MS/MS spectra searched using MaxQuant (v1.5.2.8) and Andromeda as search engine as described previously were imported as a spectral library with a score filter>0.8. Extracted ion chromatograms were generated by Skyline daily v3.4.9.9576 within 5 min of the library retention time using 3 isotopic peaks for all peptides corresponding to the spiked-in proteins and the E.coli proteins previously identified with MaxQuant. Only peptides with charge +2 and +3 were considered. Automatic peak picking was manually reviewed for the spiked-in proteins and refined with idotp > 0.75 for the E. coli proteome. The differential abundance analysis was performed by MSstats (v3.12.3) R package. description.pdf including details for data processing and statistical analysis and R script for MSstats are available in the ‘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/C5KB1M]
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Keywords: MassIVE.quant reviewed - Platinum
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