timsTOF Bibliography - Proteomics

timsTOF Bibliography

The timsTOF Pro powered by PASEF^® boosts the research capability of the labs having acquired it by offering an unprecedented, uncompromised combination of speed, sensitivity, selectivity and robustness. The reproducible measurement of Collisional Cross Section (CCS) values for every peptide has allowed to develop innovative 4D proteomics™/lipidomics™/metabolomics™ approaches, making the best use of the instrument’s selectivity. New acquisition modes are rolled out on a regular basis, like dia-PASEF^® introduced at HUPO 2019. The peer-reviewed communications listed below is a non-exhaustive list from the work initiated on the first instruments, and many more are to come.

timsTOF SCP

TITLE	AUTHOR	PUBLICATION	LINK
Circadian rhythms mediate malaria transmission potential	Bento, I.; Parrington, B.; Pascual, R. et al.	bioRxiv, preprint, 2024	https://doi.org/10.1101/2024.05.14.594221
Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis	Chandran, R.R.; Vijayaraj, P.; Garcia-Milian, R. et al.	bioRxiv, preprint, 2024	https://doi.org/10.1101/2024.06.17.599411
Single-nucleus proteomics identifies regulators of protein transport	Derks, J.; Jonson, T.; Slavov, N. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.06.17.599449
PP1 PNUTS binds the “restrictor” and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination	Erickson, B.; Fedoryshchak, R.; Fong, N. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.12.603302
Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity	Kaltenecker, D.; Horvath, I.; Al-Maskari, R. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.08.18.608300
Dysregulated Skeletal Muscle Myosin Super-relaxation in Type II, but Not Type I, Diabetes Mellitus	Lewis, C.T.A.; Moreno-Justicia, R.; Savoure, L. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.06.12.598615
An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics	Makhmut, A.; Qin, D.; Coscia, F. et al.	Molecular & Cellular Proteomics, 2024, 23, 100750	https://doi.org/10.1016/j.mcpro.2024.100750
diaPASEF analysis for HLA-I peptides enables quantification of common cancer neoantigens	Oliinyk, D.; Gurung, H.; Klaeger, S. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.30.605861
Cell Storage Conditions Impact Single-Cell Proteomic Landscapes	Onat, B.; Momenzadeh, A.; Haghani, A. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.23.604834
Tagless LysoIP method for molecular profiling of lysosomal content in clinical samples	Saarela, D.; Lis, P.; Gomes, S. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.05.17.594681
Stem-loop induced ribosome queuing in the uORF2/ ATF4 overlap fine-tunes stress-induced human ATF4 translational control	Smirnova, A.M.; Hronová, V.; Mohammad, M.P. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.07.12.548609
The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2	Suryawanshi, R.K.; Jaishankar, P.; Correy, G.J. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.08.08.606661
Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP	Wang, J.; Tan, H.; Fu, Y. et al.	Journal of the American Society for Mass Spectrometry, 2024, 35, jasms.4c00067	https://doi.org/10.1021/jasms.4c00067
Isolation and characterisation of serine proteases and metalloproteases from the venom of African puff adders	Wilkinson, M.C.; Modahl, C.; Saviola, A. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.05.31.596867

timsTOF Ultra

TITLE	AUTHOR	PUBLICATION	LINK
Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications	Ctortecka, C.; Clark, N.M.; Carr, S.A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.20.576369
Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity	Cutler, R.; Corveleyn, L.; Carr, S.A. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.05.602213
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	Oliinyk, D.; Will, A.; Meier, F. et al.	Molecular Systems Biology, 2024	https://doi.org/10.1038/s44320-024-00050-9
What’s new in single-cell proteomics	Truong, T.; Kelly, R.T.	Current Opinion in Biotechnology, 2024, 86, 103077	https://doi.org/10.1016/j.copbio.2024.103077
IMBAS-MS Discovers Organ-Specific HLA Peptide Patterns in Plasma	Wahle, M.; Thielert, M.; Mann, M. et al.	Molecular & Cellular Proteomics, 2024, 23, 100689	https://doi.org/10.1016/j.mcpro.2023.100689
Ultra-sensitive metaproteomics (uMetaP) redefines the dark field of metaproteome, enables single-bacterium resolution, and discovers hidden functions in the gut microbiome	Xian, F.; Brenek, M.; Gomez Varela, D. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.04.22.590295
Cryo-EM Structures of Saccharolobus solfataricus Initiation Complexes with Leaderless mRNAs Highlight Archaeal Features and Eukaryotic Proximity	Bourgeois, G.; Coureux, P.-D.; Chamot-Rooke, J. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.16.603699

Single Cell

Title	Authors	Publication	Link
What’s new in single-cell proteomics	Truong, T.; Kelly, R.T.	Current Opinion in Biotechnology, 2024, 86, 103077	https://doi.org/10.1016/j.copbio.2024.103077
Dysregulated Skeletal Muscle Myosin Super-relaxation in Type II, but Not Type I, Diabetes Mellitus	Lewis, C.T.A.; Moreno-Justicia, R.; Savoure, L. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.06.12.598615
An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis	Gu, L.; Li, Z.; Wang, Q. et al.	preprint; bioRxiv, 2022	https://doi.org/10.1101/2022.01.02.474723
Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity	Cutler, R.; Corveleyn, L.; Carr, S.A. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.05.602213
Automated Single-Cell Proteomics Providing Sufficient Proteome Depth to Study Complex Biology beyond Cell Type Classifications	Ctortecka, C.; Clark, N. M.; Carr, S.A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.20.576369
Single Cell Proteomics by Mass Spectrometry Reveals Deep Epigenetic Insight and New Targets of a Class Specific Histone Deacetylase Inhibitor	Orsburn, B. C.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.05.574437
A Framework for Ultra-Low-Input Spatial Tissue Proteomics	Makhmut, A.; Qin, D. et al.	Cell Systems 2023, S2405471223002879	https://doi.org/10.1016/j.cels.2023.10.003
Spatial Single-Cell Mass Spectrometry Defines Zonation of the Hepatocyte Proteome	Rosenberger, F. A.; Thielert, M.; Mann, M. et al.	Nat Methods 2023	https://doi.org/10.1038/s41592-023-02007-6
Time-of-Flight Fragmentation Spectra Generated by the Proteomic Analysis of Single Human Cells Do Not Exhibit Atypical Fragmentation Patterns	Orsburn, B. C.	J. Proteome Res. 2023, acs.jproteome.2c00715	https://doi.org/10.1021/acs.jproteome.2c00715
Optimizing Single Cell Proteomics Using Trapped Ion Mobility Spectrometry for Label-Free Experiments	Mun, D.-G.; Bhat, F. A. et al.	Analyst 2023, 10.1039.D3AN00080J	https://doi.org/10.1039/D3AN00080J
Robust Dimethyl‐based Multiplex‐DIA Doubles Single‐cell Proteome Depth via a Reference Channel	Thielert, M.; Itang, E. C.; Mann, M. et al.	Molecular Systems Biology 2023, e11503	https://doi.org/10.15252/msb.202211503
Label‐Free Single Cell Proteomics Utilizing Ultrafast LC and MS Instrumentation: A Valuable Complementary Technique to Multiplexing	Matzinger, M.; Mayer, R. L.; Mechtler, K.	Proteomics 2023, 2200162	https://doi.org/10.1002/pmic.202200162
Increasing the Throughput of Sensitive Proteomics by PlexDIA	Derks, J.; Leduc, A.; Slavov, N. et al.	Nat Biotechnol 2023, 41 (1), 50–59	https://doi.org/10.1038/s41587-022-01389-w
High Throughput Single Cell Proteomic Analysis of Organ Derived Heterogeneous Cell Populations by Nanoflow Dual Trap Single Column Liquid Chromatography	Kreimer, S.; Binek, A.; Van Eyk, J. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.01.06.522908
Acetic acid is a superior acidifier for sub-nanogram and single cell proteomic studies	Orsburn, B. C.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.08.01.551522
An Ultra-Sensitive and Easy-to-Use Multiplexed Single-Cell Proteomic Analysis	Li, C.; Gu, L.; Li. et al.	preprint; Systems Biology, 2022	https://doi.org/10.1101/2022.01.02.474723
Deep Visual Proteomics Defines Single-Cell Identity and Heterogeneity	Mund, A.; Coscia, F.; Mann, M. et al.	Nat Biotechnol 2022, 40 (8), 1231–1240	https://doi.org/10.1038/s41587-022-01302-5
Insights into Protein Post-Translational Modification Landscapes of Individual Human Cells by Trapped Ion Mobility Time-of-Flight Mass Spectrometry	Orsburn, B. C.; Yuan, Y.; Bumpus, N. N.	Nat Commun 2022, 13 (1), 7246	https://doi.org/10.1038/s41467-022-34919-w
Single Cell Proteomics Using a Trapped Ion Mobility Time-of-Flight Mass Spectrometer Provides Insight into the Post-Translational Modification Landscape of Individual Human Cells	Orsburn, B. C.	preprint; Biochemistry, 2022	https://doi.org/10.1101/2022.02.12.480144
Ultra‐high Sensitivity Mass Spectrometry Quantifies Single‐cell Proteome Changes upon Perturbation	Brunner, A.; Thielert, M.; Mann, M. et al.	Molecular Systems Biology 2022, 18 (3), e10798	https://doi.org/10.15252/msb.202110798
Unbiased Spatial Proteomics with Single-Cell Resolution in Tissues	Mund, A.; Brunner, A.-D.; Mann, M. et al.	Molecular Cell 2022, 82 (12), 2335–2349	https://doi.org/10.1016/j.molcel.2022.05.022
Single-Cell Proteomic and Transcriptomic Analysis of Macrophage Heterogeneity	Specht, H.; Emmott, E.; Slavov, N. et al.	preprint; Immunology, 2019	https://doi.org/10.1101/665307

Immunopeptidomics – COVID-19 Section

Title	Authors	Publication	Link
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF	Adams, C.; Gabriel, W.; Laukens, K. et al.	preprint; Bioinformatics, 2023	https://doi.org/10.1101/2023.07.17.549401
Interferon-α promotes neo-antigen formation and preferential HLA-B-restricted antigen presentation in pancreatic β-cells	Carré, A.; Zhou, Z.; Ternette, N. et al.	preprint; Immunology, 2023	https://doi.org/10.1101/2023.09.15.557918
HLAII peptide presentation of infliximab increases when complexed with TNF	Casasola-LaMacchia, A.; Seward, R.J.; Tourdot, S. et al.	Front. Immunol., 2022, 13, 932252	https://doi.org/10.3389/fimmu.2022.932252
A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines	Feola, S.; Chiaro, J.; Lehtiö, J. et al.	preprint; Cancer Biology, 2021	https://doi.org/10.1101/2021.06.08.447483
PeptiCHIP: a novel microfluidic-based chip platform for tumour antigen landscape identification	Feola, S.; Haapala, M.; Peltonen, K. et al.	preprint; 2021	https://doi.org/10.21203/rs.3.rs-156531/v1
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model	Carapito, C.; Martens, L.; Tenzer, S. et al.	Nat Commun., 2024, 15, 2288	https://doi.org/10.1038/s41467-024-46380-y
timsTOF mass spectrometry-based immunopeptidomics refines tumor antigen identification	Gravel, N.H.; Nelde, A.; Bauer, J. et al.	preprint; 2023	https://doi.org/10.21203/rs.3.rs-2402111/v1
Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes	Hartman, K.; Steiner, G.; Ducret, A. et al.	Biology, 2023, 12, 1265	https://doi.org/10.3390/biology12091265
TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification	Hoenisch Gravel, N.; Nelde, A.; Bauer, J. et al.	Nat Commun., 2023, 14, 7472	https://doi.org/10.1038/s41467-023-42692-7
PRR adjuvants restrain high stability peptides presentation on APCs	Li, B.; Zhang, J.; He, T. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.05.20.594923
diaPASEF analysis for HLA-I peptides enables quantification of common cancer neoantigens	Oliinyk, D.; Gurung, H.; Klaeger, S. et al.	preprint; bioRxiv, 2024	https://doi.org/10.1101/2024.07.30.605861
Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry	Phulphagar, K.M.; Ctortecka, C.; Carr, S.A. et al.	preprint; Immunology, 2023	https://doi.org/10.1101/2023.03.10.532106
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning	Tran, N.H.; Peng, C.; Lei, Q. et al.	preprint; bioRxiv, 2022	https://doi.org/10.1101/2022.07.05.497667
Discovers Organ-Specific HLA Peptide Patterns in Plasma	Wahle, M.; Thielert, M.; Mann, M. et al.	IMBAS-MS Molecular & Cellular Proteomics, 2024, 23, 100689	https://doi.org/10.1016/j.mcpro.2023.100689
The potential of plasma HLA peptides beyond neoepitopes	Wahle, M.; Thielert, M.; Mann, M. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.09.05.556309
Endogenous HLA-A*02:01 restricted antigen derived from H3.3K27M is insufficient for effective immune-targeting of Diffuse Midline Glioma	Wang, S.S.; Pandey, K.; Purcell, A.W. et al.	Molecular Therapy - Oncolytics, 2023	https://doi.org/10.1016/j.omto.2023.08.005

Biology – COVID-19 Section

Title	Authors	Publication	Link
SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection	Garvanska, D. H.; Alvarado, R. E.; Mann, M. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.09.01.555899
Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19	Mairpady Shambat, S.; Gómez-Mejia, A. et al.	PLoS Pathog 2022, 18	https://doi.org/10.1371/journal.ppat.1010176
Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry	Roberts, D.S.; Mann, M.; Ge, Y. et al.	preprint; Biochemistry 2022	https://doi.org/10.1101/2022.02.09.479776
Immune response pattern across the asymptomatic, symptomatic and convalescent periods of COVID-19	Chen, Y.; Zhang, N.; Wong, C.C.L. et al.	Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2022, 1870	https://doi.org/10.1016/j.bbapap.2021.140736
Multi-level inhibition of coronavirus replication by chemical ER stress	Shaban, M.S.; Müller, C. et al.	Nat Commun 2021, 12, 5536	https://doi.org/10.1038/s41467-021-25551-1
Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study	IMPACC Manuscript Writing Team†, on behalf of the IMPACC Network Steering Committee‡	Sci. Immunol. 2021, 6, eabf3733	https://doi.org/10.1126/sciimmunol.abf3733
DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients	Mun, D.-G.; Vanderboom, P.M. et al.	J. Proteome Res. 20, 2021, 4165–4175	https://doi.org/10.1021/acs.jproteome.1c00506
Proteomic Analysis Identifies Prolonged Disturbances in Pathways Related to Cholesterol Metabolism and Myocardium Function in the COVID-19 Recovery Stage	Chen, Y.; Yao, H.; Wong, C.C.L. et al.	J. Proteome Res 2021	https://doi.org/10.1021/acs.jproteome.1c00054
SARS-CoV-2 infects human pancreatic ß cells and elicits ß cell impairment	Wu, C.-T.; Lidsky, P.V.; Jackson, P.K. et al.	Cell Metabolism 2021	https://doi.org/10.1016/j.cmet.2021.05.013
Second-Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern	Kovacech, B.; Fialova, L. et al.	preprint; Microbiology 2021	https://doi.org/10.1101/2021.06.09.447527
A Blood Atlas of COVID-19 Defines Hallmarks of Disease Severity and Specificity; COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium	Ahern, D. J.; Ai, Z.; Fischer, R. et al.	preprint; Infectious Diseases (except HIV/AIDS) 2021	https://doi.org/10.1101/2021.05.11.21256877
Systematic Functional Analysis of SARS-CoV-2 Proteins Uncovers Viral Innate Immune Antagonists and Remaining Vulnerabilities	Hayn, M.; Hirschenberger, M. et al.	Cell Reports 2021, 109126	https://doi.org/10.1016/j.celrep.2021.109126
Large Scale Discovery of Coronavirus-Host Factor Protein Interaction Motifs Reveals SARS-CoV-2 Specific Mechanisms and Vulnerabilities	Kruse, T.; Benz, C.; Mann, M. et al.	Biochemistry 2021	https://doi.org/10.1101/2021.04.19.440086
The COVIDome Explorer Researcher Portal	Sullivan, K. D.; Galbraith, M. D. et al.	Allergy and Immunology 2021	https://doi.org/10.1101/2021.03.04.21252945
Structural O-Glycoform Heterogeneity of the SARS-CoV-2 Spike Protein Receptor-Binding Domain Revealed by Native Top-Down Mass Spectrometry	Roberts, D. S.; Mann, M. W.; Ge, Y. et al.	preprint; Biochemistry 2021	https://doi.org/10.1101/2021.02.28.433291
Structural and Functional Characterization of SARS-CoV-2 RBD Domains Produced in Mammalian Cells	Gstöttner, C.; Zhang, T.; Wuhrer, M. et al.	preprint; Biochemistry 2021	https://doi.org/10.1101/2021.02.23.432424
High-Resolution Longitudinal Serum Proteome Trajectories in COVID-19 Reveal Patients-Specific Seroconversion	Geyer, P. E.; Arend, F. M. et al.	preprint; Infectious Diseases (except HIV/AIDS) 2021	https://doi.org/10.1101/2021.02.22.21252236
The Host Interactome of Spike Expands the Tropism of SARS-CoV-2	Bamberger, C.; Pankow, S.; Yates, J. et al.	preprint; Molecular Biology 2021	https://doi.org/10.1101/2021.02.16.431318
Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients	Thomas, T.; Stefanoni, D. et al.	Proteome Res. 2020, 19 (11), 4455–4469	https://doi.org/10.1021/acs.jproteome.0c00606
Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein (preprint).	Nikolaev, E.; Indeykina, M.; Borchers, C. et al.	Molecular Biology 2020	https://doi.org/10.1101/2020.05.24.113043
Immune Suppression in the Early Stage of COVID-19 Disease	Tian, W.; Zhang, N.; Wong, C. C. L. et al.	Nat Commun 2020, 11 (1), 5859	https://doi.org/10.1038/s41467-020-19706-9
SARS-CoV-2 Induced CYP19A1 Expression in the Lung Correlates with Increased Aromatization of Testosterone-to-Estradiol in Male Golden Hamsters	Stanelle-Bertram, S.; Schaumburg, B. et al.	preprint; In Review 2020	https://doi.org/10.21203/rs.3.rs-107474/v1
Transcriptional and Proteomic Insights into the Host Response in Fatal COVID-19 Cases	Wu, M.; Chen, Y. et al.	Proc Natl Acad Sci USA 2020, 117 (45), 28336–28343	https://doi.org/10.1073/pnas.2018030117
Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level	D’Alessandro, A.; Thomas, T. et al.	Proteome Res. 2020, 19 (11), 4417–4427	https://doi.org/10.1021/acs.jproteome.0c00365

Biology

Title	Authors	Publication	Link
Combining Data Independent Acquisition with Spike-in SILAC (DIA-SiS) Improves Proteome Coverage and Quantification	Welter, A. S.; Gerwien, M.; Kerridge, R. et al.	Molecular & Cellular Proteomics 100839. 2024	https://doi.org/10.1016/j.mcpro.2024.100839
Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell	Wang, Y.; Guan, Z.-Y.; Shi, S.-W. et al.	Nat Commun 15, 1279. 2024	https://doi.org/10.1038/s41467-024-45659-4
Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP	Wang, J.; Tan, H.; Fu, Y. et al.	J. Am. Soc. Mass Spectrom. jasms.4c00067	https://doi.org/10.1021/jasms.4c00067
IMBAS-MS Discovers Organ-Specific HLA Peptide Patterns in Plasma	Wahle, M.; Thielert, M.; Mann, M. et al.	Molecular & Cellular Proteomics 23, 100689. 2024	https://doi.org/10.1016/j.mcpro.2023.100689
Parallel accumulation‐serial fragmentation method for in‐depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer	Vu, H. M.; Huh, S.; Lee, J. H. et al.	Proteomics Clinical Apps 2300053. 2024	https://doi.org/10.1002/prca.202300053
timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery	Vitko, D.; Chou, W.-F.; Nouri Golmaei, S. et al.	Proteome Res. acs.jproteome.3c00646. 2024	https://doi.org/10.1021/acs.jproteome.3c00646
Cerebrospinal fluid shotgun proteomics identifies distinct proteomic patterns in cerebral amyloid angiopathy rodent models and human patients	Vervuurt, M.; Schrader, J. M.; Wessels, H. J. C. T. et al.	Acta Neuropathologica Communications 12,6	https://doi.org/10.1186/s40478-023-01698-4
What’s new in single-cell proteomics	Truong, T.; Kelly, R.T. et al.	Current Opinion in Biotechnology 86, 103077. 2024	https://doi.org/10.1016/j.copbio.2024.103077
Transporter Protein Expression of Corneal Epithelium in Rabbit and Porcine: Evaluation of Models for Ocular Drug Transport Study	Ramsay, E.; Montaser, A. B.; Niitsu, K. et al.	Mol. Pharmaceutics 21, 3204–3217. 2024	https://doi.org/10.1021/acs.molpharmaceut.3c01210
Optimizing differential expression analysis for proteomics data via high-performing rules and ensemble inference	Peng, H.; Wang, H.; Kong, W. et al.	Nat Commun 15, 3922. 2024	https://doi.org/10.1038/s41467-024-47899-w
µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics	Oliinyk, D.; Will, A.; Schneidmadel, F. R. et al.	Mol Syst Biol. 2024	https://doi.org/10.1038/s44320-024-00050-9
The social and structural architecture of the yeast protein interactome	Michaelis, A. C.; Brunner, A.-D.; Mann, M. et al.	Nature 624, 192–200. 2023	https://doi.org/10.1038/s41586-023-06739-5
Neat plasma proteomics: getting the best out of the worst	Metatla, I.; Roger, K.; Guerrera, I. C. et al.	Clin Proteom 21, 22. 2024	https://doi.org/10.1186/s12014-024-09477-6
An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics	Makhmut, A.; Qin, D.; Coscia, F. et al.	Molecular & Cellular Proteomics 23, 100750. 2024	https://doi.org/10.1016/j.mcpro.2024.100750
Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023	Lou, R.; Shui, W.	Molecular & Cellular Proteomics 23, 100712. 2024	https://doi.org/10.1016/j.mcpro.2024.100712
Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease	Kolic, J.; Sun, W. G.; Foster, L. J. et al.	Cell Metabolism 36, 1619-1633.e5. 2024	https://doi.org/10.1016/j.cmet.2024.06.001
The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics?	Jiang, Y.; DeBord, D.; Van Eyk, J. E. et al.	Proteome Res. acs.jproteome.4c00248. 2024	https://doi.org/10.1021/acs.jproteome.4c00248
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model	Carapito, C.; Martens, L.; Tenzer, S. et al.	Nat Commun 15, 2288. 2024	https://doi.org/10.1038/s41467-024-46380-y
Bottom-up Histone Post-translational Modification Analysis using Liquid Chromatography, Trapped Ion Mobility Spectrometry, and Tandem Mass Spectrometry	Fuller, C. N.; Valadares Tose, L.; Vitorino, F. N. L. et al.	J. Proteome Res. acs.jproteome.4c00177. 2024	https://doi.org/10.1021/acs.jproteome.4c00177
Protein-Centric Analysis of Personalized Antibody Repertoires Using LC-MS-Based Fab-Profiling on a timsTOF	Fiala, J.; Schuster, D.; Heck, A. J. R. et al.	J. Am. Soc. Mass Spectrom. jasms.4c00076. 2024	https://doi.org/10.1021/jasms.4c00076
Database selection for shotgun metaproteomic of low-diversity dairy microbiomes	Da Silva Duarte, V.; De Paula Dias Moreira, L.; Skeie, S. B. et al.	International Journal of Food Microbiology 110706. 2024	https://doi.org/10.1016/j.ijfoodmicro.2024.110706
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	Berthias, F.; Bilgin, N.; Jensen, O. N. et al.	2024. Proteomics 2200471	https://doi.org/10.1002/pmic.202200471
Maximizing Glycoproteomics Results through an Integrated Parallel Accumulation Serial Fragmentation Workflow	Baerenfaenger, M.; Post, M. A.; Wessels, H. J. C. T. et al.	Anal. Chem. 2024, 96, 8956–8964.	https://doi.org/10.1021/acs.analchem.3c05874
Automated Single-Cell Proteomics Providing Sufficient Proteome Depth to Study Complex Biology beyond Cell Type Classifications	Ctortecka, C.; Clark, N. M. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.20.576369
What Do the Proteins Say about Maternal-Fetal Communication in Buffaloes?	Codognoto, V. M.; de Souza, F. F. et al.	Journal of Proteomics 2024, 290, 105023	https://doi.org/10.1016/j.jprot.2023.105023
Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Bacillus Subtilis Cells and Spores	Huang, Y.; Swarge, B. N. et al.	J. Proteome Res. 2024, acs.jproteome.3c00386	https://doi.org/10.1021/acs.jproteome.3c00386
Enhanced Feature Matching in Single-Cell Proteomics Characterizes Response to IFN-γ and Reveals Co-Existence of Different Cell States	Krull, K. K.; Ali, S. A.; Krijgsveld, J.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.01.10.575010
Single Cell Proteomics by Mass Spectrometry Reveals Deep Epigenetic Insight and New Targets of a Class Specific Histone Deacetylase Inhibitor	Orsburn, B. C.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.05.574437
Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens	Wessels, H. J. C. T.; van Gool, A. J.; Willems, E. et al.	iScience 26, 107257. 2023	https://doi.org/10.1016/j.isci.2023.107257
Interactive Effects of Dietary Isoleucine and Valine Ratios to Lysine in Response to Varying Leucine to Lysine Ratios on Pectoralis Major Muscle Protein Expression in Commercial Broilers	Almendares, C. I.; Ventura, D. E. et al.	Journal of Animal Science 2023, 101 (Supplement_3), 195–196	https://doi.org/10.1093/jas/skad281.237
A Framework for Ultra-Low-Input Spatial Tissue Proteomics	Makhmut, A.; Qin, D. et al.	Cell Systems 2023, S2405471223002879	https://doi.org/10.1016/j.cels.2023.10.003
A Region‐resolved Proteomic Map of the Human Brain Enabled by High‐throughput Proteomics	Tüshaus, J.; Sakhteman, A.; Kuster, B. et al.	The EMBO Journal 2023, e114665	https://doi.org/10.15252/embj.2023114665
Archaeal GPN-Loop GTPases Involve a Lock-Switch-Rock Mechanism for GTP Hydrolysis	Korf, L.; Ye, X. et al.	mBio 2023, e00859-23	https://doi.org/10.1128/mbio.00859-23
Community-Based Peptidomic Clustering Reveals Pathogen-Specific Proteolytic Signatures in Wounds	Hartman, E.; Forsberg, F.; Malmström, J. et al.	preprint; Bioinformatics, 2023	https://doi.org/10.1101/2023.12.28.573527
Deep Proteomics Reveals Incorporation of Unedited Proteins into Mitochondrial Protein Complexes in Arabidopsis	Rugen, N.; Senkler, M. et al.	Plant Physiology 2023, kiad655	https://doi.org/10.1093/plphys/kiad655
Deep Topographic Proteomics of a Human Brain Tumour	Davis, S.; Scott, C. et al.	Nat Commun 2023, 14 (1), 7710	https://doi.org/10.1038/s41467-023-43520-8
Distinct Molecular Profiles of Skull Bone Marrow in Health and Neurological Disorders	Kolabas, Z. I.; Kuemmerle, L. B. et al.	Cell 2023, 186 (17), 3706-3725.e29	https://doi.org/10.1016/j.cell.2023.07.009
Disturbed Electron Transport beyond PSI Changes Metabolome and Transcriptome in Zn-Deficient Soybean	Andresen, E.; Morina, F. et al.	Biochimica et Biophysica Acta (BBA) - Bioenergetics 2023, 149018	https://doi.org/10.1016/j.bbabio.2023.149018
DSE Inhibits Melanoma Progression by Regulating Tumor Immune Cell Infiltration and VCAN	Xia, L.; Feng, M. et al.	Cell Death Discov. 2023, 9 (1), 373	https://doi.org/10.1038/s41420-023-01676-8
Effects of Polyphosphate Metabolism Mutations on Biofilm, Capsule Formation and Virulence Traits in Hypervirulent ST23 Klebsiella Pneumoniae SGH10	Rojas, D.; Marcoleta, A. E. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.09.15.557991
Endogenous HLA-A*02:01 Restricted Antigen Derived from H3.3K27M Is Insufficient for Effective Immune-Targeting of Diffuse Midline Glioma	Wang, S. S.; Pandey, K.; Purcell, A. W. et al.	Molecular Therapy - Oncolytics 2023, S237277052300058X	https://doi.org/10.1016/j.omto.2023.08.005
Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes	Hartman, K.; Steiner, G. et al.	Biology 2023, 12 (9), 1265	https://doi.org/10.3390/biology12091265
Exploiting Ion‐mobility Mass Spectrometry for Unraveling Proteome Complexity	Perchepied, S.; Zhou, Z. et al.	J of Separation Science 2023, 46 (18), 2300512	https://doi.org/10.1002/jssc.202300512
Fast Proteomics with dia-PASEF and Analytical Flow-Rate Chromatography	Szyrwiel, L.; Gille, C. et al.	Proteomics 2023, 2300100	https://doi.org/10.1002/pmic.202300100
Functional Characterization of a Lytic Polysaccharide Monooxygenase from Schizophyllum Commune That Degrades Non-Crystalline Substrates	Østby, H.; Christensen, I. A. et al.	Sci Rep 2023, 13 (1), 17373	https://doi.org/10.1038/s41598-023-44278-1
Global Lactylome Reveals Lactylation-Dependent Mechanisms Underlying TH 17 Differentiation in Experimental Autoimmune Uveitis	Fan, W.; Wang, X. et al.	Sci. Adv. 2023, 9 (42), eadh4655	https://doi.org/10.1126/sciadv.adh4655
High-Throughput Single-Cell Proteomic Analysis of Organ-Derived Heterogeneous Cell Populations by Nanoflow Dual-Trap Single-Column Liquid Chromatography	Kreimer, S.; Binek, A.; Van Eyk, J. et al.	Anal. Chem. 2023, 95 (24), 9145–9150	https://doi.org/10.1021/acs.analchem.3c00213
Human Visceral Adipose Tissue Microvascular Endothelial Cell Isolation and Establishment of Co-Culture with White Adipocytes to Analyze Cell-Cell Communication	Chaurasiya, V.; Pham, D. D. et al.	Experimental Cell Research 2023, 113819	https://doi.org/10.1016/j.yexcr.2023.113819
In Vivo Protein Turnover Rates in Varying Oxygen Tensions Nominate MYBBP1A as a Mediator of the Hyperoxia Response	Chen, X.; Haribowo, A. G. et al.	Sci. Adv. 2023, 9 (49), eadj4884	https://doi.org/10.1126/sciadv.adj4884
Insight into Ionic Strength-Induced Solubilization of Myofibrillar Proteins from Silver Carp ( Hypophthalmichthys Molitrix ): Structural Changes and 4D Label-Free Proteomics Analysis	Li, X.; Zhang, N. et al.	J. Agric. Food Chem. 2023, acs.jafc.3c04254	https://doi.org/10.1021/acs.jafc.3c04254
Integrated Proteome and Malonylome Analyses Reveal the Potential Meaning of TLN1 and ACTB in End-Stage Renal Disease	Tan, R.; Li, D. et al.	Proteome Sci 2023, 21 (1), 18	https://doi.org/10.1186/s12953-023-00211-y
Ionmob: A Python Package for Prediction of Peptide Collisional Cross-Section Values	Teschner, D.; Martens, L.; Tenzer, S. et al.	Bioinformatics 2023, btad486	https://doi.org/10.1093/bioinformatics/btad486
M-Protein Diagnostics in Multiple Myeloma Patients Using Ultra-Sensitive Targeted Mass Spectrometry and an off-the-Shelf Calibrator	Wijnands, C.; Langerhorst, P.; van Gool, A. J. et al.	Clinical Chemistry and Laboratory Medicine (CCLM) 2023, 0 (0)	https://doi.org/10.1515/cclm-2023-0781
Metabolic Disruption Impairs Ribosomal Protein Levels, Resulting in Enhanced Aminoglycoside Tolerance	Orman, M.A.; Shiraliyev, R.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.12.20.572673
Microanalytical Mass Spectrometry with Super-Resolution Microscopy Reveals a Proteome Transition During Development of the Brain’s Circadian Pacemaker	Choi, S. B.; Vatan, T. et al.	Anal. Chem. 2023, acs.analchem.3c01987	https://doi.org/10.1021/acs.analchem.3c01987
Multi-omic Analysis of Guided and Unguided Forebrain Organoids Reveal Differences in Cellular Composition and Metabolic Profiles	Øhlenschlæger, M. S.; Jensen, P. et al.	preprint; Neuroscience, 2023	https://doi.org/10.1101/2023.12.21.572871
Multi omics based Analysis of the Regulatory Mechanism of Gypenosides on Bile Acids in Hypercholesterolemic Mice	Feng, C.; Yang, Y. et al.	Exp Ther Med 2023, 26 (3), 438	https://doi.org/10.3892/etm.2023.12136
Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens	Kardell, O.; Von Toerne, C.; Mann, M. et al.	J. Proteome Res. 2023, acs.jproteome.3c00473	https://doi.org/10.1021/acs.jproteome.3c00473
DDA-PASEF and DiaPASEF Acquired Cell Line Proteomic Datasets with Deliberate Batch Effects	Wang, H.; Lim, K. P. et al.	MultiPro: Sci Data 2023, 10 (1), 858	https://doi.org/10.1038/s41597-023-02779-8
Nitroxoline Resistance Is Associated with Significant Fitness Loss and Diminishes in Vivo Virulence of Escherichia Coli	Deschner, F.; Risch, T. et al.	Microbiol Spectr 2023, e03079-23	https://doi.org/10.1128/spectrum.03079-23
Plasma Glycoproteomics Delivers High-Specificity Disease Biomarkers by Detecting Site-Specific Glycosylation Abnormalities	Wessels, H. J. C. T.; Kulkarni, P.; van Gool, A. J. et al.	Journal of Advanced Research 2023, S2090123223002394	https://doi.org/10.1016/j.jare.2023.09.002
Potential Bioactive Peptides Obtained after in Vitro Gastrointestinal Digestion of Wine Lees from Sequential Fermentations	de Paula Dias Moreira, L.; Corich, V. et al.	Food Research International 2023, 113833	https://doi.org/10.1016/j.foodres.2023.113833
Propranolol Reduces the Accumulation of Cytotoxic Aggregates in C9orf72-ALS/FTD in Vitro Models	Seidel, M.; Rajkumar, S. et al.	Current Research in Neurobiology 2023, 5, 100105	https://doi.org/10.1016/j.crneur.2023.100105
Proteomic Profiling of Advanced Melanoma Patients to Predict Therapeutic Response to Anti-PD-1 Therapy	Zila, N.; Eichhoff, O. M.; Aebersold, R. et al.	Clinical Cancer Research 2023	https://doi.org/10.1158/1078-0432.CCR-23-0562
Quantification of 782 Plasma Peptides by Multiplexed Targeted Proteomics	Lesur, A.; Bernardin, F. et al.	J. Proteome Res. 2023, 22 (6), 1630–1638	https://doi.org/10.1021/acs.jproteome.2c00575
Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis	Zakopcanik, M.; Kavan, D. et al.	J. Proteome Res. 2023, acs.jproteome.3c00390	https://doi.org/10.1021/acs.jproteome.3c00390
Robust Dimethyl‐based Multiplex‐DIA Doubles Single‐cell Proteome Depth via a Reference Channel	Thielert, M.; Itang, E. C.; Mann, M. et al.	Molecular Systems Biology 2023, e11503	https://doi.org/10.15252/msb.202211503
Spatial Single-Cell Mass Spectrometry Defines Zonation of the Hepatocyte Proteome	Rosenberger, F. A.; Thielert, M.; Mann, M. et al.	Nat Methods 2023	https://doi.org/10.1038/s41592-023-02007-6
Structure and Dynamics of Endogenous Cardiac Troponin Complex in Human Heart Tissue Captured by Native Nanoproteomics	Chapman, E. A.; Roberts, D. S.; Ge, Y. et al.	Nat Commun 2023, 14 (1), 8400	https://doi.org/10.1038/s41467-023-43321-z
STT3A-Mediated Viral N-Glycosylation Underlies the Tumor Selectivity of Oncolytic Virus M1	Song, D.; Jia, X. et al.	Oncogene 2023	https://doi.org/10.1038/s41388-023-02872-7
The Bone–Liver Interaction Modulates Immune and Hematopoietic Function through Pinch-Cxcl12-Mbl2 Pathway	He, T.; Zhou, B. et al.	Cell Death Differ 2023	https://doi.org/10.1038/s41418-023-01243-9
Time-Sequential Fibroblast-to-Myofibroblast Transition in Elastin-Variable 3D Hydrogel Environments by Collagen Networks	Do, N. T.; Lee, S. Y. et al.	Biomater Res 2023, 27 (1), 103	https://doi.org/10.1186/s40824-023-00439-x
TOFIMS Mass Spectrometry-Based Immunopeptidomics Refines Tumor Antigen Identification	Hoenisch Gravel, N.; Nelde, A. et al.	Nat Commun 2023, 14 (1), 7472	https://doi.org/10.1038/s41467-023-42692-7
Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis	Liu, F. C.; Ridgeway, M. E. et al.	J. Am. Soc. Mass Spectrom. 2023, jasms.3c00187	https://doi.org/10.1021/jasms.3c00187
Ultra-High-Throughput Mapping of the Chemical Space of Asymmetric Catalysis Enables Accelerated Reaction Discovery	Nie, W.; Wan, Q. et al.	Nat Commun 2023, 14 (1), 6671	https://doi.org/10.1038/s41467-023-42446-5
Oxonium Ion–Guided Optimization of Ion Mobility–Assisted Glycoproteomics on the timsTOF Pro	Mukherjee, S.; Jankevics, A. et al.	Molecular & Cellular Proteomics 2023, 22 (2), 100486	https://doi.org/10.1016/j.mcpro.2022.100486
Linkage-Specific Identification and Quantification of Sialylated Glycans by TIMS-TOF MS through Conjugation with Metal Complexes	Li, Y.; Wang, H. et al.	Talanta 2023, 253, 123995	https://doi.org/10.1016/j.talanta.2022.123995
Glycoproteomic Analyses of Influenza A Viruses Using TimsTOF Pro MS	Wong, T. L.; Mooney, B. P. et al.	Proteome Res. 2023, 22 (1), 62–77	https://doi.org/10.1021/acs.jproteome.2c00469
Benchmarking Commonly Used Software Suites and Analysis Workflows for DIA Proteomics and Phosphoproteomics	Lou, R.; Cao, Y. et al.	Nat Commun 2023, 14 (1), 94	https://doi.org/10.1038/s41467-022-35740-1
Multi-Omics Based Anti-Inflammatory Immune Signature Characterizes Long COVID-19 Syndrome	Kovarik, J. J.; Bileck, A. et al.	iScience 2023, 26 (1), 105717	https://doi.org/10.1016/j.isci.2022.105717
Increasing the Throughput of Sensitive Proteomics by PlexDIA	Derks, J.; Leduc, A. et al.	Nat Biotechnol 2023, 41 (1), 50–59	https://doi.org/10.1038/s41587-022-01389-w
A Combined Lipidomic and Proteomic Profiling of Arabidopsis Thaliana Plasma Membrane	Bahammou, D.; Recorbet, G. et al.	preprint; Plant Biology, 2023	https://doi.org/10.1101/2023.05.14.540643
A Label-Free Approach for Relative Spatial Quantitation of c-Di-GMP in Microbial Biofilms	McCaughey, C.; Trebino, M. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.10.10.561783
A Protein Blueprint of the Diatom CO2 -Fixing Organelle	Nam, O.; McKenzie, C. et al	preprint; Cell Biology, 2023	https://doi.org/10.1101/2023.10.26.564148
A Single-Sample Workflow for Joint Metabolomic and Proteomic Analysis of Clinical Specimens	Gegner, H.; Naake, T. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.11.07.561857
Acetic Acid Is a Superior Acidifier for Sub-Nanogram and Single Cell Proteomic Studies	Orsburn, B. C.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.08.01.551522
Age-Associated Aberrations of Cumulus-Oocyte Interaction and Microfilamentous Structure in the Zona Pellucida Decline Female Fertility	Ishikawa-Yamauchi, Y.; Emori, C. et al.	preprint; Developmental Biology, 2023	https://doi.org/10.1101/2023.12.30.573680
ATR Promotes MTORC1 Activation via de Novo Cholesterol Synthesis in P16-Low Cancer Cells	Tangudu, N. K.; Huang, Z. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.10.27.564195
BioE3 Enables the Identification of Bona Fide Targets of E3 Ligases	Barroso-Gomila, O.; Merino-Cacho, L. et al.	preprint; Cell Biology, 2023	https://doi.org/10.1101/2023.08.18.553883
Biological and Genetic Determinants of Red Blood Cell Glycolysis	Nemkov, T.; Stephenson, D. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.09.11.557250
Borrowing Transcriptional Kinases to Activate Apoptosis	Sarott, R.; Gourisankar, S. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.10.23.563687
Caspase-2 Protects against Ferroptotic Cell Death	Dawar, S.; Benitez, M. C. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.08.22.553791
Characterisation of the Butyrate Production Pathway in Probiotic MIYAIRI588 by a Combined Whole Genome-Proteome Approach	Wood, L.; Omorotionmwan, B. B. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.08.20.554021
Comparative Omics Reveals Unanticipated Metabolic Rearrangements in a High-Oil Mutant of Plastid Acetyl-CoA Carboxylase	Kataya, A.; Da Silva Nascimento, J. R. et al.	preprint; Plant Biology, 2023	https://doi.org/10.1101/2023.08.31.555777
Comprehensive Multi-Omic Analysis Reveals Distinct Molecular Features in Early and Advanced Stages of Hepatocellular Carcinoma	Fan, M.; Hu, J. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.12.17.570960
«Control of the Phage Defense Mechanism by Quorum Sensing (QS) in Clinical Isolates of Klebsiella Pneumoniae »	Barrio-Pujante, A.; Bleriot, I. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.12.05.570179
Deep MALDI-MS Spatial Omics Guided by Quantum Cascade Laser Mid-Infrared Imaging Microscopy	Gruber, L.; Schmidt, S.; Hopf, C. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.12.14.571637
Degradation of Fatty Acid Export Protein1 by Rhomboid-Like Protease11 Contributes to Cold Tolerance in Arabidopsis	John, A.; Kraemer, M. et al.	preprint; Plant Biology, 2023	https://doi.org/10.1101/2023.10.26.564161
Direct Translation of Incoming Retroviral RNA Genomes	Koppke, J.; Keller, L.-E. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.05.02.539066
Dissecting the Properties of Circulating IgG against Group A Streptococcus through a Combined Systems Antigenomics-Serology Workflow	Chowdhury, S.; Gomez Toledo, A. et al.	preprint; Immunology, 2023	https://doi.org/10.1101/2023.11.07.565977
Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs	Van Bergen, W.; Fiala, J.; Heck, A. J. R. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.10.19.562725
ECM-Focused Proteomic Analysis of Ear Punch Regeneration in Acomys Cahirinus	McCabe, M. C.; Okamura, D. M. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.10.11.561940
Evolutionarily Conserved Ovarian Fluid Proteins Are Responsible for Extending Egg Viability in Salmonid Fish	Gueho, A.; Zarski, D. et al.	preprint; Evolutionary Biology, 2023	https://doi.org/10.1101/2023.09.05.556347
Ex Vivo Structures from Spinach Leaves	Wang, J.; Johansen, N. T. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.10.13.562012
Fragment Ion Intensity Prediction Improves the Identification Rate of Non-Tryptic Peptides in timsTOF	Adams, C.; Gabriel, W. et al.	preprint; Bioinformatics, 2023	https://doi.org/10.1101/2023.07.17.549401
Generation of “OP7 Chimera” Defective Interfering Particle Preparations Free of Infectious Influenza A Virus That Shows Antiviral Efficacy in Mice	Dogra, T.; Pelz, L. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.08.16.553516
H3K27me3 Spreading Organizes Canonical PRC1 Chromatin Architecture to Regulate Developmental Programs	Krug, B.; Hu, B. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.11.28.567931
High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF	Bayne, E. F.; Buck, K. M.; Ge, Y. et al.	preprint; Systems Biology, 2023	https://doi.org/10.1101/2023.08.17.553758
Hsf1 and the Molecular Chaperone Hsp90 Support a “Rewiring Stress Response” Leading to an Adaptive Cell Size Increase in Chronic Stress	Maiti, S.; Bhattacharya, K. et al.	preprint; Cell Biology, 2023	https://doi.org/10.1101/2023.01.25.525547
Human Serum Enriched After Absorption of Fish Cartilage Hydrolysate Enhances the Healing of Primary Human Dermal Fibroblasts Through the Expression of Proteins with Anti-Inflammatory and Immunomodulatory Properties	Le Faouder, J.; Gueho, A. et al.	preprint; Biology and Life Sciences, 2023	https://doi.org/10.20944/preprints202312.0550.v1
Inhibition of Mitochondrial Protein Import and Proteostasis by a Pro-Apoptotic Lipid	Fita-Torró, J.; Garrido-Huarte, J. L. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.11.06.565743
Insulin and Exercise-Induced Phosphoproteomics of Human Skeletal Muscle Identify REPS1 as a New Regulator of Muscle Glucose Uptake	Larsen, J. K.; Lindqvist, C. B. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.11.10.566644
Integrated Proteomics Identifies Troponin I Isoform Switch as a Regulator of a Sarcomere-Metabolism Axis During Cardiac Regeneration	Aballo, T. J.; Mann, M. M.; Ge, Y. et al.	preprint; Developmental Biology, 2023	https://doi.org/10.1101/2023.10.20.563389
Interferon-α Promotes Neo-Antigen Formation and Preferential HLA-B-Restricted Antigen Presentation in Pancreatic β-Cells	Carré, A.; Zhou, Z.; Ternette, N. et al.	preprint; Immunology, 2023	https://doi.org/10.1101/2023.09.15.557918
Loss of Carnitine Palmitoyltransferase 1a Reduces Docosahexaenoic Acid-Containing Phospholipids and Drives Sexually Dimorphic Liver Disease in Mice	Zelows, M. M.; Cady, C. et al.	preprint; Physiology, 2023	https://doi.org/10.1101/2023.08.17.553705
Loss-of-Function Cancer-Associated Mutations in the EIF4G2 Non-Canonical Translation Initiation Factor	Meril, S.; Bhalsen, M. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.08.22.554280
Massively Parallel Sample Preparation for Multiplexed Single-Cell Proteomics Using NPOP	Leduc, A.; Koury, L.; Slavov, N. et al.	preprint; Bioengineering, 2023	https://doi.org/10.1101/2023.11.27.568927
Maximizing Glycoproteomics Results through an Integrated PASEF Workflow	Baerenfaenger, M.; Post, M. A.; Van Gool, A. J. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.12.21.570555
Modeling the Simultaneous Dynamics of Proteins in Blood Plasma and the Cerebrospinal Fluid in Human in Vivo	Giroux, P.; Vialaret, J. et al.	preprint; Systems Biology, 2023	https://doi.org/10.1101/2023.12.28.573559
MTORC1 Regulates the Metabolic Switch of Postnatal Cardiomyocytes During Regeneration	Paltzer, W. G.; Aballo, T. J. et al.	preprint; Developmental Biology, 2023	https://doi.org/10.1101/2023.09.12.557400
Multi-Omics Profiling of Candida Albicans Grown on Solid Versus Liquid Media	Alhameed, R. A.; Semreen, M. H. et al.	Microorganisms 2023, 11(12), 2831	https://doi.org/10.3390/microorganisms11122831
Multi-Tiered Actions of Legionella Effectors to Modulate Host Rab10 Dynamics	Kubori, T.; Arasaki, K. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.06.02.543523
Multiomics Analysis Revealed Anti-Freezing Mechanism of Staphylococcus Aureus in Its Anti-Freezing Strain	Youzhi, W.; Linjun, S. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.10.02.560408
No Trade-off between Ovary Activation and Immune Protein Expression in Female Bumble Bees (Bombus Impatiens)	McAfee, A.; Chapman, A. et al.	preprint; Physiology, 2023	https://doi.org/10.1101/2023.10.27.564231
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P97 Dysfunction Underlies a Loss of Quality Control of Damaged Membrane Proteins and Promotes Oxidative Stress and Sickling in Sickle Cell Disease	Song, A.; Wen, A. Q. et al.	The FASEB Journal 2022, 36 (5)	https://doi.org/10.1096/fj.202101500RR
Absolute Quantification of Viral Proteins during Single-Round Replication of MDCK Suspension Cells	Küchler, J.; Püttker, S. et al.	Journal of Proteomics 2022, 259, 104544	https://doi.org/10.1016/j.jprot.2022.104544
P-NCS-Bn-NODAGA as a Bifunctional Chelator for Radiolabeling with the 186Re/99mTc-Tricarbonyl Core: Radiochemistry with Model Complexes and a GRPR-Targeting Peptide	Kankanamalage, P.; Hoerres, R. et al.	Nuclear Medicine and Biology 2022, 108–109, 1–9	https://doi.org/10.1016/j.nucmedbio.2022.01.004
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The Meta-Substituted Isomer of TMPyP Enables More Effective Photodynamic Bacterial Inactivation than Para-TMPyP In Vitro	Schulz, S.; Ziganshyna, S. et al.	Microorganisms 2022, 10 (5), 858	https://doi.org/10.3390/microorganisms10050858
An Anti-Influenza A Virus Microbial Metabolite Acts by Degrading Viral Endonuclease PA	Zhao, J.; Wang, J. et al.	Nat Commun 2022, 13 (1), 2079	https://doi.org/10.1038/s41467-022-29690-x
Phosphatidylcholines (PCs) Serve as Biomarkers for Prognosis of Esophageal Squamous Cell Carcinoma (ESCC) and Compromise Antitumor Efficacy of Focal Adhesion Kinase (FAK) Inhibitor	Zhan, Q.; Chen, J. et al.	preprint; In Review, 2022	https://doi.org/10.21203/rs.3.rs-1556187/v1
Development of NanoLuc-Targeting Protein Degraders and a Universal Reporter System to Benchmark Tag-Targeted Degradation Platforms	Grohmann, C.; Magtoto, C. M. et al.	Nat Commun 2022, 13 (1), 2073	https://doi.org/10.1038/s41467-022-29670-1
Specific and Reversible Enrichment of Early-Stage Glycated Proteome Based on Thiazolidine Chemistry and Palladium-Mediated Cleavage	Wu, L.; Fei, W. et al.	Anal. Chem. 2022, 94 (13), 5213–5220	https://doi.org/10.1021/acs.analchem.1c03648
Sickle-like Inertial Microfluidic System for Online Rare Cell Separation and Tandem Label-Free Quantitative Proteomics (Orcs-Proteomics)	Wang, L.; Abdulla, A. et al.	Analytical Chemistry 2022	https://doi.org/10.1021/acs.analchem.2c00679
DNA Damage Contributes to Neurotoxic Inflammation in Aicardi-Goutières Syndrome Astrocytes	Giordano, A. M. S.; Luciani, M. et al.	Journal of Experimental Medicine 2022, 219 (4), e20211121	https://doi.org/10.1084/jem.20211121
Downregulation of KRAB Zinc Finger Proteins in 5-Fluorouracil Resistant Colorectal Cancer Cells	Chauvin, A.; Bergeron, D. et al.	BMC Cancer 2022, 22 (1), 363	https://doi.org/10.1186/s12885-022-09417-3
Fritted Tip Capillary Column with Negligible Dead Volume Facilitated Ultrasensitive and Deep Proteomics	Yang, Y.; Su, Y. et al.	Analytica Chimica Acta 2022, 1201, 339615	https://doi.org/10.1016/j.aca.2022.339615
FAST-IT: F Ind A S Imple T Est — I n T IA (Transient Ischaemic Attack): A Prospective Cohort Study to Develop a Multivariable Prediction Model for Diagnosis of TIA through Proteomic Discovery and Candidate Lipid Mass Spectrometry, Neuroimaging and Machine Learning — Study Protocol	Milton, A. G.; Lau, S. et al.	BMJ Open 2022, 12 (4), e045908	https://doi.org/10.1136/bmjopen-2020-045908
Mitochondrial Protein Hyperacetylation Underpins Heart Failure with Preserved Ejection Fraction in Mice	Liu, X.; Zhang, Y. et al.	Journal of Molecular and Cellular Cardiology 2022, 165, 76–85	https://doi.org/10.1016/j.yjmcc.2021.12.015
Proteomic Datasets of HeLa and SiHa Cell Lines Acquired by DDA-PASEF and DiaPASEF	Huang, Z.; Kong, W. et al.	Data in Brief 2022, 41, 107919	https://doi.org/10.1016/j.dib.2022.107919
Integrative Proteomic and Phosphoproteomic Profiling of Invasive Micropapillary Breast Carcinoma	Chen, X.; Lin, Y. et at al.	Journal of Proteomics 2022, 257, 104511	https://doi.org/10.1016/j.jprot.2022.104511
Low-Intensity Blast Induces Acute Glutamatergic Hyperexcitability in Mouse Hippocampus Leading to Long-Term Learning Deficits and Altered Expression of Proteins Involved in Synaptic Plasticity and Serine Protease Inhibitors	Chen, S.; Siedhoff, H. R. et al.	Neurobiology of Disease 2022, 165, 105634	https://doi.org/10.1016/j.nbd.2022.105634
New Insights into the Phosphorylation of the Threonine Motif of the Β1 Integrin Cytoplasmic Domain	Böttcher, R. T.; Strohmeyer, N. et al.	Life Sci. Alliance 2022, 5 (4), e202101301	https://doi.org/10.26508/lsa.202101301
Proteomic Study of Hepatic Apoptosis Induced by Overexpression of G0S2	Qiu, Y.; Zhou, X. et al.	preprint; In Review, 2022	https://doi.org/10.21203/rs.3.rs-1342968/v1
Comprehensive Spectral Libraries for Various Rabbit Eye Tissue Proteomes	Qin, G.; Zhang, P. et al.	Sci Data 2022, 9 (1), 111	https://doi.org/10.1038/s41597-022-01241-5
Protective Mechanism of Leucine and Isoleucine against H2O2-Induced Oxidative Damage in Bovine Mammary Epithelial Cells	Wu, S.; Liu, X. et al.	Oxidative Medicine and Cellular Longevity 2022, 2022, 1–22	https://doi.org/10.1155/2022/4013575
Paeoniflorin Upregulates Mitochondrial Thioredoxin of Schwann Cells to Improve Diabetic Peripheral Neuropathy Indicated by 4D Label-Free Quantitative Proteomics	Yang, X.; Li, X. et al.	Oxidative Medicine and Cellular Longevity 2022, 2022, 1–10	https://doi.org/10.1155/2022/4775645
Chaperone-mediated autophagy controls proteomic and transcriptomic pathways to maintain glioma stem cell activity	Auzmendi-Iriarte, J.; Otaegi-Ugartemendia, M. et al.	Cancer Res 2022	https://doi.org/10.1158/0008-5472.CAN-21-2161
Reconstruction and analysis of a large-scale binary Ras-effector signaling network	Catozzi, S.; Ternet, C. et al.	Cell Commun Signal 2022, 20, 24	https://doi.org/10.1186/s12964-022-00823-5
Integrative proteomic and phosphoproteomic profiling of invasive micropapillary breast carcinoma	Chen, X.; Lin, Y. et al.	Journal of Proteomics 2022, 257	https://doi.org/10.1016/j.jprot.2022.104511
AP-4-mediated axonal transport controls endocannabinoid production in neurons	Davies, A.K.; Alecu, J.E. et al.	Nat Commun 2022, 13, 1058	https://doi.org/10.1038/s41467-022-28609-w
Combined Impact of Magnetic Force and Spaceflight Conditions on Escherichia coli Physiology	Domnin, P.A.; Parfenov, V.A.; Nikolaev, E.N. et al.	IJMS 2022, 23, 1837	https://doi.org/10.3390/ijms23031837
DNA damage contributes to neurotoxic inflammation in Aicardi-Goutières syndrome astrocytes	Giordano, A.M.S.; Luciani, M. et al.	Journal of Experimental Medicine 2022, 219	https://doi.org/10.1084/jem.20211121
Quantitative Proteomics Analysis Expands the Roles of Lysine β-Hydroxybutyrylation Pathway in Response to Environmental β-Hydroxybutyrate	Hou, W.; Liu, G. et al.	Oxidative Medicine and Cellular Longevity 2022, 1–15	https://doi.org/10.1155/2022/4592170
Diagnostic Ion Data Analysis Reduction (DIDAR) allows rapid quality control analysis and filtering of multiplexed single cell proteomics data	Jenkins, C.; Orsburn, B.C.	prepint; Biochemistry 2022	https://doi.org/10.1101/2022.02.22.481489
Nedd4-2 binding to 14-3-3 modulates the accessibility of its catalytic site and WW domains	Joshi, R.; Pohl, P. et al.	Biophysical Journal 2022, S0006349522001497	https://doi.org/10.1016/j.bpj.2022.02.025
High-light-inducible proteins HliA and HliB: pigment binding and protein–protein interactions	Konert, M.M.; Wysocka, A. et al.	Photosynth Res 2022	https://doi.org/10.1007/s11120-022-00904-z
Absolute quantification of viral proteins during single-round replication of MDCK suspension cells	Küchler, J.; Püttker, S. et al.	Journal of Proteomics 2022, 259	https://doi.org/10.1016/j.jprot.2022.104544
Ibrutinib reverses IL-6-induced osimertinib resistance through inhibition of Laminin α5/FAK signaling	Li, L.; Li, Z. et al.	Commun Biol 2022, 5, 155	https://doi.org/10.1038/s42003-022-03111-7
Detection of Mycotoxins in Highly Matrix-Loaded House-Dust Samples by QTOF-HRMS, IM-QTOF-HRMS, and TQMS: Advantages and Disadvantages	Lindemann, V.; Schmidt, J. et al.	Anal. Chem. 2022, 94, 4209–4217	https://doi.org/10.1021/acs.analchem.1c04254
Proximity proteomics of C9orf72 dipeptide repeat proteins identifies molecular chaperones as modifiers of poly-GA aggregation	Liu, F.; Morderer, D. et al.	acta neuropathol commun 2022, 10, 22	https://doi.org/10.1186/s40478-022-01322-x
Isoindolines and phthalides from the rhizomes of Ligusticum chuanxiong and their relaxant effects on the uterine smooth muscle	Liu, J.; Feng, R. et al.	Phytochemistry 2022, 198	https://doi.org/10.1016/j.phytochem.2022.113159
LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer	Murray, C.W.; Brady, J.J. et al.	Nat Commun 2022, 13, 1090	https://doi.org/10.1038/s41467-022-28619-8
Smart proteolysis samplers for pre‐lab bottom‐up protein analysis – Performance of on‐paper digestion compared to conventional digestion	Nguyen, M.T.; Halvorsen, T.G. et al.	Separation Science Plus 2022	https://doi.org/10.1002/sscp.202100062
Single Cell Proteomics Using a Trapped Ion Mobility Time-of-Flight Mass Spectrometer Provides Insight into the Post-translational Modification Landscape of Individual Human Cells	Orsburn, B.C.; Yuan, Y.; Bumpus, N.N.	preprint; Biochemistry 2022	https://doi.org/10.1101/2022.02.12.480144
Hornerin deposits in neuronal intranuclear inclusion disease: direct identification of proteins with compositionally biased regions in inclusions	Park, H.; Yamanaka, T. et al.	acta neuropathol commun 2022, 10, 28	https://doi.org/10.1186/s40478-022-01333-8
Elasnin Effectively Eradicates Daptomycin-Resistant Methicillin-Resistant Staphylococcus aureus Biofilms	Sulaiman, J.E.; Long, L. et al.	Microbiol Spectr 2022, 10	https://doi.org/10.1128/spectrum.02320-21
Time-related accurate investigation of multicomponent drug interventions in heart failure	Wang, M.; Wu, Y. et al.	Phytomedicine Plus 2022, 2	https://doi.org/10.1016/j.phyplu.2022.100242
Fritted tip capillary column with negligible dead volume facilitated ultrasensitive and deep proteomics	Yang, Y.; Su, Y. et al.	Analytica Chimica Acta 2022, 1201	https://doi.org/10.1016/j.aca.2022.339615
CPEB1 directs muscle stem cell activation by reprogramming the translational landscape	Zeng, W.; Yue, L. et al.	Nat Commun 2022, 13, 947	https://doi.org/10.1038/s41467-022-28612-1
Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro	Aballo, T.J.; Roberts, D.S. et al.	J. Proteome Res. 2021, 20, 4203–4211	https://doi.org/10.1021/acs.jproteome.1c00446
Analyzing changes in tear proteins of Sjogren’s syndrome patients with timsTOF pro	Akkurt Arslan, M.; Kolman, I. et al.	Acta Ophthalmologica 2022, 100	https://doi.org/10.1111/j.1755-3768.2022.167
Distribution of proteins in the different parts of the schirmer strip	Arslan, M.A.; Kolman, I. et al.	Acta Ophthalmologica 2022, 100	https://doi.org/10.1111/j.1755-3768.2022.179
Optimization of proteomics sample preparation for identification of host and bacterial proteins in mouse feces	Baniasad, M.; Kim, Y. et al.	Anal Bioanal Chem 2022	https://doi.org/10.1007/s00216-022-03885-z
New insights into the phosphorylation of the threonine motif of the β1 integrin cytoplasmic domain	Böttcher, R.T.; Strohmeyer, N. et al.	Life Sci. Alliance 2022, 5	https://doi.org/10.26508/lsa.202101301
The Parallel Reaction Monitoring-Parallel Accumulation–Serial Fragmentation (prm-PASEF) Approach for Multiplexed Absolute Quantitation of Proteins in Human Plasma	Brzhozovskiy, A.; Kononikhin, A et al.	Anal. Chem. 2022, 94, 2016–2022	https://doi.org/10.1021/acs.analchem.1c03782
Low-intensity blast induces acute glutamatergic hyperexcitability in mouse hippocampus leading to long-term learning deficits and altered expression of proteins involved in synaptic plasticity and serine protease inhibitors	Chen, S.; Siedhoff, H.R. et al.	Neurobiology of Disease 2022, 165	https://doi.org/10.1016/j.nbd.2022.105634
Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism	Duethorn, B.; Groll, F. et al.	Nat Commun 2022, 13, 610	https://doi.org/10.1038/s41467-022-28139-5
FASN-dependent de novo lipogenesis is required for brain development	Gonzalez-Bohorquez, D.; Gallego López, I.M. et al.	Proc Natl Acad Sci USA 2022, 119	https://doi.org/10.1073/pnas.2112040119
p-NCS-Bn-NODAGA as a bifunctional chelator for radiolabeling with the 186Re/99mTc-tricarbonyl core: Radiochemistry with model complexes and a GRPR-targeting peptide	Kankanamalage, P.; Hoerres, R. et al.	Nuclear Medicine and Biology 2022, 108–109, 1–9	https://doi.org/10.1016/j.nucmedbio.2022.01.004
Enhanced competitive protein exchange at the nano-bio interface enables ultra-deep coverage of the human plasma proteome	Hornburg, D.; Ferdosi, S. et al.	preprint; Biophysics 2022	https://doi.org/10.1101/2022.01.08.475439
Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF	Huang, Z.; Kong, W. et al.	Data in Brief 2022, 41	https://doi.org/10.1016/j.dib.2022.107919
Analysis of the molecular mechanism of inosine monophosphate deposition in Jingyuan chicken muscles using a proteomic approach	Huang, Z.; Zhang, J. et al.	Poultry Science 2022	https://doi.org/10.1016/j.psj.2022.101741
The [2Fe‐2S] protein CISD2 plays a key role in preventing iron accumulation in cardiomyocytes	Karmi, O.; Rowland, L. et al.	FEBS Letters 2022	https://doi.org/10.1002/1873-3468.14277
Altered glycosylation of several metastasis-associated glycoproteins with terminal GalNAc defines the highly invasive cancer cell phenotype	Khosrowabadi, E.; Wenta, T. et al.	Oncotarget 2022, 13, 73–89	https://doi.org/10.18632/oncotarget.28167
Mitochondrial protein hyperacetylation underpins heart failure with preserved ejection fraction in mice	Liu, X.; Zhang, Y. et al.	Journal of Molecular and Cellular Cardiology 2022, 165, 76–85	https://doi.org/10.1016/j.yjmcc.2021.12.015
Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined With Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open Reading Frame-Encoded Peptides	Peeters, M.K.R.; Baggerman, G. et al.	Front. Cell Dev. Biol. 2021, 9	https://doi.org/10.3389/fcell.2021.720570
Proteomics and Transcriptomics Uncover Key Processes for Elasnin Tolerance in Methicillin-Resistant Staphylococcus aureus	Sulaiman, J.E.; Long, L. et al.	mSystems 2022	https://doi.org/10.1128/msystems.01393-21
Protein phosphorylation in hemocytes of Fenneropenaeus chinensis in response to white spot syndrome virus infection	Tang, X.; Liu, T. et al.	Fish & Shellfish Immunology 2022, 122, 106–114	https://doi.org/10.1016/j.fsi.2022.01.038
Niban apoptosis regulator 1 promotes gemcitabine resistance by activating the focal adhesion kinase signaling pathway in bladder cancer	Tong, S.; Yin, H. et al.	J. Cancer 2022, 13, 1103–1118	https://doi.org/10.7150/jca.66248
Proteomics based markers of clinical pain severity in juvenile idiopathic arthritis	Van Der Heijden, H.; Fatou, B.; Steen, H. et al.	Pediatr Rheumatol 2022, 20, 3	https://doi.org/10.1186/s12969-022-00662-1
Doxycycline Alters the Porcine Renal Proteome and Degradome during Hypothermic Machine Perfusion	van Leeuwen, L.; Venema, L.H. et al.	CIMB 2022, 44, 559–577	https://doi.org/10.3390/cimb44020039
Investigation of Effects of the Spectral Library on Analysis of diaPASEF Data	Wen, C.; Gan, G. et al.	J. Proteome Res. 2021	https://doi.org/10.1021/acs.jproteome.1c00899
Erythrocyte transglutaminase-2 combats hypoxia and chronic kidney disease by promoting oxygen delivery and carnitine homeostasis	Xu, P.; Chen, C. et al.	Cell Metabolism 2022, 34	https://doi.org/10.1016/j.cmet.2021.12.019
Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric	Orsburn, B. C.	Proteomes 2021, 9 (3), 34	https://doi.org/10.3390/proteomes9030034
Proteomic Analysis of Tears and Conjunctival Cells Collected with Schirmer Strips Using timsTOF Pro: Preanalytical Considerations	Akkurt Arslan, M.; Kolman, I. et al.	Metabolites 2021, 12, 2	https://doi.org/10.3390/metabo12010002
Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry-Based Proteomics	Charkow, J.; Röst, H.L.	Anal. Chem. 2021, 93, 16751–16758	https://doi.org/10.1021/acs.analchem.1c01399
OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization	Cho, N.H.; Cheveralls, K.C.; Mann, M. et al.	preprint; Cell Biology 2021	https://doi.org/10.1101/2021.03.29.437450
Covalent Coupling of HIV-1 Glycoprotein Trimers to Biodegradable Calcium Phosphate Nanoparticles via Genetically Encoded Aldehyde-Tags	Damm, D.; Kostka, K. et al.	Acta Biomaterialia 2021, S1742706121008291	https://doi.org/10.1016/j.actbio.2021.12.022
Comparison of TIMS-PASEF quantitative proteomics data-analysis workflows using FragPipe, DIA-NN, and Spectronaut from a user’s perspective	Fernández-Vega, A.; Farabegoli, F. et al.	preprint; Molecular Biology 2021	https://doi.org/10.1101/2021.11.29.470373
Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules	Fojtík, L.; Fiala, J.; Novák, P. et al.	J. Am. Chem. Soc. 2021, 143, 20670–20679	https://doi.org/10.1021/jacs.1c07771
Functionalized Terpolymer-Brush-Based Biointerface with Improved Antifouling Properties for Ultra-Sensitive Direct Detection of Virus in Crude Clinical Samples	Forinová, M.; Pilipenco, A. et al.	ACS Appl. Mater. Interfaces 2021, 13, 60612–60624	https://doi.org/10.1021/acsami.1c16930
PIPP: Improving peptide identity propagation using neural networks	Hediyeh-zadeh, S.; Martin, J.; Webb, A.I. et al.	preprint; Bioinformatics 2021	https://doi.org/10.1101/2021.12.05.471338
Comprehensive Transcriptome Sequencing of Tanaidacea with Proteomic Evidences for Their Silk	Kakui, K.; Fleming, J.F. et al.	Genome Biology and Evolution 2021, 13	https://doi.org/10.1093/gbe/evab281
An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis	Li, C.; Gu, L. et al.	preprint; Systems Biology 2022	https://doi.org/10.1101/2022.01.02.474723
Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex	Loginov, D.S.; Fiala, J.; Novak, P. et al.	Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2022, 1870	https://doi.org/10.1016/j.bbapap.2021.140735
Structural amyloid plaque polymorphism is associated with distinct lipid accumulations revealed by trapped ion mobility mass spectrometry imaging	Michno, W.; Wehrli, P.M.; Hopf, C. et al.	Journal of Neurochemistry 2021	https://doi.org/10.1111/jnc.15557
A druggable addiction to de novo pyrimidine biosynthesis in diffuse midline glioma	Pal, S.; Kaplan, J.P. et al.	preprint; Cancer Biology 2021	https://doi.org/10.1101/2021.11.30.470644
De Novo Pyrimidine Synthesis is a Targetable Vulnerability in IDH Mutant Glioma	Shi, D.D.; Savani, M.R. et al.	preprint; Cancer Biology 2021	https://doi.org/10.1101/2021.11.30.470443
Antimicrobial Peptide BCp12 Inhibits Staphylococcus aureus Growth by Altering Lysine Malonylation Levels in the Arginine Synthesis Pathway	Shi, Y.; Li, Y. et al.	J. Agric. Food Chem. 2021	https://doi.org/10.1021/acs.jafc.1c05894
Application of LC-MS/MS with ion mobility for chemical analysis of propolis extracts with antimicrobial potential	Sofrenic, I.; Ljujic, J. et al.	J Serb Chem Soc 2021, 86–86	https://doi.org/10.2298/JSC210812086S
Association of Complement and MAPK Activation With SARS-CoV-2–Associated Myocardial Inflammation	Weckbach, L.T.; Schweizer, L.; Mann, M. et al.	JAMA Cardiol 2021	https://doi.org/10.1001/jamacardio.2021.5133
Investigation of Effects of the Spectral Library on Analysis of diaPASEF Data	Wen, C.; Gan, G. et al.	J. Proteome Res. 2021	https://doi.org/10.1021/acs.jproteome.1c00899
The effect of lipocalin-2 (LCN2) on apoptosis: a proteomics analysis study in an LCN2 deficient mouse model	Wu, D.; Wang, X. et al.	BMC Genomics 2021, 22, 892	https://doi.org/10.1186/s12864-021-08211-y
Multifunctional exosome-mimetics for targeted anti-glioblastoma therapy by manipulating protein corona	Wu, J.-Y.; Li, Y.-J. et al.	J Nanobiotechnol 2021, 19, 405	https://doi.org/10.1186/s12951-021-01153-3
Ultrasensitive Trace Sample Proteomics Unraveled the Protein Remodeling during Mesenchymal–Amoeboid Transition	Yang, S.; Xiong, Y. et al.	Anal. Chem. 2021	https://doi.org/10.1021/acs.analchem.1c03212
Mitochondrial C1qbp promotes differentiation of effector CD8 + T cells via metabolic-epigenetic reprogramming	Zhai, X.; Liu, K. et al.	Sci. Adv. 2021, 7	https://doi.org/10.1126/sciadv.abk0490
Effects of dietary selenium on immune function of spleen in mice	Zhang, X.; Zhang, L. et al.	Journal of Functional Foods 2022, 89	https://doi.org/10.1016/j.jff.2021.104914
Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology	Fuchs, T.; Melcher, F. et al.	Microb Cell Fact 2021, 20, 205	https://doi.org/10.1186/s12934-021-01692-2
Stability of proteins encapsulated in Michael‐type addition polyethylene glycol hydrogels	Ghassemi, Z.; Ruesing, S. et al.	Biotechnol Bioeng 2021, 118, 4840–4853	https://doi.org/10.1002/bit.27949
UPLC-MS/MS analysis and biological activity of the potato cyst nematode hatching stimulant, solanoeclepin A, in the root exudate of Solanum spp	Guerrieri, A.; Floková, K. et al.	Planta 2021, 254, 112	https://doi.org/10.1007/s00425-021-03766-2
Comparative Analysis of Dental Pulp and Periodontal Stem Cells: Differences in Morphology, Functionality, Osteogenic Differentiation and Proteome	Kotova, A.V.; Lobov, A.A. et al.	Biomedicines 2021, 9, 1606	https://doi.org/10.3390/biomedicines9111606
Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy	Lin, B.; Liu, J. et al.	BMC Genomics 2021, 22, 852	https://doi.org/10.1186/s12864-021-08155-3
Proteomic and lipidomic profiling of demyelinating lesions identifies fatty acids as modulators in lesion recovery	Penkert, H.; Bertrand, A. et al.	Cell Reports 2021, 37	https://doi.org/10.1016/j.celrep.2021.109898
Effect of age on the vascular proteome in middle cerebral arteries and mesenteric resistance arteries in mice	Rabaglino, M.B.; Wakabayashi, M. et al.	Mechanisms of Ageing and Development 2021, 200	https://doi.org/10.1016/j.mad.2021.111594
Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation	Schreiber, A.; Collins, B.C.; Aebersold, R. et al.	Molecular Cell 2021, S109727652100931X	https://doi.org/10.1016/j.molcel.2021.10.024
Systematic proteomics analysis of lysine acetylation reveals critical features of placental proteins in pregnant women with preeclampsia	Shangguan, Y.; Wang, Y. et al.	J Cell Mol Med 2021, 25, 10614–10626	https://doi.org/10.1111/jcmm.16997
Noncovalently Tagged Gas Phase Complex Ions for Screening Unknown Contaminant Metabolites in Plants	Shen, M.; Gong, X. et al.	Anal. Chem. 2021, 93, 14929–14933	https://doi.org/10.1021/acs.analchem.1c03145
Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition	Shrestha, V.; Yobi, A. et al.	Plant Physiology 2021	https://doi.org/10.1093/plphys/kiab390
A preliminary study of KAT2A on cGAS-related immunity in inflammation amplification of systemic lupus erythematosus	Tang, Y.; Li, X. et al.	Cell Death Dis 2021, 12, 1036	https://doi.org/10.1038/s41419-021-04323-1
4D-quantitative proteomics signature of asthenozoospermia and identification of extracellular matrix protein 1 as a novel biomarker for sperm motility	Yang, J.; Liu, Q. et al.	Mol. Omics 2021	https://doi.org/10.1039/D1MO00257K
Proteomic Analysis of Chrysanthemum Lateral Buds after Removing Apical Dominance Based on Label-Free Technology	Zheng, S.; Song, J. et al.	Phyton 2022, 91, 525–539	https://doi.org/10.32604/phyton.2022.017629
Red Blood Cell Proteasome in Beta-Thalassemia Trait: Topology of Activity and Networking in Blood Bank Conditions	Anastasiadi, A.T.; Tzounakas, V.L. et al.	Membranes 2021, 11, 716	https://doi.org/10.3390/membranes11090716
Proteomic Analysis of the Functional Inward Rectifier Potassium Channel (Kir) 2.1 Reveals Several Novel Phosphorylation Sites	Brown, K.A.; Anderson, C.; Ge, Y. et al.	Biochemistry 2021	https://doi.org/10.1021/acs.biochem.1c00555
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Cathepsin C Is Involved in Macrophage M1 Polarization via p38/MAPK Pathway in Sudden Cardiac Death	Dai, J.; Liu, J. et al.	Cardiovascular Therapeutics 2021, 1–12	https://doi.org/10.1155/2021/6139732
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Plasmodium sporozoites require the protein B9 to invade hepatocytes	Fernandes, P.; Loubens, M. et al.	preprint; Microbiology 2021	https://doi.org/10.1101/2021.10.25.465731
Musarin, a novel protein with tyrosine kinase inhibitory activity from Trametes versicolor, accepted inhibits colorectal cancer stem cell growth	He, Y.; Liu, S. et al.	Biomedicine & Pharmacotherapy 2021, 144, 112339	https://doi.org/10.1016/j.biopha.2021.112339
Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria	Herbert, C.J.; Labarre-Mariotte, S. et al.	Nucleic Acids Research 2021	https://doi.org/10.1093/nar/gkab789
Identification of proteins associated with Fusarium crown rot resistance in wheat using label-free quantification analysis	Jin, J.; Duan, S. et al.	Journal of Integrative Agriculture 2021, 20, 3209–3221	https://doi.org/10.1016/S2095-3119(20)63573-0
Cell-surface tethered promiscuous biotinylators enable small-scale surface proteomics of human exosomes	Kirkemo, L.L.; Elledge, S.K. et al.	preprint; Biochemistry 2021	https://doi.org/10.1101/2021.09.22.461393
Loss of the AMD-associated B3GLCT gene affects glycosylation of TSP1 without impairing secretion in retinal pigment epithelial cells 27	Lauwen, S.		https://doi.org/10.1016/j.exer.2021.108798
Effects of Tartary Buckwheat Protein on Gut Microbiome and Plasma Metabolite in Rats with High-Fat Diet	Liu, J.; Song, Y. et al.	Foods 2021, 10	https://doi.org/10.3390/foods10102457
Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex	Loginov, D.S.; Fiala, J.; Novak, P. et al.	preprint; Biochemistry 2021	https://doi.org/10.1101/2021.09.20.461051
Tyrosine phosphorylation of DEPTOR functions as a molecular switch to activate mTOR signaling	Gagné, L.; Morin, N. et al.	Journal of Biological Chemistry 2021, 297	https://doi.org/10.1016/j.jbc.2021.101291
Developing a mechanically matched decellularized spinal cord scaffold for the in situ matrix-based neural repair of spinal cord injury	Ma, Y.; Shi, H. et al.	Biomaterials 2021, 279	https://doi.org/10.1016/j.biomaterials.2021.121192
Heading towards a dead end: The role of DND1 in germ line differentiation of human iPSCs	Mall, E.M.; Lecanda, A. et al.	PLoS ONE 2021, 16	https://doi.org/10.1371/journal.pone.0258427
The social architecture of an in-depth cellular protein interactome	Michaelis, A.C.; Brunner, A.-D.; Mann, M. et al.	preprint; Systems Biology 2021	https://doi.org/10.1101/2021.10.24.465633
Differential Brain and Cerebrospinal Fluid Proteomic Responses to Acute Prenatal Endotoxin Exposure	Muk, T.; Stensballe, A. et al.	preprint; In Review 2021	https://doi.org/10.21203/rs.3.rs-910516/v1
Genome-Wide Analyses of Proteome and Acetylome in Zymomonas mobilis Under N2-Fixing Condition	Nisar, A.; Gongye, X. et al.	Front. Microbiol. 2021, 12	https://doi.org/10.3389/fmicb.2021.740555
Exploration of Proteomics Analysis of Crop Milk in Pigeons ( Columba livia ) during the Lactation Period	Shao, Y.; Ma, W. et al.	ACS Omega 2021, 6, 27726–27736	https://doi.org/10.1021/acsomega.1c02977
A stress-reduced passaging technique improves the viability of human pluripotent cells	Takahashi, K.; Okubo, C. et al.	preprint; Cell Biology 2021	https://doi.org/10.1101/2021.10.12.464142
YY1 lactylation in microglia promotes angiogenesis through transcription activation-mediated upregulation of FGF2	Wang, X.; Fan, W. et al.	preprint; In Review 2021	https://doi.org/10.21203/rs.3.rs-910016/v1
Simplifying MS1 and MS2 spectra to achieve lower mass error, more dynamic range, and higher peptide identification confidence on the Bruker timsTOF Pro	Wilding-McBride, D.; Dagley, L.F. et al.	Bioinformatics 2021	https://doi.org/10.1101/2021.10.18.464737
Global Profiling of Protein Lysine Malonylation in Eucommia ulmoides Leaves Reveals Its Role in Photosynthesis and Metabolism	Yao, X.; Shen, C. et al.	Plant Mol Biol Rep 2021	https://doi.org/10.1007/s11105-021-01319-1
PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors	Zhu, H.; Ficarro, S.B.; Marto, J.A et al.	Anal. Chem. 2021, 93, 13791–13799	https://doi.org/10.1021/acs.analchem.1c02349
