Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet

(2015) Andrew Keller et al.   MOLECULAR & CELLULAR PROTEOMICS

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

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring

(2014) Chun Wai Manson Ma et al.   JOURNAL OF PROTEOME RESEARCH

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Regulation of mRNA Trafficking by Nuclear Pore Complexes

(2014) Amandine Bonnet et al.   Genes

Profiling of Ubiquitin-like Modifications Reveals Features of Mitotic Control

(2013) Yifat Merbl et al.   CELL

Protein post-translational modifications and regulation of pluripotency in human stem cells

(2013) Yu-Chieh Wang et al.   CELL RESEARCH

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

(2013) John D. Chapman et al.   MASS SPECTROMETRY REVIEWS

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

RNA editing enters the limelight in cancer

(2013) Angela Gallo   NATURE MEDICINE

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

Post-translational modifications and the Warburg effect

(2013) T Hitosugi et al.   ONCOGENE

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

(2010) Ding Ye et al.   BIOINFORMATICS

A Novel Approach for Untargeted Post-translational Modification Identification Using Integer Linear Optimization and Tandem Mass Spectrometry

(2010) Richard C. Baliban et al.   MOLECULAR & CELLULAR PROTEOMICS

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

(2008) Judit Villén et al.   Nature Protocols