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

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

(2012) Chad R. Weisbrod et al.   JOURNAL OF PROTEOME RESEARCH

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

FDRAnalysis: A Tool for the Integrated Analysis of Tandem Mass Spectrometry Identification Results from Multiple Search Engines

(2011) David C. Wedge et al.   JOURNAL OF PROTEOME RESEARCH

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

(2010) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies

(2010) Brian C. Searle   PROTEOMICS

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

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

(2008) Brian C. Searle et al.   JOURNAL OF PROTEOME RESEARCH

A Fast SEQUEST Cross Correlation Algorithm

(2008) Jimmy K. Eng et al.   JOURNAL OF PROTEOME RESEARCH

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

(2008) Christopher Y. Park et al.   JOURNAL OF PROTEOME RESEARCH