PASEF^®

PASEF^® (Parallel Accumulation Serial Fragmentation) is an innovative mass spectrometry technology that revolutionizes proteomics analysis. PASEF^® is uniquely incorporated into Bruker's timsTOF mass spectrometers, which combine orthogonal ion mobility and time-of-flight separation to achieve unprecedented levels of selectivity, speed, and sensitivity.

PASEF^® (Parallel Accumulation Serial Fragmentation) is a revolutionary mass spectrometry technique rewriting the rules of proteome analysis. It leverages the unmatched power of time and space focusing, combining orthogonal ion mobility (IM) and time-of-flight (TOF) separations to deliver unprecedented selectivity, speed, and sensitivity.

Unlike traditional methods, PASEF^® exploits the unique Collisional Cross Section (CCS) property of peptides, a measurable fingerprint differentiating them based on size and shape. This "space focusing" via IM separates peptides with exquisite precision, even in crowded samples.

Simultaneously, "time focusing" empowers parallel accumulation of these separated ions, followed by rapid, sequential fragmentation. This ingenious design unlocks:

• Speed: PASEF^® slashes analysis time compared to conventional methods, accelerating your research pace.
• Sensitivity: By minimizing interferences and boosting signal-to-noise ratio, PASEF^® reveals low-abundance peptides previously hidden from view.
• Selectivity: CCS-based separation and time-focused fragmentation dramatically reduce background noise, ensuring confident identification and characterization of even the most challenging analytes.
  

The result? Comprehensive proteome coverage, deeper insights into complex biological systems, and faster breakthroughs in your research.

PASEF^® is not just a tool; it's a game-changer for biomolecular research, from peptides to proteins, to lipids and metabolites. If you demand cutting-edge proteomics solutions for superior speed, sensitivity, and selectivity, PASEF^® exclusively on the timsTOF is your answer.

dda-PASEF^® is a data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF^®) technology to improve the speed, sensitivity, and comprehensiveness of proteomics analysis.

DDA is a traditional proteomics method that selects and fragments peptides for identification and quantification based on their mass-to-charge ratio (m/z). PASEF^® is a new method that uses trapped ion mobility separation (TIMS) to separate peptides based on their size, shape, and charge before fragmentation. This allows for the identification of a wider range of peptides and a more comprehensive understanding of the proteome.

Here's why dda-PASEF^® stands out:

• Breakthrough coverage: Transcend m/z limitations. dda-PASEF^® leverages TIMS (Trapped Ion Mobility Separation) to resolve isobaric peptides and unveil hidden gems in your samples, leading to significantly richer proteome landscapes.
  
• MS/MS on steroids: Experience near 100% duty cycle with blistering scan speeds reaching 300 Hz. This translates to exponentially more MS/MS scans, maximizing peptide identifications and painting a comprehensive protein picture.
  
• Precise CCS insights: Gain deeper structural and functional understanding with accurate collisional cross-section (CCS) determination. This opens doors to novel biomarker discovery and unmatched analyte characterization.
  
• Real-time optimization: Conquer workflow bottlenecks with Bruker ProteoScape™ real-time data analysis. Streamline your research, maximize productivity, and extract the most value from every precious sample without delay.
  

dda-PASEF^® excels in:

• Deciphering complex proteomes: Tackle challenging samples like tissues, single cells, and PTM-laden landscapes of any species with confidence.
  
• Boosted peptide identification: Leave no stone unturned. Identify more low-abundance, isobaric peptides, and their modifications for a comprehensive protein proteome picture.
  
• Lightning-fast lipidomics: Conquer time constraints in lipid analysis and easily differentiate sub-classes and lipid species with unparalleled acquisition speeds.
  
• Biomarker discovery: Unearth novel candidates with the combined power of MS and CCS data.
  

dia-PASEF^® is a data-independent acquisition (DIA) method that uses parallel accumulation-serial fragmentation (PASEF^®) technology to attain superior speed, comprehensive and ultra-sensitive quantitative proteomics.

Here's why dia-PASEF^® stands out:

• Unparalleled sensitivity: Forget limitations. Unlike DDA, dia-PASEF^® fragments all peptides in your sample, regardless of their abundance. This unveils even the faintest whispers of protein expression, offering a truly holistic view of your proteome.
  
• Exquisite selectivity: PASEF^® technology leverages Trapped Ion Mobility Separation (TIMS) to separate peptides based on size and shape, effectively eliminating isobaric interferences. This translates to confident and accurate quantification, even for low-abundance proteins.
  
• Quantitative powerhouse: Achieve high reproducibility of quantification with dia-PASEF^®. Its robust design minimizes technical variability, ensuring reliable comparisons across samples and conditions.
  
• Deeper insights with CCS: Gain valuable structural and functional information with integrated collisional cross-section (CCS) analysis. This opens doors to novel biomarker discovery and targeted protein investigations.
  
• Efficiency meets depth: Experience shorter chromatographic gradients without compromising identification depth. dia-PASEF^® optimizes your workflow, maximizing your research output and precious sample resources.
  

dia-PASEF^® shines in:

• Comparative proteomics: Unravel differential protein expression across conditions, cell types, or disease states with unmatched sensitivity, accuracy and data completeness.
  
• Biomarker discovery: Mine your data for novel diagnostic, prognostic, or therapeutic targets with confidence in your identifications and quantifications.
  
• Protein interaction studies: Map protein-protein interactions with exceptional sensitivity and uncover subtle changes in complex networks.
• Complex Post-translational modification(PTM) profiling: Delve deeper into the intricate world of PTMs by identifying and quantifying modified peptides with precision.

If you are looking to gain the most comprehensive data while not sacrificing quantitative specificity for your biological data, dia-PASEF^® is the method for you. 

diagonal-PASEF^® is an innovative scan mode for the timsTOF platform, encompassing two advanced methods: midia-PASEF^® and synchro-PASEF^®. These methods leverage the synchronization of the TIMS ramp with the quadrupole selection window, significantly enhancing data acquisition and analysis capabilities.

• Improved quantitation and throughput: Experience faster cycle times, averaging 0.4 seconds, which boosts quantitation precision and overall throughput, making your experiments more efficient.
• Enhanced specificity and sensitivity: Benefit from the precise synchronization of the quadrupole selection window with the TIMS ramp, allowing for more accurate and sensitive detection of precursor ions and their fragments.
• Increased proteome coverage: Unlock comprehensive detection of precursor ions, significantly enhancing your proteome coverage and ensuring no critical data is missed.
• Optimized duty cycle: Enjoy a superior duty cycle compared to conventional dia-PASEF^®, which enhances both throughput and data quality, making your research more productive.

midia-PASEF^®

midia-PASEF^® offers DDA-like spectra, making it ideal for immunopeptidomics and post-translational modification (PTM) studies. Developed by Professor Stefan Tenzer, this method uses overlapping ion mobility-encoded quadrupole windows to maximize information content in DIA acquisitions. The resulting “MIDIA fingerprints” enable precise prediction of precursor m/z positions with high accuracy, typically less than 2 Th.

• High-quality deconvoluted spectra: Generate DDA-like spectra from DIA data, significantly improving database searching and de novo sequencing capabilities, and providing high-quality results for complex samples.

synchro-PASEF^®

synchro-PASEF^®, developed by Professor Matthias Mann, enhances conventional DIA by synchronizing the quadrupole selection window with the TIMS ramp. This method improves specificity, efficiency, and proteome coverage, making it advantageous for large-scale proteomics studies.

• Streamlined setup: Enjoy the simplicity of configuring just a few diagonal windows, eliminating the complexity of standard dia window allocation and accelerating your workflow. Additionally, synchro-PASEF^® data can be processed by most software solutions on the market, including Bruker ProteoScape™ and Spectronaut, ensuring seamless integration into existing workflows.

Both midia-PASEF^® and synchro-PASEF^® represent significant advancements in the timsTOF platform, providing researchers with powerful tools for comprehensive and detailed proteomic analysis.

prm-PASEF^® is a targeted proteomics method that combines the advantages of parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF^®). PRM is a specific method for the identification and quantification of known analytes in the sample, while PASEF^® is a technique that increases the sensitivity and selectivity of proteomics analysis.

Here's why prm-PASEF^® sets the standard:

• Targeted precision: Forget fishing expeditions. prm-PASEF^® lets you hone in on pre-defined protein targets, without the need to develop affinity handles like antibodies ensuring confident identification and accurate quantification of even low-abundance analytes amidst complex mixtures.
  
• Sensitivity unleashed: PASEF^®'s magic touch amplifies your signal, revealing previously hidden targets with exquisite detail. No more struggling with faint whispers of protein expression.
  
• Multiplexing master: Break free from single-target limitations. prm-PASEF^® empowers simultaneous analysis of multiple proteins in a single run, saving you time and resources while maximizing insights.
  
• TIMS-powered efficiency: Bruker's timsTOF platform fuels prm-PASEF^®'s prowess. Its Trapped Ion Mobility Separation (TIMS) technology eliminates isobaric interferences, guaranteeing reliable quantification and confident target identification.
  
• Fast forward your research: Experience shorter LC gradients without sacrificing sensitivity or selectivity. prm-PASEF^® optimizes your workflow, accelerating your research pace and maximizing your precious sample resources.
  

The prm-PASEF^® advantage: 

• Biomarker discovery and validation: Pinpoint promising candidates with confidence and translate them into reliable diagnostic or therapeutic targets.
  
• Targeted protein investigations: Deep dive into specific protein pathways, interactions, or post-translational modifications with exceptional precision.
  
• Clinical proteomics: Unravel disease mechanisms and personalize treatment strategies through accurate and reproducible protein analysis.
  
• Method development and validation: Streamline your workflows with prm-PASEF^®'s robust performance and reliable quantification.
  

If you are looking for a targeted proteomics method that offers increased sensitivity, selectivity, and multiplexing capabilities, then prm-PASEF^® is the method for you.

Discover just a few of the innovative ways that customers are using PASEF^® to advance their research. As PASEF^® technology continues to develop, we can expect to see even more innovative applications for this powerful tool.

Just a click of a button to empower you to dissect any sample.

Ready to join the PASEF^® revolution? Explore its potential today.

dda-PASEF^® variations

• caps-PASEF^®: Uses stepped collision energy (CE) to fragment precursor ions, resulting in more complete fragmentation and improved sensitivity, unlocking unmatched sensitivity for crosslinked peptides using the resolving power of TIMS.¹
• thunder-PASEF: Improves sensitivity for identifying immunopeptides by selectively fragmenting HLA peptide ligands based on their mobility and m/z, including singly charged peptides, while excluding singly charged chemical noise. This makes it a powerful tool for immunopeptidomics research.²
  
  

dia-PASEF^® variations

• slice-PASEF^®: Precise precursor ion selection at PASEF^® speeds amplifies sensitivity for the most challenging samples, including single cells and Formalin-Fixed Paraffin-Embedded (FFPE) tissues, opening new possibilities in proteomic analysis.³
• VistaScan (synchro-PASEF): A method that synchronizes the quadrupole selection window with the ion mobility dimension. This allows for more specific and sensitive detection of precursor ions and their fragment ions.⁴
• plexDIA: Allows for multiplexed proteomic analysis of multiple samples in a single experiment, increasing throughput, reducing costs, and improving data quality. It is well-suited for comparative proteomics, clinical proteomics, and biomarker discovery.⁵
  

dia-PASEF^® with dda-like spectra

• midia-PASEF^®: Combines the best of both worlds: the high-quality MS/MS spectra of dda-PASEF^® with the comprehensiveness of dia. It does this by using a mobility-specific micro-encoding of overlapping quadrupole windows to optimally cover the ion population in the ion mobility-mass to charge plane ideal applications such as immunopeptidomics research.⁶
  
  

prm-PASEF^® variations

• prm-live: Automatically adjust PRM detection windows for reproducible quantitation of 100s of a targets/min. Increases the reproducible multiplexing of targets across prm-PASEF^® acquisitions by accounting for sporadic chromatographic drifts in peptide retention time. It is well-suited for highly multiplexed targeted proteomics.⁷
  
  

1. Steigenberger, Barbara. et al. “Benefits of Collisional Cross Section Assisted Precursor Selection (Caps-PASEF) for Cross-Linking Mass Spectrometry.” Molecular & Cellular Proteomics 19, no. 10 (2020): 1677–87. https://doi.org/10.1074/mcp.ra120.002094 
2. Gomez-Zepeda D, et. al. "Thunder-DDA-PASEF enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCov-2 spike protein epitopes” Europe PMC (2023). https://europepmc.org/article/ppr/ppr628333 
3. Szyrwiel, Lukasz, et al. “Slice-PASEF: Fragmenting All Ions for Maximum Sensitivity in Proteomics.” bioRxiv , 2022. https://doi.org/10.1101/2022.10.31.514544 
4. Mann, M et. Al (2023). “Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition” Molecular & cellular proteomics: MCP, 22(2), 100489. https://doi.org/10.1016/j.mcpro.2022.100489
5. Slavov. N et. al. “Increasing the throughput of sensitive proteomics by plexDIA”. Nat Biotechnol 41, 50–59 (2023). https://doi.org/10.1038/s41587-022-01389-w 
   
6. Distler, Ute, et al. “MIDIAPASEF maximizes information content in data-independent acquisition proteomics.” bioRxiv, (2023). https://doi.org/10.1101/2023.01.30.526204
7. H. Zhu. et al. “PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors” Analytical Chemistry 2021 93 (41), 13791-13799. https://doi.org/10.1021/acs.analchem.1c02349

PASEF^® is a revolutionary mass spectrometry technology that is exclusively offered by Bruker. It is the most advanced technology available for proteomics analysis, combining the advantages of orthogonal trapped ion mobility and time-of-flight separation to deliver unprecedented levels of selectivity, speed, and sensitivity. This makes PASEF^® the ideal choice for a wide range of applications, from proteome-wide analysis to single-cell analysis.

If you are looking for the most advanced mass spectrometry technology for proteomics analysis, then PASEF^® is the clear choice. Contact Bruker today to learn more about PASEF^® and how it can help you advance your research.