Peptide features were identified with the Progenesis QI v4.0 algorithm, aligned across all files, and annotated with the peptide identification resulting from the database search result from Proteome Discovery and Mascot. Unique tryptic peptides corresponding to the spiked-in proteins were quantified using the feature areas as calculated by the Progenesis algorithm. The differential abundance analysis was performed by MSstats R package. Quantification result is the same as in RMSV000000261.3. Uninformative features and outliers were flagged by feature selection algorithm and removed for statistical analysis in MSstats R package for this reanalysis.
**Publication : Tsai TH, Choi M, Banfai B, Liu Y, MacLean BX, Dunkley T, Vitek O. (2020). Selection of features with consistent proles improves relative protein quantification in mass spectrometry experiments. Molecular & Cellular Proteomics. 2020 March 31, 19(6) 944-959, doi:10.1074/mcp.RA119.001792. PMID: 32234965.
[doi:10.25345/C56147]
[See
results attachment job
for details]
Keywords: MassIVE.quant reviewed - Platinum
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Browse Reanalysis Files | |
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