PyQuant: A Versatile Framework for Analysis of Quantitative Mass Spectrometry Data

Comprehensive Temporal Protein Dynamics during the Diauxic Shift inSaccharomyces cerevisiae

(2015) J. Patrick Murphy 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

Deletion of Genes Encoding Arginase Improves Use of “Heavy” Isotope-Labeled Arginine for Mass Spectrometry in Fission Yeast

(2015) Weronika E. Borek et al.   PLoS One

NeuCode Labels for Relative Protein Quantification

(2014) Anna E. Merrill et al.   MOLECULAR & CELLULAR PROTEOMICS

Neutron-encoded mass signatures for multiplexed proteome quantification

(2013) Alexander S Hebert et al.   NATURE METHODS

TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics

(2012) Jun Zhong et al.   MOLECULAR & CELLULAR PROTEOMICS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

MSblender: A Probabilistic Approach for Integrating Peptide Identifications from Multiple Database Search Engines

(2011) Taejoon Kwon et al.   JOURNAL OF PROTEOME RESEARCH

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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Data maximization by multipass analysis of protein mass spectra

(2010) Ravi Tharakan et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

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

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

Enhancing Peptide Identification Confidence by Combining Search Methods

(2008) Gelio Alves et al.   JOURNAL OF PROTEOME RESEARCH

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