Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry-Based Proteomics

Deep learning the collisional cross sections of the peptide universe from a million experimental values

(2021) Florian Meier et al.   Nature Communications

Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-Based Quantitation in Proteomic LC/MS/MS

(2020) Kosuke Ogata et al.   ANALYTICAL CHEMISTRY

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

(2020) Nikita Prianichnikov et al.   MOLECULAR & CELLULAR PROTEOMICS

Philosopher: a versatile toolkit for shotgun proteomics data analysis

(2020) Felipe da Veiga Leprevost et al.   NATURE METHODS

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

(2020) Florian Meier et al.   NATURE METHODS

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry

(2019) Devin K. Schweppe et al.   ANALYTICAL CHEMISTRY

PyRanges: efficient comparison of genomic intervals in Python

(2019) Endre Bakken Stovner et al.   BIOINFORMATICS

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

Parallel accumulation for 100% duty cycle trapped ion mobility-mass spectrometry

(2017) Joshua A. Silveira et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry

(2016) Sibylle Pfammatter et al.   JOURNAL OF PROTEOME RESEARCH

Now, More Than Ever, Proteomics Needs Better Chromatography

(2016) Evgenia Shishkova et al.   Cell Systems

Review on Ion Mobility Spectrometry. Part 1: current instrumentation

(2015) R. Cumeras et al.   ANALYST

Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

(2015) Florian Meier et al.   JOURNAL OF PROTEOME RESEARCH

Enhancing bottom-up and top-down proteomic measurements with ion mobility separations

(2015) Erin Shammel Baker et al.   PROTEOMICS

DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

(2014) Johan Teleman et al.   BIOINFORMATICS

Estimating Influence of Cofragmentation on Peptide Quantification and Identification in iTRAQ Experiments by Simulating Multiplexed Spectra

(2014) Honglan Li et al.   JOURNAL OF PROTEOME RESEARCH

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry

(2014) Bo Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation

(2011) Saw Yen Ow et al.   PROTEOMICS

Note: Integration of trapped ion mobility spectrometry with mass spectrometry

(2011) F. A. Fernandez-Lima et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies

(2010) Stephane Houel et al.   JOURNAL OF PROTEOME RESEARCH

Enhanced Sensitivity in Proteomics Experiments Using FAIMS Coupled with a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer†

(2009) Julian Saba et al.   JOURNAL OF PROTEOME RESEARCH

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies

(2009) Erin Shammel Baker et al.   JOURNAL OF PROTEOME RESEARCH

Assessing the Dynamic Range and Peak Capacity of Nanoflow LC−FAIMS−MS on an Ion Trap Mass Spectrometer for Proteomics

(2008) Jesse D. Canterbury et al.   ANALYTICAL CHEMISTRY

Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues

(2008) Leroi V. DeSouza et al.   JOURNAL OF PROTEOME RESEARCH

Robust and Sensitive iTRAQ Quantification on an LTQ Orbitrap Mass Spectrometer

(2008) Marcus Bantscheff et al.   MOLECULAR & CELLULAR PROTEOMICS