Computational protocol: Extracellular Matrix Dynamics in Hepatocarcinogenesis: a Comparative Proteomics Study of PDGFC Transgenic and Pten Null Mouse Models

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Protocol publication

[…] Acquired data were processed using the X!Tandem search algorithm and PeptideProphet and ProteinProphet statistical tools , . The tandem mass spectra were searched against the mouse International Protein Index protein sequence database (IPI, version 3.34, The following search criteria were used in all cases: trypsin specificity, 2.5 Da of mass accuracy for the parent ion and methionine oxidation as a variable modification and when specified, lysine oxidation was added as a variable modification. Relative abundance scores were calculated for individual proteins based on total peptide counts normalized to account for the total amount of protein in the mixture. […]

Pipeline specifications

Software tools PeptideProphet, ProteinProphet
Databases IPI
Application MS-based untargeted proteomics
Organisms Mus musculus, Homo sapiens
Diseases Fatty Liver, Carcinoma, Hepatocellular, Liver Cirrhosis, Neoplasms, Adenoma, Liver Cell