Integration of Transcriptomic And Proteomic Analyses Reveals Several Levels of Metabolic Regulation In The Excess Starch And Early Senescent Leaf Mutant lses1 In Rice	Chen, Z.; Wang, Y. et al.	preprint; In Review 2021	https://doi.org/10.21203/rs.3.rs-805903/v1
Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System	Gnanasekaran, T.; Assis Geraldo, J. et al.	mSystems 6 2021	https://doi.org/10.1128/mSystems.00232-21
Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra	Gutenbrunner, P.; Kyriakidou, P. et al.	preprint; Bioinformatics 2021	https://doi.org/10.1101/2021.09.04.458985
Upregulation of α enolase (ENO1) crotonylation in colorectal cancer and its promoting effect on cancer cell metastasis	Hou, J.-Y.; Cao, J. et al.	Biochemical and Biophysical Research Communications 2021, 578, 77–83	https://doi.org/10.1016/j.bbrc.2021.09.027
Characterization of the microRNA Transcriptomes and Proteomics of Cochlea Tissue-derived Small Extracellular Vesicles From Different Age of Mice After Birth	Jiang, P.; Ma, X. et al.	preprint; In Review 2021	https://doi.org/10.21203/rs.3.rs-823336/v1
Drone honey bees (Apis mellifera ) are disproportionately sensitive to abiotic stressors despite expressing high levels of stress response proteins	McAfee, A.; Metz, B. et al.	preprint; Cell Biology 2021	https://doi.org/10.1101/2021.08.28.456261
Evaluation of a Bruker timsTOF Pro for Native Mass Spectrometry	Panczyk, E.; Snyder, D. et al.	preprint; Chemistry 2021	https://doi.org/10.33774/chemrxiv-2021-qr78t
Identification of potential autoantigens in anti-CCP-positive and anti-CCP-negative rheumatoid arthritis using citrulline-specific protein arrays	Poulsen, T.B.G.; Damgaard, D.; Stensballe, A. et al.	Sci Rep 2021, 11, 17300	https://doi.org/10.1038/s41598-021-96675-z
Thiol and Disulfide Containing Vancomycin Derivatives Against Bacterial Resistance and Biofilm Formation	Shchelik, I.S.; Gademann, K.	preprint; Microbiology 2021	https://doi.org/10.1101/2021.08.23.457343
Use of PASEF for Accelerated Protein and De Novo Sequencing with High Data Quality	Suckau, D.; Evers, W.; Beck, A. et al.	2022, In: Houen, G. (Ed.), Therapeutic Antibodies, Methods in Molecular Biology. Springer US, New York, NY, pp. 207–217	https://doi.org/10.1007/978-1-0716-1450-1_12
Accurate and automated high-coverage identification of chemically cross-linked peptides with MaxLynx	Yılmaz, Ş.; Busch, F.; Cox, J. et al.	preprint; Bioinformatics 2021	https://doi.org/10.1101/2021.08.26.457759
A Multi-omics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes	Bayne, E.F.; Simmons, A.D.; Ge, Y. et al.	preprint; Systems Biology 2021	https://doi.org/10.1101/2021.06.23.449630
Synthetic antigen-presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses	Céspedes, P.F.; Jainarayanan, A.; Fischer, R. et al.	preprint; Immunology 2021	https://doi.org/10.1101/2021.05.29.445691
Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System	Gnanasekaran, T.; Assis Geraldo, J. et al.	mSystems 2021	https://doi.org/10.1128/mSystems.00232-21
Complementing Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging with Chromatography Data for Improved Assignment of Isobaric and Isomeric Phospholipids Utilizing Trapped Ion Mobility-Mass Spectrometry	Helmer, P.O.; Nordhorn, I.D.; Zubeil, F. et al.	Anal. Chem. 2021, 93, 2135–2143	https://doi.org/10.1021/acs.analchem.0c03942
Salivary proteome of aphthous stomatitis reveals the participation of vitamin metabolism, nutrients, and bacteria	Hernández-Olivos, R.; Muñoz, M. et al.	preprint; Dentistry and Oral Medicine 2021	https://doi.org/10.1101/2021.08.01.21261411
Darwin’s bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression	Kono, N.; Ohtoshi, R. et al.	preprint; Molecular Biology 2021	https://doi.org/10.1101/2021.07.16.452619
High-Throughput Multi-attribute Analysis of Antibody-Drug Conjugates Enabled by Trapped Ion Mobility Spectrometry and Top-Down Mass Spectrometry	Larson, E.J.; Roberts, D.S.; Ge, Y. et al.	Anal. Chem. 2021, 93, 10013–10021	https://doi.org/10.1021/acs.analchem.1c00150
Comparative Proteomic Analysis to Investigate the Pathogenesis of Oral Adenoid Cystic Carcinoma	Li, W.; Zhang, Q. et al.	ACS Omega 2021, 6, 18623–18634	https://doi.org/10.1021/acsomega.1c01270
Mode of action of Elasnin as biofilm-formation eradicator of Methicillin-Resistant Staphylococcus aureus	Long, L.; Sulaiman, J.E. et al.	preprint; In Review 2021	https://doi.org/10.21203/rs.3.rs-752510/v1
Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation – Serial Fragmentation (PASEF) in Proteomics	Meier, F.; Park, M.A.; Mann, M.	Molecular & Cellular Proteomics 2021, 100138	https://doi.org/10.1016/j.mcpro.2021.100138
Investigating Closed Room Conspirators of Posttraumatic Inflammatory Response: Multi- Omics Profiles of Exosomes Derived from Intestinal Epithelial Cells Under Ischemia Reperfusion Injury	Senda, A.; Kojima, M. et al.	preprint; In Review 2021	https://doi.org/10.21203/rs.3.rs-792334/v1
Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows	Van Den Bossche, T.; Kunath, B.J. et al.	preprint; Microbiology 2021	https://doi.org/10.1101/2021.03.05.433915
AlphaTims: Indexing trapped ion mobility spectrometry – time of flight data for fast and easy accession and visualization	Willems, S.; Voytik, E.; Mann, M. et al.	preprint; Bioinformatics 2021	https://doi.org/10.1101/2021.07.27.453933
Integrative proteomics and phosphoproteomics reveals phosphorylation networks involved in the maintenance and expression of embryogenic competence in sugarcane callus	Xavier, L.R.; Almeida, F.A. et al.	preprint; Plant Biology 2021	https://doi.org/10.1101/2021.07.22.453415
Integrative proteomic and metabolomic analyses reveal the mechanism by which bismuth enables Helicobacter pylori eradication	Yao, X.; Xiao, S.; Zhou, L.	Helicobacter 2021	https://doi.org/10.1111/hel.12846
Comparative analyses of the venom components in the salivary gland transcriptomes and saliva proteomes of some heteropteran insects	Yoon, K.A.; Kim, W. et al.	Insect Science 2021, 1744-7917.12955	https://doi.org/10.1111/1744-7917.12955
MaxDIA enables library-based and library-free data-independent acquisition proteomics	Sinitcyn, P.; Hamzeiy, H.; Cox, J. et al.	Nat Biotechnol, 2021	https://doi.org/10.1038/s41587-021-00968-7
A Multi-omics Strategy Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes	Bayne, E.F.; Simmons, A.D.; Ge, Y. et al.	preprint; Systems Biology, 2021	https://doi.org/10.1101/2021.06.23.449630
Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale	Bob, K.; Teschner, D.; Tenzer, S. et al.	preprint; Bioinformatics, 2021	https://doi.org/10.1101/2021.07.01.450702
Fragmentation and Mobility Separation of Peptide and Protein Ions in a Trapped-Ion Mobility Device	Borotto, N.B.; Graham, K.A.	Anal. Chem., 2021	https://doi.org/10.1021/acs.analchem.1c01188
Metabolomic Profiling of Human Urine Samples Using LC-TIMS-QTOF Mass Spectrometry	Di Poto, C.; Tian, X. et al.	J. Am. Soc. Mass Spectrom., 2021	https://doi.org/10.1021/jasms.0c00467
BCAR1 plays critical roles in the formation and immunoevasion of invasive circulating tumor cells in lung adenocarcinoma	Mao, C.-G.; Jiang, S. et al.	Int. J. Biol. Sci., 2021, 17, 2461–2475	https://doi.org/10.7150/ijbs.61790
Insight into the collagen-degrading activity of a serine protease in the latex of Ficus carica cultivar Masui Dauphine	Nishimura, K.; Higashiya, K. et al.	Bioscience, Biotechnology, and Biochemistry, 2021, 85, 1147–1156	https://doi.org/10.1093/bbb/zbab025
The differences of muscle proteins between neon flying squid (Ommastrephes bartramii) and jumbo squid (Dosidicus gigas) mantles via physicochemical and proteomic analyses	Shui, S.; Yao, H. et al.	Food Chemistry, 2021, 364, 130374	https://doi.org/10.1016/j.foodchem.2021.130374
Global profiling of RNA-binding protein target sites by LACE-seq	Su, R.; Fan, L.-H.; Wong, C.C.L et al.	Nat Cell Biol, 2021, 23, 664–675	https://doi.org/10.1038/s41556-021-00696-9
Physiological and Proteomic Responses of Pitaya to PEG-Induced Drought Stress	Wang, A.; Ma, C. et al.	Agriculture, 2021, 11, 632	https://doi.org/10.3390/agriculture11070632
A cell-sorting-based nano-scale pipeline for cell-type specific proteomics in plants	Wang, H.; Li, R. et al.	preprint; Plant Biology, 2021	https://doi.org/10.1101/2021.07.06.451220
Proteomics and bioinformatics reveal insights into neuroinflammation in the acute to subacute phases in rat models of spinal cord contusion injury	Yao, X.; Liu, Z. et al.	FASEB, 2021, 35	https://doi.org/10.1096/fj.202100081RR
Nuclear receptors NHR-49 and NHR-79 promote peroxisome proliferation to compensate for aldehyde dehydrogenase deficiency in C. elegans	Zeng, L.; Li, X. et al.	PLoS Genet, 2021, 17	https://doi.org/10.1371/journal.pgen.1009635
Multi-omics analyses of human colorectal cancer revealed three mitochondrial genes potentially associated with poor outcomes of patients	Zhang, W.; Lin, L. et al.	J Transl Med, 2021, 19, 273	https://doi.org/10.1186/s12967-021-02939-7
Integrative multiplatform-based molecular profiling of human colorectal cancer reveals proteogenomic alterations underlying mitochondrial inactivation	Zhang, W.; Tang, D. et al.	Am J Cancer Res, 2021, 11, 2893–2910	https://pubmed.ncbi.nlm.nih.gov/34249434
Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro	Aballo, T.J.; Roberts, D.S.; Ge, Y. et al.	preprint; Systems Biology, 2021	https://doi.org/10.1101/2021.05.24.445470
DeGlyPHER: an ultrasensitive method for analysis of viral spike N-glycoforms	Baboo, S.; Diedrich, J.K.; Yates, J.R. et al.	preprint; Biochemistry, 2021	https://doi.org/10.1101/2021.05.13.444041
Identification of proximal SUMO-dependent interactors using SUMO-ID	Barroso-Gomila, O.; Trulsson, F.; Azkargorta, M. et al.	preprint; Biochemistry, 2020	https://doi.org/10.1101/2020.12.28.424528
Synthetic Antigen Presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses	Céspedes, P.F.; Jainarayanan, A.; Fischer, R. et al.	preprint; Immunology, 2021	https://doi.org/10.1101/2021.05.29.445691
Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles	De Vrieze, J.; Heyer, R. et al.	preprint; Bioengineering, 2021	https://doi.org/10.1101/2021.05.28.446109
A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines	Feola, S.; Chiaro, J.; Lehtiö, J. et al.	preprint; Cancer Biology, 2021	https://doi.org/10.1101/2021.06.08.447483
PeptiCHIP: a novel microfluidic-based chip platform for tumour antigen landscape identification	Feola, S.; Haapala, M.; Lehtiö, J. et al.	preprint; In Review, 2021	https://doi.org/10.21203/rs.3.rs-156531/v1
Immunomodulation of T Helper Cells by Tumor Microenvironment in Oral Cancer Is Associated With CCR8 Expression and Rapid Membrane Vitamin D Signaling Pathway	Fraga, M.; Yáñez, M. et al.	Front. Immunol., 2021, 12	https://doi.org/10.3389/fimmu.2021.643298
Two-dimensional guanidinium-based covalent organic nanosheets for controllable recognition and specific enrichment of global/multi-phosphopeptides	He, Y.; Huang, W. et al.	Talanta, 2021, 233	https://doi.org/10.1016/j.talanta.2021.122497
A ciliopathy complex builds distal appendages to initiate ciliogenesis	Kumar, D.; Rains, A. et al.	preprint; Cell Biology, 2021	https://doi.org/10.1101/2021.03.01.433418
High resolution analysis of proteome dynamics during Bacillus subtilis sporulation	Tu, Z.; Dekker, H.L.; Kramer, G. et al.	preprint; Microbiology, 2021	https://doi.org/10.1101/2021.05.20.445030
LRRC23 is a conserved component of the radial spoke that is necessary for sperm motility and male fertility in mice	Zhang, X.; Sun, J. et al.	preprint; Cell Biology, 2021	https://doi.org/10.1101/2021.06.01.446532
Ribosome-Inactivating Proteins of Bougainvillea Glabra Uncovered Polymorphism and Active Site Divergence	Lin, Y.; Xu, L. et al.	Toxins 2021, 13 (5), 331	https://doi.org/10.3390/toxins13050331
Integrated Phospho-Proteogenomic and Single-Cell Transcriptomic Analysis of Meningiomas Establishes Robust Subtyping and Reveals Subtype-Specific Immune Invasion	Blume, C.; Dogan, H.; Mann, M. et al.	preprint; Genomics, 2021	https://doi.org/10.1101/2021.05.11.443369
Tetrahydrocurcumin Ameliorates Alzheimer’s Pathological Phenotypes by Inhibition of Microglial Cell Cycle Arrest and Apoptosis via Ras/ERK Signaling	Xiao, Y.; Dai, Y. et al.	Biomedicine & Pharmacotherapy 2021, 139	https://doi.org/10.1016/j.biopha.2021.111651
Hypoxic Acclimation Improves Cardiac Redox Homeostasis and Protects Heart against Ischemia-Reperfusion Injury through Upregulation of O-GlcNAcylation	Ou, W.; Liang, Y et al.	Redox Biology 2021, 101994	https://doi.org/10.1016/j.redox.2021.101994
DNA Binding Mode, Photophysical Properties and Recommendations for Use of SYBR Gold	Kolbeck, P. J.; Vanderlinden, W. et al.	Molecular Structure, Nucleic Acids Research 2021, gkab265	https://doi.org/10.1093/nar/gkab265
Comprehensive Plasma Proteomics by Orthogonal Protease Digestion	Fossati, A.; Richards, A. L. et al.	preprint; Systems Biology, 2021	https://doi.org/10.1101/2021.04.28.441706
Multicomponent Nature Underlies the Extraordinary Mechanical Properties of Spider Dragline Silk	Kono, N.; Nakamura, H. et al.	preprint; Molecular Biology, 2021	https://doi.org/10.1101/2021.04.22.441049
MiRNAs and Their Gene Targets—A Clue to Differentiate Pregnancies with Small for Gestational Age Newborns, Intrauterine Growth Restriction, and Preeclampsia	Timofeeva, A. V.; Fedorov, I. S. et al.	Diagnostics 2021, 11 (4), 729	https://doi.org/10.3390/diagnostics11040729
The Autophagy Receptor TAX1BP1 (T6BP) Is a Novel Player in Antigen Presentation by MHC-II Molecules	Pereira, M.; Richetta, C.; Pionneau, C. et al.	preprint; Immunology, 2021	https://doi.org/10.1101/2021.04.21.440798
Conformational Interconversion of MLKL and Disengagement from RIPK3 Precede Cell Death by Necroptosis	Garnish, S. E.; Meng, Y. et al.	Nat Commun 2021, 12 (1), 2211	https://doi.org/10.1038/s41467-021-22400-z
Comprehensive Analysis of Lysine Succinylation in Paper Mulberry (Broussonetia Papyrifera)	Dong, Y.; Li, P. et al.	First BMC Genomics 2021, 22 (1), 255	https://doi.org/10.1186/s12864-021-07567-5
Benefits of Ion Mobility Separation and Parallel Accumulation–Serial Fragmentation Technology on TimsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis	Loginov, D. S.; Fiala, J. et al.	ACS Omega 2021, 6 (15), 10352–10361	https://doi.org/10.1021/acsomega.1c00732
SLPI Is a Critical Mediator That Controls PTH-Induced Bone Formation	Morimoto, A.; Kikuta, J. et al.	Nat Commun 2021, 12 (1), 2136	https://doi.org/10.1038/s41467-021-22402-x
Analysis of Peptide Stereochemistry in Single Cells by Capillary Electrophoresis–Trapped Ion Mobility Spectrometry Mass Spectrometry	Mast, D. H.; Liao, H.-W.; Sweedler, J. V. et al.	Anal. Chem. 2021, 93 (15), 6205–6213	https://doi.org/10.1021/acs.analchem.1c00445
Simplified High-Throughput Methods for Deep Proteome Analysis on the TimsTOF Pro	Sandow, J. J.; Infusini, G.; Webb, A. I. et al.	preprint; Biochemistry, 2019	https://doi.org/10.1101/657908
Ti4+-Immobilized Hierarchically Porous Zirconium-Organic Frameworks for Highly Efficient Enrichment of Phosphopeptides	He, Y.; Zheng, Q. et al.	Microchim Acta 2021, 188 (5), 150	https://doi.org/10.1007/s00604-021-04760-x
Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry Based Workflow	Charkow, J.; Röst, H. L.	preprint; Bioinformatics, 2021	https://doi.org/10.1101/2021.04.01.438072
Elongation Factor EEF2 Kinase and Autophagy Jointly Promote Survival of Cancer Cells	Lenchine, R. V.; Rao, S. R. et al.	Biochemical Journal 2021, 478 (8), 1547–1569	https://doi.org/10.1042/BCJ20210126
Proteome-Scale Endogenous Tagging Enables the Cartography of Human Cellular Organization	Cho, N. H.; Cheveralls, K. C.; Mann, M. et al.	OpenCell; preprint; Cell Biology, 2021	https://doi.org/10.1101/2021.03.29.437450
Hippocampal Proteomic Analysis Reveals Activation of Necroptosis and Ferroptosis in a Mouse Model of Chronic Unpredictable Mild Stress-Induced Depression	Huang, Y.; Zhu, L. et al.	Behavioural Brain Research 2021, 407, 113261	https://doi.org/10.1016/j.bbr.2021.113261
Developing a Multivariable Prediction Model for Functional Outcome after Reperfusion Therapy for Acute Ischaemic Stroke: Study Protocol for the Targeting Optimal Thrombolysis Outcomes (TOTO) Multicentre Cohort Study	Holliday, E.; Lillicrap, T. et al.	BMJ Open 2020, 10 (4), e038180	https://doi.org/10.1136/bmjopen-2020-038180
Cross-Linking/Mass Spectrometry Combined with Ion Mobility on a TimsTOF Pro Instrument for Structural Proteomics	Ihling, C. H.; Piersimoni, L. et al.	preprint; Biochemistry, 2021	https://doi.org/10.1101/2021.03.26.437136
Temporarily Epigenetic Repression in Bergmann Glia Regulates the Migration of Granule Cells	Chen, S.; Zhang, K. et al.	Adv. Sci. 2021, 2003164	https://doi.org/10.1002/advs.202003164
Ubiquitin Specific Peptidase 32 Acts as an Oncogene in Epithelial Ovarian Cancer by Deubiquitylating Farnesyl-Diphosphate Farnesyltransferase 1	Nakae, A.; Kodama, M. et al.	Biochemical and Biophysical Research Communications 2021, 552, 120–127	https://doi.org/10.1016/j.bbrc.2021.03.049
Open and Easy Access to TimsTOF Raw Data	Łącki, M. K.; Startek, M. P. et al.	OpenTIMS, TimsPy, and TimsR: J. Proteome Res. 2021, 20 (4), 2122–2129	https://doi.org/10.1021/acs.jproteome.0c00962
High Sensitivity Dia-PASEF Proteomics with DIA-NN and FragPipe	Demichev, V.; Yu, F. et al.	preprint; Bioinformatics, 2021	https://doi.org/10.1101/2021.03.08.434385
Packed Red Blood Cells Inhibit T-Cell Activation via ROS-Dependent Signaling Pathways	Gerner, M. C.; Bileck, A. et al.	Journal of Biological Chemistry 2021, 296, 100487	https://doi.org/10.1016/j.jbc.2021.100487
Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows	Van Den Bossche, T.; Kunath, B. J. et al.	preprint; Microbiology, 2021	https://doi.org/10.1101/2021.03.05.433915
A Ciliopathy Complex Builds Distal Appendages to Initiate Ciliogenesis	Kumar, D.; Rains, A. et al.	preprint; Cell Biology, 2021	https://doi.org/10.1101/2021.03.01.433418
Global Proteomic Analysis of Extracellular Matrix in Mouse and Human Brain Highlights Relevance to Cerebrovascular Disease	Pokhilko, A.; Brezzo, G. et al.	Cereb Blood Flow Metab 2021, 0271678X2110043	https://doi.org/10.1177/0271678X211004307
