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
entries per page
| 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 |
timsTOF Ultra
entries per page
| 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 |
Showing 1 to 7 of 7 entries
Single Cell
entries per page
| 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 |
Immunopeptidomics – COVID-19 Section
entries per page
| 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 |
Biology – COVID-19 Section
entries per page
| 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 |
Biology
entries per page
| 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 |
Biology - Preprints
entries per page
| 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 |
Chemistry
entries per page
| 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 |
For Research Use Only. Not for use in clinical diagnostic procedures.