A spectral library was generated using all available raw files from the original publication using the Pulsar search engine integrated in Spectronaut 11(11.0.15038) with default settings. The uniprot yeast reference proteome was used for the spectrum centric data analysis for library generation. DIA data was then analyzed using default settings and exported using the built in MSstats Report (v3.7.3) export schema. The differential abundance analysis was performed by MSstats (v3.10.6) 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/C5WB2S]
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Keywords: MassIVE.quant reviewed - Platinum
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