Deep Learning the Collisional Cross Sections of the Peptide Universe from a Million Experimental Values	Meier, F.; Köhler, N. D. et al.	Nat Commun 2021, 12 (1), 1185	https://doi.org/10.1038/s41467-021-21352-8
Comparison of Lipidome Profiles of Caenorhabditis Elegans—Results from an Inter-Laboratory Ring Trial	Spanier, B.; Laurençon, A. et al.	Metabolomics 2021, 17 (3), 25	https://doi.org/10.1007/s11306-021-01775-6
Insight into the Collagen-Degrading Activity of a Serine Protease in the Latex of Ficus Carica Cultivar Masui Dauphine	Nishimura, K.; Higashiya, K. et al.	Bioscience, Biotechnology, and Biochemistry 2021, 85 (5), 1147–1156	https://doi.org/10.1093/bbb/zbab025
Genome-Wide CRISPRi Screening Identifies OCIAD1 as a Prohibitin Client and Regulatory Determinant of Mitochondrial Complex III Assembly in Human Cells	Vasseur, M. L.; Friedman, J. R. et al.	preprint; Cell Biology, 2021	https://doi.org/10.1101/2021.02.16.431450
KCTD19 Associates with ZFP541 and HDAC1 and Is Required for Meiotic Exit in Male Mice	Oura, S.; Koyano, T. et al.	preprint; Developmental Biology, 2021	https://doi.org/10.1101/2021.02.12.430913
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Unraveling the Phosphoproteome with Trapped Ion Mobility Spectrometry (TIMS)	Ishihama, Y.	Drug Discovery World, January 2021
Acute Post-Injury Blockade of Α2δ-1 Calcium Channel Subunits Prevents Pathological Autonomic Plasticity after Spinal Cord Injury	Brennan, F. H.; Noble, B. T. et al.	Cell Reports 2021, 34 (4), 108667	https://doi.org/10.1016/j.celrep.2020.108667
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A CRISPR-Based Genome-Wide Screen for Adipogenesis Reveals New Insights into Mitotic Expansion and Lipogenesis	Hilgendorf, K. I.; Johnson, C. T. et al.	preprint; Molecular Biology, 2020	https://doi.org/10.1101/2020.07.13.201038
Divergent Molecular Signatures of Regeneration and Fibrosis during Wound Repair	Mascharak, S.; desJardins-Park, H. E. et al.	preprint; Cell Biology, 2020	https://doi.org/10.1101/2020.12.17.423181
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In-Depth Proteomic Analysis of Plasmodium Berghei Sporozoites Using Trapped Ion Mobility Spectrometry with Parallel Accumulation-Serial Fragmentation	Hamada, S.; Pionneau, C. et al.	preprint; Microbiology, 2020	https://doi.org/10.1101/2020.11.26.400192
Licorice Ameliorates Cisplatin-Induced Hepatotoxicity Through Antiapoptosis, Antioxidative Stress, Anti-Inflammation, and Acceleration of Metabolism	Man, Q.; Deng, Y. et al.	Front. Pharmacol. 2020, 11, 563750	https://doi.org/10.3389/fphar.2020.563750
Multi-Omics Profiling of Living Human Pancreatic Islet Donors Reveals Heterogeneous Beta Cell Trajectories toward Type 2 Diabetes	Wigger, L.; Barovic, M. et al.	preprint; Bioinformatics, 2020	https://doi.org/10.1101/2020.12.05.412338
Nuclear Receptor NHR-49 Promotes Peroxisome Proliferation to Compensate for Aldehyde Dehydrogenase Deficiency in C. Elegans	Zeng, L.; Li, X. et al.	preprint; Cell Biology, 2020	https://doi.org/10.1101/2020.12.04.411637
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The MPK 8‐ TCP 14 Pathway Promotes Seed Germination in Arabidopsis	Zhang, W.; Cochet, F. et al.	Plant J 2019, 100 (4), 677–692	https://doi.org/10.1111/tpj.14461
The Marine Bivalve Molluscs Pathogen Vibrio Neptunius Produces the Siderophore Amphibactin Which Is Widespread in Molluscs Microbiota	Galvis, F.; Ageitos, L. et al.	Environ Microbiol 2020, 1462-2920.15312	https://doi.org/10.1111/1462-2920.15312
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Antagonistic Regulation by CPN60A and CLPC1 of TRXL1 That Regulates MDH Activity Leading to Plant Disease Resistance and Thermotolerance	Pant, B. D.; Oh, S. et al.	Cell Reports 2020, 33 (11), 108512	https://doi.org/10.1016/j.celrep.2020.108512
Pharmacological Targeting of Vacuolar H+-ATPase via Subunit V1G Combats Multidrug-Resistant Cancer	Wang, Y.; Zhang, L. et al.	Cell Chemical Biology 2020, 27 (11), 1359-1370.e8	https://doi.org/10.1016/j.chembiol.2020.06.011
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Effect of (R)‐salbutamol on the Switch of Phenotype and Metabolic Pattern in LPS‐induced Macrophage Cells	Wang, S.; Liu, F. et al.	Cell Mol Med 2020, 24 (1), 722–736	https://doi.org/10.1111/jcmm.14780
Label-Free Quantitative Phosphoproteomics Reveals Signaling Dynamics Involved in Embryogenic Competence Acquisition in Sugarcane	Almeida, F. A.; Passamani, L. Z. et al.	Proteome Res. 2020, 19 (10), 4145–4157	https://doi.org/10.1021/acs.jproteome.0c00652
The Occurrence of Sulfated Salicinoids in Poplar and Their Formation by Sulfotransferase1	Lackus, N. D.; Müller, A. et al.	Plant Physiol. 2020, 183 (1), 137–151	https://doi.org/10.1104/pp.19.01447
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LUZP1, a Novel Regulator of Primary Cilia and the Actin Cytoskeleton, Is a Contributing Factor in Townes-Brocks Syndrome	Bozal-Basterra, L.; Gonzalez-Santamarta, M. et al.	eLife 2020, 9, e55957	https://doi.org/10.7554/eLife.55957
Ectosomal PKM2 Promotes HCC by Inducing Macrophage Differentiation and Remodeling the Tumor Microenvironment	Hou, P.; Luo, L. et al.	Molecular Cell 2020, 78 (6), 1192-1206.e10	https://doi.org/10.1016/j.molcel.2020.05.004
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Targeting Fibroblast Activation Protein: Radiosynthesis and Preclinical Evaluation of an 18 F-Labeled FAP Inhibitor	Toms, J.; Kogler, J. et al.	Nucl Med 2020, 61 (12), 1806–1813	https://doi.org/10.2967/jnumed.120.242958
Effects of a Pyroglutamyl Pentapeptide Isolated from Fermented Barley Extract on Atopic Dermatitis-like Skin Lesions in Hairless Mouse	Maruoka, N.; Watanabe, B. et al.	Bioscience, Biotechnology, and Biochemistry 2020, 84 (8), 1696–1705	https://doi.org/10.1080/09168451.2020.1762480
Accelerating Protein Biomarker Discovery and Translation from Proteomics Research for Clinical Utility	Chen, J.; Zheng, N.	Bioanalysis 2020, 12 (20), 1469–1481	https://doi.org/10.4155/bio-2020-0198
Generation of a Collision Cross Section Library for Multi-Dimensional Plant Metabolomics Using UHPLC-Trapped Ion Mobility-MS/MS	Schroeder, M.; Meyer, S. W. et al.	Metabolites 2019, 10 (1), 13	https://doi.org/10.3390/metabo10010013
Dynamic Rewiring of the Human Interactome by Interferon Signaling	Kerr, C. H.; Skinnider, M. A. et al.	Genome Biol 2020, 21 (1), 140	https://doi.org/10.1186/s13059-020-02050-y
The Impact of AckA, Pta, and AckA-Pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia Coli K-12	Schütze, A.; Benndorf, D. et al.	Front. Microbiol. 2020, 11, 233	https://doi.org/10.3389/fmicb.2020.00233
Arachidyl Amido Cholanoic Acid Improves Liver Glucose and Lipid Homeostasis in Nonalcoholic Steatohepatitis via AMPK and MTOR Regulation	Fernández-Ramos, D.; Lopitz-Otsoa, F. et al.	MWJG 2020, 26 (34), 5101–5117	https://doi.org/10.3748/wjg.v26.i34.5101
Semiquantitative Proteomic Research of Protein Plasma Profile of Volunteers in 21-Day Head-Down Bed Rest	Kashirina, D. N.; Brzhozovskiy, A. G. et al.	Front. Physiol. 2020, 11, 678	https://doi.org/10.3389/fphys.2020.00678
An Effector Caspase Sp-Caspase First Identified in Mud Crab Scylla Paramamosain Exhibiting Immune Response and Cell Apoptosis	Li, J.; Dong, L. et al.	Fish & Shellfish Immunology 2020, 103, 442–453	https://doi.org/10.1016/j.fsi.2020.05.045
Developing a Multivariable Prediction Model for Functional Outcome after Reperfusion Therapy for Acute Ischaemic Stroke: Study Protocol for the Targeting Optimal Thrombolysis Outcomes (TOTO) Multicentre Cohort Study	Holliday, E.; Lillicrap, T. et al.	Levi, CBMJ Open 2020, 10 (4), e038180	https://doi.org/10.1136/bmjopen-2020-038180
Prenatal Endotoxin Exposure Induces Fetal and Neonatal Renal Inflammation via Innate and Th1 Immune Activation in Preterm Pigs	Muk, T.; Jiang, P.-P. et al.	Front. Immunol. 2020, 11, 565484	https://doi.org/10.3389/fimmu.2020.565484
Multiple Signaling Roles of CD3ε and Its Application in CAR-T Cell Therapy	Wu, W.; Zhou, Q. et al.	Cell 2020, 182 (4), 855-871.e23	https://doi.org/10.1016/j.cell.2020.07.018
Identification of Modified Peptides Using Localization-Aware Open Search	Yu, F.; Teo, G. C. et al.	INat Commun 2020, 11 (1), 4065	https://doi.org/10.1038/s41467-020-17921-y
Connecting the Dots on Vertical Transmission of SARS-CoV-2 Using Protein-Protein Interaction Network Analysis – Potential Roles of Placental ACE2 and ENDOU	Jing, H.; Ackerman, W. E. et al.	Placenta 2021, 104, 16–19	https://doi.org/10.1016/j.placenta.2020.11.001
Arachidyl Amido Cholanoic Acid Improves Liver Glucose and Lipid Homeostasis in Nonalcoholic Steatohepatitis via AMPK and MTOR Regulation	Fernández-Ramos, D.; Lopitz-Otsoa, F. et al.	WJG 2020, 26 (34), 5101–5117	https://doi.org/10.3748/wjg.v26.i34.5101
Deep learning the collisional cross sections of the peptide universe from a million training samples (preprint)	Meier, F., Köhler, N.D. et al.	Systems Biology, 2021	https://doi.org/10.1101/2020.05.19.102285
Benefits of Collisional Cross Section Assisted Precursor Selection (Caps-PASEF) for Cross-Linking Mass Spectrometry	Steigenberger, B.; van den Toorn, H. et al.	Mol Cell Proteomics 2020, mcp	https://doi.org/10.1074/mcp.RA120.002094
Ethanolamine Phosphate on the Second Mannose as Bridge in GPI Anchored Proteins: Towards Understanding Inherited PIGG Deficiency	Ishida, M.; Maki, Y. et al.	preprint; Molecular Biology, 2020	https://doi.org/10.1101/2020.11.26.399477
Phosphorylation profile of human AQP2 in urinary exosomes by LC–MS/MS phosphoproteomic analysis	Sakai, M., Yamamoto, K. et al.	Clin Exp Nephrol, 2020	https://doi.org/10.1007/s10157-020-01899-4
Enrichment-Free Identification of Native Definitive (EnFIND) O-glycoproteome of antibodies in autoimmune diseases (preprint)	Sun, X., Cheng, J. et al.	Systems Biology, 2020	https://doi.org/10.1101/2020.07.15.204511
Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant (preprint)	Yu, F., Haynes, S.E. et al.	Bioinformatics, 2020	https://doi.org/10.1101/2020.03.19.999334
Cytoplasmic MRNA Recapping Has Limited Impact on Proteome Complexity	Agana, B. A.; Wysocki, V. H. et al.	Open Biol. 2020, 10 (11), 200313	https://doi.org/10.1098/rsob.200313
Proteomic profiling of mitochondrial-derived vesicles in brain reveals enrichment of respiratory complex sub-assemblies and small TIM chaperones (preprint)	Roberts, R.F., Bayne, A.N. et al.	Biochemistry, 2020	https://doi.org/10.1101/2020.07.06.189993
c-Src Promotes Tumorigenesis and Tumor Progression by Activating PFKFB3	Ma, H., Zhang, J. et al.	Cell Reports 2020, 30, 4235-4249.e6	https://doi.org/10.1016/j.celrep.2020.03.005
Dephosphorylation of cGAS by PPP6C impairs its substrate binding activity and innate antiviral response	Li, M., Shu, H.-B.	Protein Cell 2020, 11, 584–599	https://doi.org/10.1007/s13238-020-00729-3
An intracellular membrane protein GEP1 regulates xanthurenic acid induced gametogenesis of malaria parasites	Jiang, Y., Wei, J. et al.	Nat Commun 2020, 11, 1764	https://doi.org/10.1038/s41467-020-15479-3
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MaxQuant software for ion mobility enhanced shotgun proteomics	Prianichnikov, N., Koch, H. et al.	Mol Cell Proteomics, 2020	https://doi.org/10.1074/mcp.TIR119.001720
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MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas (preprint)	Tsugawa, H., Ikeda, K. et al.	Bioinformatics, 2020	https://doi.org/10.1101/2020.02.11.944900
Characterization and regulation of extracellular vesicles in the lumen of the ovine uterus	O’Neil, E.V., Burns, G.W. et al.	Biology of Reproduction 2020, 102, 1020–1032	https://doi.org/10.1093/biolre/ioaa019
Low collision energy fragmentation in structure-specific glycoproteomics analysis	Sanda, M., Benicky, J. et al.	Anal. Chem. 2020	https://doi.org/10.1021/acs.analchem.0c00519
Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging	Neumann, E.K., Migas, L.G. et al.	Mass Spectrometry n.d., 9
Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-based Quantitation in Proteomic LC/MS/MS	Ogata, K., Ishihama, Y.	Anal. Chem. 2020	https://doi.org/10.1021/acs.analchem.0c01695
An effector caspase Sp-caspase first identified in mud crab Scylla paramamosain exhibiting immune response and cell apoptosis	Li, J., Dong, L. et al.	Fish & Shellfish Immunology 2020, S1050464820303715	https://doi.org/10.1016/j.fsi.2020.05.045
Exploration of human cerebrospinal fluid: A large proteome dataset revealed by trapped ion mobility time-of-flight mass spectrometry	Macron, C., Lavigne, R. et al.	Data in Brief 2020, 31, 105704	https://doi.org/10.1016/j.dib.2020.105704
Developing a multivariable prediction model for functional outcome after reperfusion therapy for acute ischaemic stroke: study protocol for the Targeting Optimal Thrombolysis Outcomes (TOTO) multicentre cohort study	Holliday, E., Lillicrap, T. et al.	BMJ Open 2020, 10, e038180	https://doi.org/10.1136/bmjopen-2020-038180
Biallelic variants in SLC35C1 as a cause of isolated short stature with intellectual disability	Knapp, K.M., Luu, R. et al.	J Hum Genet, 2020	https://doi.org/10.1038/s10038-020-0764-4
Quantitative Proteomic Analysis of Chikungunya Virus-Infected Aedes aegypti Reveals Proteome Modulations Indicative of Persistent Infection	Cui, Y., Liu, P. et al.	J. Proteome Res. 2020	https://doi.org/10.1021/acs.jproteome.0c00173
Relative Quantitation of Subclass-Specific Murine IgG Fc N -Glycoforms by Multiple Reaction Monitoring	Han, J., Liu, Q. et al.	ACS Omega 2020, 5, 8564–8571	https://doi.org/10.1021/acsomega.9b04412
Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts	Vasilopoulou, C.G., Sulek, K. et al.	Nat Commun 2020, 11, 331	https://doi.org/10.1038/s41467-019-14044-x
In-depth proteomics and natural peptidomics analyses reveal antibacterial peptides in human endometrial fluid	Azkargorta, M., Bregón-Villahoz, M. et al.	Journal of Proteomics 2020, 103652	https://doi.org/10.1016/j.jprot.2020.103652
The Complex Response of Free and Bound Amino Acids to Water Stress During the Seed Setting Stage in Arabidopsis	Yobi, A., Bagaza, C. et al.	Plant J 2020, tpj.14668	https://doi.org/10.1111/tpj.14668
Combination of intact, middle-up and bottom-up levels to characterize 7 therapeutic monoclonal antibodies by capillary electrophoresis	Giorgetti, J., Beck, A. et al.	Mass spectrometry. Journal of Pharmaceutical and Biomedical Analysis, 2020, 182, 113107	https://doi.org/10.1016/j.jpba.2020.113107
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Identification of 56 Proteins Involved in Embryo–Maternal Interactions in the Bovine Oviduct	Banliat, C., Tsikis, G. et al.	IJMS 2020, 21, 466	https://doi.org/10.3390/ijms21020466
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Single-Cell Proteomic and Transcriptomic Analysis of Macrophage Heterogeneity	Specht, H.; Emmott, E.; Slavov, N. et al.	preprint; Immunology, 2019	https://doi.org/10.1101/665307
Simplified high-throughput methods for deep proteome analysis on the timsTOF Pro	Sandow, J. J, Infusini, G. et al.	Biochemistry, 2019, doi:10.1101/657908
Cathepsin B/ SAPC inhibition deregulates apoptosis-related proteins in neuronal cells exposed to supernatants from HIV-infected macrophages	Melendez L, PhD , Zenon-Melendez C, et al.	J Biomol Tech. 2020, 31(Suppl):S19
Trapped ion mobility spectrometry (TIMS) and parallel accumulation - serial fragmentation (PASEF) enable in-depth lipidomics from minimal sample amounts	Vasilopoulou, C. G. et al.	Systems Biology, 2019, doi:10.1101/654491
Regulation of macrophage activity by surface receptors contained within Borrelia burgdorferi-enriched phagosomal fractions	Carreras-González, A., Barriales, D. et al.	PLoS Pathog 2019, 15, e1008163	https://doi.org/10.1371/journal.ppat.1008163
The MPK8-TCP14 pathway promotes seed germination in Arabidopsis	Zhang, W.; Cochet, F. et al.	The Plant Journal, 2019	https://doi.org/10.1111/tpj.14461
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Characterization of an evolutionarily conserved calcitonin signalling system in a lophotrochozoan, the Pacific oyster (Crassostrea gigas)	Schwartz, J.; Réalis-Doyelle, E. et al.	Journal of Experimental Biology, 2019	https://doi:10.1242/jeb.201319
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Mass spectrometry analysis of mouse hematopoietic stem cells and their progenitors reveals differential expression within and between proteome and transcriptome throughout adult and aged hematopoiesis (preprint)	Zaro, B.W.; Noh, J.J. et al.	Cell Biology, 2019	https://doi.org/10.1101/836692
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Protein 18 Is Involved in Chloroplast Function and Thylakoid Formation	Espinoza-Corral, R.; Heinz, S. et al.	Plastoglobular Journal of Experimental Botany 2019, 70 (15), 3981–3993	https://doi.org/10.1093/jxb/erz177
SUMO-Binding Entities (SUBEs) as Tools for the Enrichment, Isolation, Identification, and Characterization of the SUMO Proteome in Liver Cancer	Lopitz-Otsoa, F.; Delgado, T. C. et al.	JoVE 2019, No. 153, 60098	https://doi.org/10.3791/60098
Methods and Guidelines for Measurement of Glucagon in Plasma	Holst, J. J.; Wewer Albrechtsen, N. J.	IJMS 2019, 20 (21), 5416	https://doi.org/10.3390/ijms20215416
Sclerotinia Sclerotiorum Circumvents Flavonoid Defenses by Catabolizing Flavonol Glycosides and Aglycones	Chen, J.; Ullah, C. et al.	Plant Physiol. 2019, 180 (4), 1975–1987	https://doi.org/10.1104/pp.19.00461
A. Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms	Garabedian, A.; Baird, M. A. et al.	Anal. Chem. 2018, 90 (4), 2918–2925	https://doi.org/10.1021/acs.analchem.7b05224
Online Parallel Accumulation-Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer	Meier, F.; Brunner, A.D. et al.	Mol Cell Proteomics. 2018 Dec;17(12):2534-2545
Parallel accumulation – serial fragmentation (PASEF): Multiplying sequencing speed and sensitivity by synchronized scans in a trapped ion mobility device	Meier, F.; Beck, S. et al.	J Proteome Res. 2015 Dec 4;14(12):5378-87

Biology - Preprints

Title	Authors	Publication	Link
mini-Complexome Profiling (mCP), an FDR-controlled workflow for global targeted detection of protein complexes	Amedei, H.; Paul, N.; Foo, B. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.04.22.590599
Global organization of phenylpropanoid and anthocyanin pathways revealed by proximity labeling of trans-cinnamic acid 4-hydroxylase (CYP73A412) in Petunia inflata petal protoplasts	Aravena-Calvo, J.; Busck-Mellor, S.; Laursen, T.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.04.05.588085
Identification of druggable targets from the interactome of the Androgen Receptor and Serum Response Factor pathways in prostate cancer	Azam, H.; Veale, C.; Zitzmann, K. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.08.15.608046
Synchronized Temporal-spatial Analysis via Microscopy and Phoshoproteomics (STAMP) of Quiescence	Aziz-Zanjani, M.O.; Turn, R.E.; Xu, L.A. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.06.24.600542
Low-dose colchicine treatment improves vasorelaxation, reduces arterial remodeling and attenuates blood pressure increases in spontaneously hypertensive rats	Baldwin, S.N.; Bastrup, J.A.; Van Der Horst, J. et al.	preprint; Physiology, 2024	https://doi.org/10.1101/2024.07.31.604256
Dbf4-Dependent Kinase Finetunes INO80 Function at Chromosome Replication Origins	Bansal, P.; Lahiri, S.; Kumar, C. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.06.10.598178
Multi-omic analyses unveil temporal and spatial distribution of specialized metabolites in seeds of Camelina sativa	Barreda, L.; Brosse, C.; Boutet, S. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.05.31.596893
A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage	Barrett, J.; Naduthodi, M.I.S.; Mao, Y. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.04.09.588658
Circadian rhythms mediate malaria transmission potential	Bento, I.; Parrington, B.; Pascual, R. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.05.14.594221
Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome	Beusch, C.M.; Dawood, A.S.; Ozdilek, A. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.05.14.593504
Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics	Biggs, G.S.; Cawood, E.E.; Vuorinen, A. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.07.25.605137
Identification of a new family of peptidoglycan transpeptidases reveals atypical crosslinking is essential for viability in Clostridioides difficile	Bollinger, K.W.; Müh, U.; Ocius, K.L. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.03.14.584917
Cryo-EM Structures of Saccharolobus solfataricus Initiation Complexes with Leaderless mRNAs Highlight Archaeal Features and Eukaryotic Proximity	Bourgeois, G.; Coureux, P.-D.; Lazennec-Schurdevin, C. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.07.16.603699
Discovery of a novel antifungal compound, ilicicolin K, through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei	Burger, I.; Schmal, M.; Peikert, K. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.06.20.599701
Lysosomal signalling pathways influence heart rhythm, and regulate atrial function	Capel, R.A.; Akerman, E.; Rog-Zielinska, E.A. et al.	preprint; Physiology, 2024	https://doi.org/10.1101/2024.06.10.597905
Synaptic synergy of T cell receptor and interleukin 2 receptor in CD8+ T cells	Capera, J.; Jainarayanan, A.K.; Valvo, S. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.08.13.607831
Structure and dynamics determine G protein coupling specificity at a class A GPCR	Casiraghi, M.; Wang, H.; Brennan, P. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.03.28.587240
Molecular insights into G protein specificity and biased agonism at the β 2 -adrenergic receptor	Casiraghi, M.; Wang, H.; Brennan, P. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.03.28.587240
Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis	Chandran, R.R.; Vijayaraj, P.; Garcia-Milian, R. et al.	preprint; Pathology, 2024	https://doi.org/10.1101/2024.06.17.599411
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics	Chen, C.-W.; Lin, P.-Y.; Lai, Y.-M. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.02.26.582001
Reprogramming neuroblastoma by diet-enhanced polyamine depletion	Cherkaoui, S.; Yang, L.; McBride, M. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.01.07.573662
Signal transduction pathways controlling Ins2 gene activity and β cell state transitions	Chu, C.M.J.; Sabbineni, B.; Cen, H.H. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.06.06.597838
High resolution cryo-EM of V-ATPase in native synaptic vesicles	Coupland, C.E.; Karimi, R.; Bueler, S.A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.04.01.587493
Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications	Ctortecka, C.; Clark, N.M.; Boyle, B. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.20.576369
Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity	Cutler, R.; Corveleyn, L.; Ctortecka, C. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.07.05.602213
Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α	Delaveris, C.S.; Kong, S.; Glasgow, J. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.03.20.585970
Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics	Dens, C.; Adams, C.; Laukens, K. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.05.02.592141
Single-nucleus proteomics identifies regulators of protein transport	Derks, J.; Jonson, T.; Leduc, A. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.06.17.599449
Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers Enables Affinity Tagging	Di Ianni, A.; Ihling, C.H.; Vranka, T. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.03.29.587196
Extracellular vesicles from microglial cells activated by abnormal heparan sulfate oligosaccharides from Sanfilippo patients impair neuronal dendritic arborization	Dias, C.; Ballout, N.; Morla, G. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.05.22.595318
Coupling of secondary metabolite production in Bacillus subtilis	Dinesen, C.; Vertot, M.; Jarmusch, S.A. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.08.15.608099
Astrogliosis and Neuroinflammation Underlie Scoliosis Upon Cilia Dysfunction	Djebar, M.; Anselme, I.; Pezeron, G. et al.	preprint; Developmental Biology, 2024	https://doi.org/10.1101/2024.02.22.581530
RNA G-quadruplex dynamic steers the crosstalk between protein synthesis and energy metabolism	Dumas, L.; Shin, S.; Rigaud, Q. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.01.29.577192
Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15	Ebenwaldner, C.; García Saura, A.G.; Ekström, S. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.04.04.588081
Latent infection of an active giant endogenous virus in a unicellular green alga	Erazo-Garcia, M.P.; Sheyn, U.; Barth, Z.K. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.09.03.611062
PP1 PNUTS binds the “restrictor” and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination	Erickson, B.; Fedoryshchak, R.; Fong, N. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.07.12.603302
HumanIslets: An integrated platform for human islet data access and analysis	Ewald, J.D.; Lu, Y.; Ellis, C.E. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.06.19.599613
Dynamic in vivo mapping of the methylproteome using a chemoenzymatic approach	Farhi, J.; Jones, R.B.; Lee, R.S. et al.	preprint; Biochemistry, 2022	https://doi.org/10.1101/2022.07.22.501130
A Lipid Atlas of the Human Kidney	Farrow, M.A.; Tideman, L.E.M.; Neumann, E.K. et al.	preprint; Biochemistry, 2022	https://doi.org/10.1101/2022.04.07.487155
Caspase cleavage of Influenza A virus M2 disrupts M2-LC3 interaction and regulates virion production	Figueras-Novoa, C.; Akutsu, M.; Murata, D. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.04.04.588074
Setdb1 safeguards genome integrity in muscle stem cells to allow for regenerative myogenesis and inflammation	Garcia, P.; Jarassier, W.; Brun, C. et al.	preprint; Cell Biology, 2023	https://doi.org/10.1101/2023.06.08.544190
Endogenous viral elements constitute a complementary source of antigens for personalized cancer vaccines	Garde, C.; Pavlidis, M.A.; Garces, P. et al.	preprint; Cancer Biology, 2023	https://doi.org/10.1101/2023.03.23.533908
Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT)	Geyer, F.H.; Ritter, A.; Kinn-Gurzo, S. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.07.17.603708
Insulin regulates lymphatic endothelial function via palmitoylation	Gonzalez-Nieves, S.; Wei, X.; McQuillan, J. et al.	preprint; Physiology, 2024	https://doi.org/10.1101/2024.05.06.592341
An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis	Gu, L.; Li, Z.; Wang, Q. et al.	preprint; Systems Biology, 2022	https://doi.org/10.1101/2022.01.02.474723
Tracing active bugs in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesised proteins	Hellwig, P.; Kautzner, D.; Heyer, R. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.08.27.609880
Proteomic Analysis Reveals Trilaciclib-Induced Senescence	Hermosilla-Trespaderne, M.; Hu-Yang, M.X.; Dannoura, A. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.03.12.584620
Highly Repeatable Tissue Proteomics for Kidney Transplant Pathology: Technical and Biological Validation of Protein Analysis using LC-MS/MS	Hofstraat, R.; Marx, K.; Blatnik, R. et al.	preprint; Pathology, 2024	https://doi.org/10.1101/2024.06.14.599091
The X-Linked Intellectual Disability gene, ZDHHC9 , is important for oligodendrocyte subtype determination and myelination	Hollman, R.B.; Wild, A.R.; O’Leary, T.P. et al.	preprint; Neuroscience, 2023	https://doi.org/10.1101/2023.08.08.552342
The cryo-EM structure of ASK1 reveals an asymmetric architecture allosterically modulated by TRX1	Honzejkova, K.; Kosek, D.; Obsilova, V. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.12.20.572539
Non-mechanical disruption of Bacillus subtilis spores allows sensitive and deep characterization of the minimal proteome for resuming a cellular lifestyle	Huang, Y.; De Koster, A.; Tu, Z. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.03.08.584050
Loss of SPNS1, a lysosomal transporter, in the nervous system causes dysmyelination and white matter dysplasia	Ichimura, Y.; Sugiura, Y.; Katsuragi, Y. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.05.29.596535
Increased Cholesterol Synthesis Drives Neurotoxicity in Patient Stem Cell-Derived Model of Multiple Sclerosis	Ionescu, R.-B.; Nicaise, A.M.; Reisz, J.A. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.01.16.575826
Degradome analysis to identify direct protein substrates of small-molecule degraders	Jochem, M.; Schrempf, A.; Wagner, L.-M. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.28.577572
Urinary multi-omics reveal non-invasive diagnostic biomarkers in clear cell renal cell carcinoma	Jonsson, G.; Hofmann, M.; Oliveira, T. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.08.12.607453
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures	Justice, J.L.; Greco, T.M.; Hutton, J.E. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.09.07.611843
Post-proline cleaving enzymes also show specificity to reduced cysteine	Kalaninová, Z.; Portašiková, J.M.; Jirečková, B. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.07.12.603020
Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity	Kaltenecker, D.; Horvath, I.; Al-Maskari, R. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.08.18.608300
Ketomimetic Nutrients Trigger a Dual Metabolic Defense in Breast Cancer Cells	Kamra, M.; Chen, Y.-I.; Delgado, P. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.07.03.601966
Ketomimetic Medium Promotes Metastatic Disposition and Chemoresistance in Breast Cancer Cells through Hypersialylation and Lipid Synthesis	Kamra, M.; Chen, Y.-I.; Delgado, P. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.07.03.601966
High-Recovery Desalting Tip Columns for a Wide Variety of Peptides in Mass Spectrometry-based Proteomics	Kanao, E.; Tanaka, S.; Tomioka, A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.07.19.604362
TLN468 changes the pattern of tRNA used to read through premature termination codons in CFTR	Karri, S.; Cornu, D.; Serot, C. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.02.02.526440
Targeting high-risk multiple myeloma genotypes with optimized anti-CD70 CAR-T cells	Kasap, C.; Izgutdina, A.; Patiño-Escobar, B. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.02.24.581875
Cyclase-associated protein 1 (CAP1) represses MRTF-SRF-dependent gene expression in the mouse cerebral cortex	Khudayberdiev, S.; Weiss, K.; Heinze, A. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.02.26.582060
The N-degron pathway governs autophagy to promote thermotolerance in Arabidopsis	Kim, S.H.; Park, J.S.; Lee, M.-H. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.07.17.604022
Flavonoid metabolism and its different physiological roles in plant cold acclimation	Kitashova, A.; Lehmann, M.: Schwenkert, S. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.06.13.598861
Ultra-deep proteomics by Thin-diaPASEF with a 60-cm long column system	Konno, R.; Ishikawa, M.; Nakajima, D. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.04.26.591246
The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins	Körner, C.; Schäfer, J.-H.; Esch, B.M. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.01.30.577963
Deep learning-based proteomics enables accurate classification of bulk and single-cell samples	Krull, K.K.; Kühn, A.; Höhn, J. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.02.03.578734
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows	Kwon, Y.; Woo, J.; Yu, F. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.03.04.583367
Screening of leaf extraction and storage conditions for eco-metabolomics studies	Lang, J.: Ramos, S.E.; Smohunova, M. et al.	preprint; Plant Biology, 2023	https://doi.org/10.1101/2023.06.26.546251
Personalized Molecular Signatures of Insulin Resistance and Type 2 Diabetes (preprint). Biochemistry	Larsen, J.K.; Stocks, B.; Henderson, J. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.02.06.578994
Radioproteomics stratifies molecular response to antifibrotic treatment in pulmonary fibrosis	Lauer, D.; Magnin, C.Y.; Kolly, L. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.03.27.586923
Koina: Democratizing machine learning for proteomics research	Lautenbacher, L.; Yang, K.L.; Kockmann, T. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.06.01.596953
Discovery of chemical marker for maidong (roots of Ophiopogon japonicus and Liriope spicata): a feature-based molecular networking approach	Lei, F.; Saldanha, L.L.; Weckerle, C. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.07.30.605840
Dysregulated Skeletal Muscle Myosin Super-relaxation in Type II, but Not Type I, Diabetes Mellitus	Lewis, C.T.A.; Moreno-Justicia, R.; Savoure, L. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.06.12.598615
PRR adjuvants restrain high stability peptides presentation on APCs	Li, B.; Zhang, J.; He, T. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.05.20.594923
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data	Li, K.; Teo, G.C.; Yang, K.L. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.05.25.595875
Knocking out the carboxyltransferase interactor 1 (CTI1) in Chlamydomonas boosted oil content by fivefold without affecting cell growth	Li, Z.; Kim, M.; Da Silva Nascimento, J.R. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.09.03.611075
Transcription-Coupled Repair of DNA Interstrand Crosslinks by UVSSA	Liebau, R.C.; Waters, C.; Ahmed, A. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.05.10.538304
Similar, but not the same: multi-omics comparison of human valve interstitial cells and osteoblast osteogenic differentiation expanded with an estimation of data-dependent and data-independent PASEF	Lobov, A.; Kuchur, P.; Boyarskaya, N. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.04.03.587893
N-Terminal proteomics reveals distinct protein degradation patterns in different types of human atherosclerotic plaques	Lorentzen, L.G.; Yeung, K.; Eldrup, N. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.05.14.594251
Prkra dimer senses double-stranded RNAs to dictate global translation efficiency	Lu, T.; Ma, P.; Chen, A. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.07.16.603655
MYCN inhibits TrkC-mediated differentiation in neuroblastoma cells via disruption of the PKA signalling pathway	Maher, S.; Wynne, K.; Zhernovkov, V. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.08.07.606961
T cell correction pipeline for Inborn Errors of Immunity	Mamia, K.; Kolbeinsdottir, S.; Li, Z. et al.	preprint; Bioengineering, 2024	https://doi.org/10.1101/2024.09.03.610811
Trajectory Analysis of Hepatic Stellate Cell Differentiation Reveals Metabolic Regulation of Cell Commitment and Fibrosis	Martínez García De La Torre, R.A.; Vallverdú, J.; Xu, Q. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.02.15.577777
A mouse model of cardiac AL amyloidosis unveils mechanisms of tissue accumulation and toxicity of amyloid fibrils	Martinez-Rivas, G.; Ayala, M.; Bender, S. et al.	preprint; Pathology, 2024	https://doi.org/10.1101/2024.07.18.604040
SCF FBXL5 ubiquitin ligase regulates stability of von-Hippel Lindau protein and the HIF1α-dependent response to hypoxia	Mayank, A.K.; Pandey, V.; Lien, K. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.01.29.577840
Zika virus remodels and hijacks IGF2BP2 ribonucleoprotein complex to promote viral replication organelle biogenesis	Mazeaud, C.; Pfister, S.; Owen, J.E. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.12.08.570783
Population origin, body mass, and viral infections influence drone honey bee (Apis mellifera) heat tolerance	McAfee, A.; Metz, B.N.; Connor, P. et al.	preprint; Physiology, 2024	https://doi.org/10.1101/2024.05.12.593456
Microbial metabolomics’ latest SICRIT: Soft ionization by Chemical Reaction in-Transfer mass spectrometry	McAtamney, A.; Ferranti, A.; Ludvik, D.A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.07.17.604007
The Pseudogene RPS27AP5 Reveals Novel Ubiquitin and Ribosomal Protein Variants Involved in Specialised Ribosomal Functions	Meller, A.; Lévesque, D.; Raisch, J. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.02.05.578897
ANKRD55 interacts with an IFT-B-like complex in microglia	Mena, J.; Navarro, R.T.; Díez-García, J. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.03.18.584613
In-depth study of MPV17: a molecular travel unveiling a mitochondrial calcium regulation function	Meurant, S.; Amato, I.; Mauclet, L. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.04.12.589178
Lipid A double bond position determination using ozone and laser-induced dissociation	Mikhael, A.; Pětrošová, H.; Smith, D. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.02.15.580351
Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle	Moller, E.; Britt, M.; Zhou, F. et al.	preprint; Biophysics, 2024	https://doi.org/10.1101/2024.01.22.576751
Identification of high sugar diet-induced dysregulated metabolic pathways in muscle using tissue-specific metabolic models in Drosophila	Moon, S.J.; Hu, Y.; Dzieciatkowska, M. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.04.24.591006
Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies	Morderer, D.; Wren, M.C.; Liu, F. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.03.25.585597
USP24 is an ISG15 cross-reactive deubiquitinase that mediates IFN-I production by de-ISGylating the RNA helicase MOV10	Mukhopadhyay, R.; Draganov, S.D.; Akkermans, J.J.L.L. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.09.06.611391
A Lipidomics-Based Method to Eliminate Negative Urine Culture in General Population	Nartey, L.K.; Mikhael, A.; Pětrošová, H. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.04.11.589091
Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes	Nemkov, T.; Stephenson, D.; Earley, E.J. et al.	preprint; Biochemistry, 2023	https://doi.org/10.1101/2023.09.11.557250
diaPASEF analysis for HLA-I peptides enables quantification of common cancer neoantigens	Oliinyk, D.; Gurung, H.; Zhou, Z. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.07.30.605861
Cell Storage Conditions Impact Single-Cell Proteomic Landscapes	Onat, B.; Momenzadeh, A.; Haghani, A. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.07.23.604834
Non-canonical Metabolic and Molecular Effects of Calorie Restriction Are Revealed by Varying Temporal Conditions	Pak, H.H.; Grossberg, A.N.; Sanderfoot, R.R. et al.	preprint; Physiology, 2024	https://doi.org/10.1101/2024.02.15.580502
dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples	Panigrahi, A.; Hunt, A.L.; Assis, D. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.08.09.607341
SFRP1 upregulation causes hippocampal synaptic dysfunction and memory impairment	Pereyra, G.; Mateo, M.I.; Martin-Bermejo, M.J. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.04.04.588100
CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote	Perrin, A.J.; Dowson, M.; Dowle, A.A. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.02.28.582475
Estimating essential phenotypic and molecular traits from integrative biodiversity data	Peters, K.; Ziegler, J.; Neumann, S.	preprint; Ecology, 2024	https://doi.org/10.1101/2024.04.02.587699
Anisotropic Articular Cartilage Biofabrication based on Decellularized Extracellular Matrix	Puiggali-Jou, A.; Hui, I.; Baldi, L. et al.	preprint; Bioengineering, 2024	https://doi.org/10.1101/2024.07.30.605411
Cell-autonomous targeting of arabinogalactan by host immune factors inhibits mycobacterial growth	Qin, L.; Xu, J.; Chen, J. et al.	preprint; Immunology, 2023	https://doi.org/10.1101/2023.10.05.561003
Free Amino Acids Accelerate the Time-Dependent Inactivation of Rat Liver Nucleotide Pyrophosphatase / Phosphodiesterase Enpp3 elicited by EDTA	Romero, A.; Cumplido-Laso, G.; Fernández, A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.06.27.601032
Protein surface chemistry encodes an adaptive resistance to desiccation	Romero-Perez, P.S.; Moran, H.M.; Horani, A. et al.	preprint; Biophysics, 2024	https://doi.org/10.1101/2024.07.28.604841
EXCRETE enables deep proteomics of the microbial extracellular environment	Russo, D.A.; Oliinyk, D.; Pohnert, G. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.03.01.582910
Tagless LysoIP method for molecular profiling of lysosomal content in clinical samples	Saarela, D.; Lis, P.; Gomes, S. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.05.17.594681
Saturated fatty acid-Coenzyme A supplementation restores neuronal energy levels, synaptic function, and protein homeostasis in hereditary spastic paraplegia	Saber, S.H.; Yak, N.; Yong, X.L.H. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2023.12.31.573799
MS2Lipid: a lipid subclass prediction program using machine learning and curated tandem mass spectral data	Sakamoto, N.; Oka, T.; Matsuzawa, Y. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.05.16.594510
Endoplasmic reticulum stress signaling actively contributes to therapy resistance in colorectal cancer	Sasaki, D.; Sato, N.; Wilhelm, D. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.01.07.574523
Microbial consortia driving lignocellulose transformation in agricultural woodchip bioreactors	Schiml, V.; Walter, J.; Hagen, L.H. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.07.11.603112
Label-free Assessment of Complement-Dependent Cytotoxicity of Therapeutic Antibodies via a Whole-Cell MALDI Mass Spectrometry Bioassay	Schmidt, S.; Geisel, A.; Enzlein, T. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.05.03.592336
Mass Spectrometry Imaging of the Subchondral Bone in Osteoarthritis Reveals Tissue Remodeling of Extracellular Matrix Proteins that Precede Cartilage Loss	Schurman, C.A.; Bons, J.; Woo, J.J. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.08.03.606482
The Small GTPase Rho5 - Yet Another Player in Yeast Glucose Signaling	Schweitzer, F.; Bischof, L.; Walter, S. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.07.29.605593
Single Cell MALDI-MSI Analysis of Lipids and Proteins within a Replicative Senescence Fibroblast Model	Sekera, E.R.; Rosas, L.; Holbrook, J.H. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.03.13.584140
Elevated phagocytic capacity directs innate spinal cord repair	Shaw, D.K.; Saraswathy, V.M.; McAdow, A.R. et al.	preprint; Neuroscience, 2024	https://doi.org/10.1101/2024.06.11.598515
Electrophoresis-Correlative Ion Mobility Deepens Single-cell Proteomics in Capillary Electrophoresis Mass Spectrometry	Shen, B.; Zhou, F.; Nemes, P.	preprint; Developmental Biology, 2024	https://doi.org/10.1101/2024.09.11.612533
Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance	Shiraliyev, R.; Orman, M.A.	preprint; Microbiology, 2024	https://doi.org/10.1101/2023.12.20.572673
Aspergillus dsRNA virus drives fungal fitness and pathogenicity in the mammalian host	Shlezinger, N.; Lerer, V.; Rocha, M. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2024.02.16.580674
Tau phosphorylation impedes functionality of protective tau envelopes	Siahaan, V.; Weissova, R.; Lanska, E. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.03.25.586522
MassDash: A Web-based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization	Sing, J.C.; Charkow, J.; AlHigaylan, M. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.01.15.575772
Stem-loop induced ribosome queuing in the uORF2/ ATF4 overlap fine-tunes stress-induced human ATF4 translational control	Smirnova, A.M.; Hronová, V.; Mohammad, M.P. et al.	preprint; Molecular Biology, 2023	https://doi.org/10.1101/2023.07.12.548609
msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Immunofluorescence Microscopy Data Processing and Analysis	Spangenberg, P.; Bessler, S.; Widera, L. et al.	preprint; Bioinformatics, 2024	https://doi.org/10.1101/2024.08.24.609403
Resolving multi-image spatial lipidomic responses to inhaled toxicants by machine learning	Stevens, N.C.; Shen, T.; Martinez, J. et al.	preprint; Pharmacology and Toxicology, 2024	https://doi.org/10.1101/2024.07.05.602264
Negative regulation of APC/C activation by MAPK-mediated attenuation of Cdc20 Slp1 under stress	Sun, L.; Chen, X.; Song, C. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.04.02.587770
The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2	Suryawanshi, R.K.; Jaishankar, P.; Correy, G.J. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.08.08.606661
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning	Tran, N.H.; Peng, C.; Lei, Q. et al.	preprint; Bioinformatics, 2022	https://doi.org/10.1101/2022.07.05.497667
The balance between antiviral and antibacterial responses during M. tuberculosis infection is regulated by the ubiquitin ligase CBL	Truong, T.; Martin, K.E.; Salemi, M.R. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.05.15.594178
Systematic Optimization of Activity-Based Protein Profiling for Identification of Polysorbate-Degradative Enzymes in Biotherapeutic Drug Substance Down to 10 ppb	Tsukidate, T.; Liu, A.P.; Rivera, S. et al.	preprint; Bioengineering, 2024	https://doi.org/10.1101/2024.08.29.610306
diaPASEF Enables High-throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development	Tsukidate, T.; Stiving, A.Q.; Rivera, S. et al.	preprint; Bioengineering, 2024	https://doi.org/10.1101/2024.02.21.581388
The Non-Phototrophic Hypocotyl3 (NPH3)-domain protein NRL5 is a trafficking-associated GTPase essential for drought resistance	Upadhyay-Tiwari, N.; Huang, X.-J.; Lee, Y.-C. et al.	preprint; Plant Biology, 2023	https://doi.org/10.1101/2023.05.10.540297
Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease	Urbauer, E.; Aguanno, D.; Mindermann, N. et al.	preprint; Microbiology, 2023	https://doi.org/10.1101/2023.07.27.549844
Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells	Van Bentum, M.; Klinger, B.; Sieber, A. et al.	preprint; Systems Biology, 2024	https://doi.org/10.1101/2024.05.13.593849
ATP-Binding Cassette Family C member 1 constrains metabolic responses to high-fat diet in male mice	Villalobos, E.; Miguelez-Crespo, A.; Morgan, R.A. et al.	preprint; Physiology, 2024	https://doi.org/10.1101/2024.01.23.576896
Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry	Wang, A.; Fekete, E.E.F.; Creskey, M. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.03.13.584844
Architecture of intact mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis	Wang, C.; Ma, C.; Chang, S. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.02.01.578502
Rab7 deficiency induces lysosome formation from recycling endosomes leading to an increased degradation of cell surface proteins	Wang, G.M.; Xu, P.; Yu, K. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.05.13.593900
Combining data independent acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification	Welter, A.S.; Gerwien, M.; Kerridge, R. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.05.03.592381
Proteomic profiling of IDH-wildtype Glioblastoma Tissue and Serum uncovers prognostic Subtypes and Marker Candidates	Werner, T.; Schäfer, A.; Hennes, M. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.02.29.582688
Drug Metabolism and Transport Capacity of Endothelial Cells, Pericytes, and Astrocytes: Implications for CNS Drug Disposition	Wilkins, H.N.; Knerler, S.A.; Warshanna, A. et al.	preprint; Pharmacology and Toxicology, 2024	https://doi.org/10.1101/2024.08.01.606165
Isolation and characterisation of serine proteases and metalloproteases from the venom of African puff adders	Wilkinson, M.C.; Modahl, C.; Saviola, A. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.05.31.596867
. Mining Yeast Diversity Unveils Novel Targets for Improved Heterologous Laccase Production in Saccharomyces cerevisiae	Wong, R.W.K.; Foo, M.; Lay, J.R.S. et al.	preprint; Molecular Biology, 2024	https://doi.org/10.1101/2024.08.26.609787
Ultra-sensitive metaproteomics (uMetaP) redefines the dark field of metaproteome, enables single-bacterium resolution, and discovers hidden functions in the gut microbiome	Xian, F.; Brenek, M.; Krisp, C. et al.	preprint; Microbiology, 2024	https://doi.org/10.1101/2024.04.22.590295
Post-death Vesicles of Senescent Bone Marrow Mesenchymal Stromal Polyploids Promote Macrophage Aging and Breast Cancer	Xie, B.; Fan, M.; Wang, C.X. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.03.06.583755
Wounding perception by jasmonate-mediated JAZ condensation in plants	Yan, Z.-W.; Liu, J.; Chen, H.-C. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.03.28.587122
PVRL2 Suppresses Anti-tumor Immunity Through PVRIG- and TIGIT-Independent Pathways	Yang, J.; Wang, L.; Byrnes, J.R. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.01.26.577132
Deficiency in a special dynein DNAH12 causes male infertility by impairing DNAH1 and DNALI1 recruitment in humans and mice	Yang, M.; Hussain, H.M.J.; Khan, M. et al.	preprint; Genetics, 2024	https://doi.org/10.1101/2024.06.20.599934
The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation	Yu, K.; Guo, S.S.; Bassermann, F. et al.	preprint; Cell Biology, 2024	https://doi.org/10.1101/2024.05.14.594138
Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells	Zhang, N.; Gao, S.; Peng, H. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.04.27.591460
pH-Controlled chemoselective rapid azo-coupling reaction (CRACR) enables global profiling of serotonylation proteome in cancer cells	Zhang, N.; Wu, J.; Gao, S. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.05.10.593574
Implementation of pupylation-based proximity labelling in plant biology reveals regulatory factors in cellulose biosynthesis	Zheng, S.; Khammy, O.; Marie Noack, L.C. et al.	preprint; Plant Biology, 2024	https://doi.org/10.1101/2024.01.09.574788
Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma	Zheng, X.; Pedersen, L.M.; Bzorek, M. et al.	preprint; Cancer Biology, 2024	https://doi.org/10.1101/2024.06.12.598635
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment	Zhu, B.; Bai, Y.; Yeo, Y.Y. et al.	preprint; Immunology, 2024	https://doi.org/10.1101/2024.03.04.583400
Endogenously produced hydrogen cyanide serves as a novel mammalian gasotransmitter	Zuhra, K.; Petrosino, M.; Janickova, L. et al.	preprint; Biochemistry, 2024	https://doi.org/10.1101/2024.06.03.597146

