Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

Biosaur: An open‐source Python software for LC/MS1 peptide feature detection with ion‐mobility support

(2021) Daniil A. Abdrakhimov et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes

(2020) Mark V. Ivanov et al.   ANALYTICAL CHEMISTRY

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

(2020) Dorte B. Bekker-Jensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

(2020) Fengchao Yu et al.   MOLECULAR & CELLULAR PROTEOMICS

Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing

(2020) Jana Zecha et al.   MOLECULAR & CELLULAR PROTEOMICS

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

(2020) Christoph B. Messner et al.   Cell Systems

Quantitative shotgun proteome analysis by direct infusion

(2020) Jesse G. Meyer et al.   NATURE METHODS

SW-Tandem: A Highly Efficient Tool for Large-Scale Peptide Sequencing with Parallel Spectrum Dot Product on Sunway TaihuLight

(2019) Chuang Li et al.   BIOINFORMATICS

Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags while Significantly Reducing Instrument Time

(2019) Jonathan R. Krieger et al.   JOURNAL OF PROTEOME RESEARCH

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction

(2019) Joerg Doellinger et al.   MOLECULAR & CELLULAR PROTEOMICS

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics

(2018) Lev I. Levitsky et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of In-Solution, FASP, and S-Trap Based Digestion Methods for Bottom-Up Proteomic Studies

(2018) Katelyn R. Ludwig et al.   JOURNAL OF PROTEOME RESEARCH

Improved Peptide Retention Time Prediction in Liquid Chromatography through Deep Learning

(2018) Chunwei Ma et al.   ANALYTICAL CHEMISTRY

S-Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics

(2018) Milkessa HaileMariam et al.   JOURNAL OF PROTEOME RESEARCH

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

(2018) Wout Bittremieux et al.   JOURNAL OF PROTEOME RESEARCH

A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

(2018) Nicolai Bache et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Scavager: a versatile postsearch validation algorithm for shotgun proteomics based on gradient boosting

(2018) Mark V. Ivanov et al.   PROTEOMICS

MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity

(2017) Mark V. Ivanov et al.   JOURNAL OF PROTEOME RESEARCH

SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes

(2017) Matthieu David et al.   JOURNAL OF PROTEOME RESEARCH

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

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

(2017) Andy T Kong et al.   NATURE METHODS

Sample Clean-up Strategies for ESI Mass Spectrometry Applications in Bottom-up Proteomics: Trends from 2012 to 2016

(2017) Ria Marni Tubaon et al.   PROTEOMICS

Predictive chromatography of peptides and proteins as a complementary tool for proteomics

(2016) Irina A. Tarasova et al.   ANALYST

Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing

(2016) Ludovic C. Gillet et al.   Annual Review of Analytical Chemistry

Dinosaur: A Refined Open-Source Peptide MS Feature Detector

(2016) Johan Teleman et al.   JOURNAL OF PROTEOME RESEARCH

Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach

(2016) Lev I. Levitsky et al.   JOURNAL OF PROTEOME RESEARCH

Modified filter-aided sample preparation (FASP) method increases peptide and protein identifications for shotgun proteomics

(2016) Mao-wei Ni et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Enhancement of mass spectrometry performance for proteomic analyses using high-field asymmetric waveform ion mobility spectrometry (FAIMS)

(2015) Eric Bonneil et al.   JOURNAL OF MASS SPECTROMETRY

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

LC-MS alignment in theory and practice: a comprehensive algorithmic review

(2013) R. Smith et al.   BRIEFINGS IN BIOINFORMATICS

High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics

(2012) Kristian E Swearingen et al.   Expert Review of Proteomics

Mass spectrometry for translational proteomics: progress and clinical implications

(2012) Erin Baker et al.   Genome Medicine

Identification of phosphorylated human peptides by accurate mass measurement alone

(2011) Yuan Mao et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

(2011) Benjamin J. Diament et al.   JOURNAL OF PROTEOME RESEARCH

Training, Selection, and Robust Calibration of Retention Time Models for Targeted Proteomics

(2010) Luminita Moruz et al.   JOURNAL OF PROTEOME RESEARCH

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments

(2008) Christophe D. Masselon et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY