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Module Three : ProteinPilot Peptide Summary
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ProteinPilot™ is a proteomics software program used for analysis of peptide tandem mass spectrometry data and for relative quantification of proteins using the iTRAQ® technology and other modes of stable isotope labeling. Raw data acquired on AB Sciex instruments such as MALDI-TOF/TOF 4800 or QSTAR systems is searched against protein sequence databases; the Paragon scoring algorithm provides confidence levels for protein hits, and the ProGroup algorithm tool (PMID: 17533153) groups related and homologous proteins. The highlights of the software include: a user-friendly interface, simultaneous prediction of hundreds of peptide modifications (~175) and non-tryptic cleavages, the ability to perform quantification at the protein iso-form level, and a sophisticated FDR (false discovery rate) analysis that includes protein- and peptide-level reports. The newest version of ProteinPilot™ also supports identification of peptides and proteins from data acquired on non-AB Sciex instruments after conversion of raw data into *.mgf file format. The tutorial will include an introduction to the software followed by iTRAQ® Data analysis workflow and FDR analysis overviews.
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