Chemistry

Title	Authors	Publication	Link
Development of Approach for Flavonoid Profiling of Biotechnological Raw Materials IRIS SIBIRICA L. by HPLC with High‐resolution Tandem Mass Spectrometry	Karpitskiy, D. A.; Bessonova, E. A. et al.	Phytochemical Analysis 2022, 33 (6), 869–878	https://doi.org/10.1002/pca.3135
Ordered Micropattern Arrays Fabricated by Lung-Derived DECM Hydrogels for Chemotherapeutic Drug Screening	Zhu, X.; Li, Y. et al.	Materials Today Bio 2022, 15, 100274	https://doi.org/10.1016/j.mtbio.2022.100274
Dual-Resolving of Positional and Geometric Isomers of C=C Bonds via Bifunctional Photocycloaddition-Photoisomerization Reaction System	Feng, G.; Gao, M.; et al.	Nat Commun 2022, 13 (1), 2652	https://doi.org/10.1038/s41467-022-30249-z
Development of Disulfide-Functionalized Peptides Covalently Binding G Protein-Coupled Receptors	Einsiedel, J.; Schmidt, M. F. et al.	Bioorganic & Medicinal Chemistry 2022, 61, 116720	https://doi.org/10.1016/j.bmc.2022.116720
Isoindolines and phthalides from the rhizomes of Ligusticum chuanxiong and their relaxant effects on the uterine smooth muscle	Liu, J., Feng, R. et al.	Phytochemistry 2022, 198, 113159	https://doi.org/10.1016/j.phytochem.2022.113159
Noncovalently Tagged Gas Phase Complex Ions for Screening Unknown Contaminant Metabolites in Plants	Shen, M., Gong. X. et al.	Anal. Chem. 2021, 93, 45, 14929–14933	https://doi.org/10.1021/acs.analchem.1c03145
Trapped Ion Mobility Incorporated in LC–HRMS Workflows as an Integral Analytical Platform of High Sensitivity: Targeted and Untargeted 4D-Metabolomics in Extra Virgin Olive Oil	Drakopoulou, S.K.; Damalas, D.E. et al.	J. Agric. Food Chem. 2021, 69, 15728–15737	https://doi.org/10.1021/acs.jafc.1c04789
Feature-based molecular networking in the GNPS analysis environment	Nothias, L.-F.; Petras, D. et al.	Nat Methods 2020, 17, 905–908	https://doi.org/10.1038/s41592-020-0933-6
Facile synthesis of Ti4+-immobilized magnetic covalent organic frameworks for enhanced phosphopeptide enrichment	He, Y.; Zhang, S. et al.	Talanta 2021, 235, 122789	https://doi.org/10.1016/j.talanta.2021.122789
Thiol and Disulfide Containing Vancomycin Derivatives Against Bacterial Resistance and Biofilm Formation	Shchelik, I.S.; Gademann, K.	preprint; Microbiology 2021	https://doi.org/10.1101/2021.08.23.457343
Automated Chiral Analysis of Amino Acids Based on Chiral Derivatization and Trapped Ion Mobility–Mass Spectrometry	Will, J. M.; Behrens, A. et al.	Anal. Chem. 2020, acs.analchem.0c03481	https://doi.org/10.1021/acs.analchem.0c03481
Evaluation of Trapped Ion Mobility Spectrometry Source Conditions Using Benzylammonium Thermometer Ions	Naylor, C.N.; Ridgeway, M.E. et al.	J. Am. Soc. Mass Spectrom. 2021, 31, 1593–1602	https://doi.org/10.1021/jasms.0c00151
Fast Online Separation and Identification of Electrochemically Generated Isomeric Oxidation Products by Trapped Ion Mobility-Mass Spectrometry	Fangmeyer, J.; Scheeren, S. et al.	Anal. Chem. 2019, acs.analchem.9b04337	https://doi.org/10.1021/acs.analchem.9b04337
Solvent Adducts in Ion Mobility Spectrometry: Toward an Alternative Reaction Probe for Thermometer Ions	Morsa, D.; Hanozin, E. et al.	J. Am. Soc. Mass Spectrom. 2020, jasms.0c00108	https://doi.org/10.1021/jasms.0c00108
Integration of •SO4−-based AOP mediated by reusable iron particles and a sulfidogenic process to degrade and detoxify Orange II	Yu, X.; Sun, J. et al.	Water Research 2020, 174, 115622	https://doi.org/10.1016/j.watres.2020.115622
Trends in trapped ion mobility – Mass spectrometry instrumentation	Ridgeway, M.E.; Bleiholder, C. et al.	TrAC Trends in Analytical Chemistry 2019, 116, 324–331	https://doi.org/10.1016/j.trac.2019.03.030
Integration of •SO4−-Based AOP Mediated by Reusable Iron Particles and a Sulfidogenic Process to Degrade and Detoxify Orange II	Yu, X.; Sun, J. et al.	Water Research 2020, 174, 115622	https://doi.org/10.1016/j.watres.2020.115622
Metal–Peptide Rings Form Highly Entangled Topologically Inequivalent Frameworks with the Same Ring- and Crossing-Numbers	Sawada, T.; Saito, A. et al.	Nat Commun 2019, 10 (1), 921	https://doi.org/10.1038/s41467-019-08879-7
Comparing Empty and Filled Fullerene Cages with High-Resolution Trapped Ion Mobility Spectrometry	Hennrich, F.; Schneider, E. et al.	J. Am. Soc. Mass Spectrom. 2019, 30 (10), 1973–1980	https://doi.org/10.1007/s13361-019-02250-2
Nanogymnastics: Visualization of Intercluster Reactions by High-Resolution Trapped Ion Mobility Mass Spectrometry	Baksi, A.; Schneider, E. K. et al.	J. Phys. Chem. C 2019, 123 (46), 28477–28485	https://doi.org/10.1021/acs.jpcc.9b08686
Imidazole-Modified G-Quadruplex DNA as Metal-Triggered Peroxidase	Punt, P. M.; Clever, G.	Chem. Sci. 2019, 10 (8), 2513–2518	https://doi.org/10.1039/C8SC05020A
Effective Liquid Chromatography–Trapped Ion Mobility Spectrometry–Mass Spectrometry Separation of Isomeric Lipid Species	Jeanne Dit Fouque, K.; Ramirez, C. E. et al.	Anal. Chem. 2019, 91 (8), 5021–5027	https://doi.org/10.1021/acs.analchem.8b04979
Visible-Light-Driven [2 + 2] Photocycloadditions between Benzophenone and C═C Bonds in Unsaturated Lipids	Li, H.-F.; Cao, W. et al.	J. Am. Chem. Soc. 2020, 142 (7), 3499–3505	https://doi.org/10.1021/jacs.9b12120
Helicenes Fused with Hexafluorocyclopentene (HFCP): Synthesis, Structure, and Properties: Helicenes Fused with Hexafluorocyclopentene (HFCP): Synthesis, Structure, and Properties	Agou, T.; Kohara, M. et al.	Eur. J. Org. Chem. 2020, 2020 (12), 1871–1880	https://doi.org/10.1002/ejoc.202000152
Visible-Transparent Aromatic Polymers Obtained by the Polycondensation of a Bis(Trifluorovinyl)Benzene with Bisphenols	Agou, T.; Yoshinari, K. et al.	Macromolecules 2020, 53 (8), 2942–2949	https://doi.org/10.1021/acs.macromol.0c00157
Tacticity, Molecular Weight, and Temporal Control by Lanthanide Triflate-Catalyzed Stereoselective Radical Polymerization of Acrylamides with an Organotellurium Chain Transfer Agent	Imamura, Y.; Fujita, T. et al.	Polym. Chem. 2020, 11 (44), 7042–7049	https://doi.org/10.1039/D0PY01280G
Flavonoids and Other Phenolics in Herbs Commonly Used in Norwegian Commercial Kitchens	Slimestad, R.; Fossen, T. et al.	Food Chemistry 2020, 309, 125678	https://doi.org/10.1016/j.foodchem.2019.125678
“Conformation Pinning” by Anion Attachment Enabling Separation of Isomeric Steroid Monomers by Ion Mobility Spectrometry	Cole, R. B.; Bayat, P. et al.	J Mass Spectrom 2020, 55 (12)	https://doi.org/10.1002/jms.4657
Synthesis of Trialkylamines with Extreme Steric Hindrance and Their Decay by a Hofmann-like Elimination Reaction	Banert, K.; Hagedorn, M. et al.	J. Org. Chem. 2020, 85 (21), 13630–13643	https://doi.org/10.1021/acs.joc.0c01790
Oxidative Formation of Disulfide Bonds by a Chemiluminescent 1,2-Dioxetane under Mild Conditions	Sauer, C. S.; Köckenberger, J. et al.	J. Org. Chem. 2020, 85 (14), 9331–9338	https://doi.org/10.1021/acs.joc.0c00569
Linear Size Contraction of Ligand Protected Ag 29 Clusters by Substituting Ag with Cu	Baksi, A.; Schneider, E. K. et al.	ACS Nano 2020, 14 (11), 15064–15070	https://doi.org/10.1021/acsnano.0c05082
A Recyclable Photocatalytic Tea-Bag-like Device Model Based on Ultrathin Bi/C/BiOX (X = Cl, Br) Nanosheets	Li, H.; Long, B. et al.	Applied Surface Science 2020, 515, 145967	https://doi.org/10.1016/j.apsusc.2020.145967
Hydroperoxylated vs Dihydroxylated Lipids: Differentiation of Isomeric Cardiolipin Oxidation Products by Multidimensional Separation Techniques	Helmer, P. O.; Behrens, A. et al.	Anal. Chem. 2020, 92 (17), 12010–12016	https://doi.org/10.1021/acs.analchem.0c02605
Hydrophilic Spacer-Arm Containing Magnetic Nanoparticles for Immobilization of Proteinase K: Employment for Speciation of Proteins for Mass Spectrometry-Based Analysis	Bayramoglu, G.; Kayili, H. M. et al.	Talanta 2020, 206, 120218	https://doi.org/10.1016/j.talanta.2019.120218
Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry	Morsa, D.; Hanozin, E. et al.	Anal. Chem. 2020, 92 (6), 4573–4582	https://doi.org/10.1021/acs.analchem.9b05850
LC-Trapped Ion Mobility Spectrometry-TOF MS Differentiation of 2- and 3-Disulfide-Bonded Isomers of the μ-Conotoxin PIIIA	Schmitz, T.; Pengelley, S. et al.	Anal. Chem. 2020, 92 (16), 10920–10924	https://doi.org/10.1021/acs.analchem.0c02151

For Research Use Only. Not for use in clinical diagnostic procedures.