Peptide features were identified with the Progenesis algorithm (v4.0.6403), aligned across all files, and annotated with the peptide identification resulting from the database search result from Comet. Unique semi-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 (v3.13.5) R package. Details for data processing and statistical analysis are available in description.pdf ('Methods' folder).
**Publication : Choi et al. (Under revision) MSstats increases the reproducibility of detecting differentially abundant proteins across tools that process raw mass spectra.
[doi:10.25345/C53149]
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results attachment job
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Keywords: MassIVE.quant reviewed - Platinum
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