Proteomics; Tandem Mass Spectrometry/methods; Computational Biology; Software

(HUPO)-PSI; (Human Proteome Organization) ­ Proteomics Standards Initiative; AMT; ATAQS; Accurate Mass Tag; Application programming interface; Automated and Targeted Analysis with Quantitative SRM; Bioinformatics; CV; Controlled Vocabulary; DAO; Data Access Object; Databases; EBI; European Bioinformatics Institute; FDR; False Discovery Rate; GUI; Graphical User Interface; ICAT; ICPL; IPTL; ISB; Institute for Systems Biology; Isobaric Peptide Termini Labeling; Isobaric Tag for Relative and Absolute Quantitation; Isotope-Coded Affinity Tags; Isotope-Coded Protein Label; JPL; Java Proteomic Library; LC-MS; LIMS; Laboratory Information Management System; Liquid Chromatography­Mass Spectrometry; MGF; MIAPE; MS; Mascot Generic Format; Mass Spectrometry; Minimum Information About a Proteomics Experiment; Open source software; PASSEL; PRIDE; PRoteomics IDEntifications (database); PSM; PTM; Peptide Spectrum Match; PeptideAtlas SRM Experiment Library; Post-Translational Modifications; Proteomics; RT; Retention Time; SILAC; SRM; Selected Reaction Monitoring; Software libraries; Stable Isotope Labeling by Amino acids in Cell culture; TMT; TOPP; TPP; Tandem Mass Tag; The OpenMS Proteomics Pipeline; Trans-Proteomic Pipeline; emPAI; exponentially modified Protein Abundance Index; iTRAQ