pyQms enables universal and accurate quantification of mass spectrometry data

Supplemental Data

• Supplemental Data (.zip, 50.8 MB) - Annotated peptide spectra as required by MCP guidelines.
• Supplemental figures (.pdf, 6.6 MB) - Supplemental figures 1 - 15 including descriptions.
• Supplemental methods (.pdf, 83 KB) - Supplemental methods.
• Supplemental table descriptions (.pdf, 66 KB) - Supplemental table descriptions for STable 1 - 12
• Supplemental Table S1 (.xlsx, 20 KB) - Overview of quantification engines for DDA and DIA mass spectrometry data.
• Supplemental Table S2 (.xlsx, 1.9 MB) - All identified peptides in the pulse gold standard data set.
• Supplemental Table S3 (.xlsx, 365 KB) - Identified peptides and protein sequence coverage.
• Supplemental Table S4 (.xlsx, 2.7 MB) - Retention time windows.
• Supplemental Table S5 (.xlsx, 455 KB) - Retention time alignment functions for the Bruderer et al. dataset.
• Supplemental Table S6 (.xlsx, 10 KB) - Intensity alignment correction factors.
• Supplemental Table S7 (.xlsx, 89 KB) - DDA quantification results for the spiked-in-proteins of the DDA data set from Bruderer et al. (2015).
• Supplemental Table S8 (.xlsx, 738 KB) - Complete curated spectral library used for the DIA quantification approach.
• Supplemental Table S9 (.xlsx, 56 KB) - DIA quantification results for the spiked-in-proteins of the DIA data set from Bruderer et al. (2015).
• Supplemental Table S10 (.xlsx, 9 KB) - T-test results on master mix level for the DDA and DIA approaches by pyQms.
• Supplemental Table S11 (.xlsx, 11 KB) - T-test results on protein level for the DDA and DIA approaches by pyQms.
• Supplemental Table S12 (.xlsx, 10 KB) - Header/sample descriptions for the supplemental table headers.
• Fasta database (.zip, 16.4 MB) - C reinhardtii fasta database for pulse chase gold standard dataset