Search engine processor: Filtering and organizing peptide spectrum matches

Arginylation and Methylation Double Up to Regulate Nuclear Proteins and Nuclear Architecture In Vivo

(2011) Sougata Saha et al.   CHEMISTRY & BIOLOGY

Can the false-discovery rate be misleading?

(2011) Rodrigo Barboza et al.   PROTEOMICS

Analyzing marginal cases in differential shotgun proteomics

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

YADA: a tool for taking the most out of high-resolution spectra

(2009) Paulo C. Carvalho et al.   BIOINFORMATICS

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data

(2009) Paulo C Carvalho et al.   Proteome Science

PatternLab for proteomics: a tool for differential shotgun proteomics

(2008) Paulo C Carvalho et al.   BMC BIOINFORMATICS

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

(2008) Eric W. Deutsch et al.   PHYSIOLOGICAL GENOMICS