Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

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

(2017) Andy T Kong et al.   NATURE METHODS

Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation

(2016) Inamul Hasan Madar et al.   ANALYTICAL CHEMISTRY

Modeling Protein Excited-state Structures from “Over-length” Chemical Cross-links

(2016) Yue-He Ding et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides

(2016) Boris Bogdanow et al.   MOLECULAR & CELLULAR PROTEOMICS

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

(2016) Johannes Griss et al.   NATURE METHODS

The potential clinical impact of the release of two drafts of the human proteome

(2015) Iakes Ezkurdia et al.   Expert Review of Proteomics

pFind–Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

(2015) Hao Chi et al.   Journal of Proteomics

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

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

Illuminating the dark matter of shotgun proteomics

(2015) Owen S Skinner et al.   NATURE BIOTECHNOLOGY

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

pQuant Improves Quantitation by Keeping out Interfering Signals and Evaluating the Accuracy of Calculated Ratios

(2014) Chao Liu et al.   ANALYTICAL CHEMISTRY

Space–time wiring specificity supports direction selectivity in the retina

(2014) Jinseop S. Kim et al.   NATURE

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

(2012) Viktor Granholm et al.   Journal of Proteomics

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

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

pParse: A method for accurate determination of monoisotopic peaks in high-resolution mass spectra

(2011) Zuo-F ei Yuan et al.   PROTEOMICS

Spectral Dictionaries

(2008) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY