Protein Quantification in Formaldehyde-Treated Cells

Protein-level SWATH-MS quantitative dataset for formaldehyde (FA) treated cells (or ‘ProtSWATH’ in short). This dataset was published in a previous study in which HeLa Kyoto cells were treated with or without 200 μM FA for 5 h (62 (link)). The SWATH-MS measurement was performed on a SCIEX 5600 plus TripleTOF instrument. The proteome changes induced by FA treatment was demonstrated to be minimal and specific, with <1% of the detected proteins showed statistically significant reductions (P < 0.05, Benjamini–Hochberg adjusted), presenting a challenging case for relative label free quantification at the protein level, for which the proteomic analysis has been already matured (26 (link)). To analyze ‘ProtSWATH’ dataset, a spectral library containing mass spectrometric assays for 10 000 human proteins (63 (link)) and 1% peptide and 1% protein-FDR (29 (link)) were applied to Spectronaut based analysis (57 (link),58 (link)). In particular, the MS2 peak area of the top3 most abundant peptides were averaged and summarized for protein quantification. No PTM score was needed.