Proteomics data analysis
MS spectra were processed using Proteome Discoverer (Thermo Fisher
Scientific, version) and the MS Amada identification algorithm (Dorfer
et al., 2014). The MS/MS data were queried against the CHO-K1 proteome
available from UniProtKB (proteome ID : UP000001075, downloaded Sept 3,
2018) and the “common Repository of Adventitious Proteins” database
(cRAP) for contaminants available on the Global Proteome Machine website
(downloaded Oct 30, 2018)(Consortium, 2018; Craig et al., 2004).
Precursor mass tolerance was set at 10ppm. Fragment mass tolerance was
set at 0.02ppm. Methionine oxidation and protein N-terminal acetylation
were defined as dynamic modifications. Cysteine carbamidomethylation,
TMT adduction on Lysine and on protein N-terminal were defined as a
fixed modification. Peptides and assembled proteins were searched at a
false discovery rate (FDR) of 1%. A minimum of one unique peptide per
protein was required for protein identification. For TMT quantification,
the ratios of the TMT reporter ion intensities between samples and the
internal standard (label 131C), generated by proteome discoverer for
each proteins, were used. These ratios were extracted for the
statistical analysis in R.