Table 1.
Coverage and input amount | Average number of proteins and site-localized PTMs quantified per replicate; no. of fractions and mass spectrometry runs |
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---|---|---|---|---|
Proteome | pS, pT, pY | K(GG) | K(Ac) | |
Low (1 mg per SILAC label) | 1,991 (± 213); 1 | 5,466 (± 615); 1 | 2,078 (± 578); 1 | 317 (± 55); 1 |
Medium (2.5 mg per SILAC label) | 5,603 (± 129); 8 | 12,913 (± 1,136); 4 | 4,924 (± 1,208); 2 | 799 (± 30); 2 |
High (7.5 mg per SILAC label) | 7,897 (± 104); 24 | 20,800 (± 1,879); 12 | 15,408 (± 2,000); 6 | 3,190 (± 317); 6 |
Average numbers of quantified proteins and fully localized PTM sites per replicate (n = 3) are shown with s.d. For protein quantification we required at least two unique or razor peptides and ratios per protein. PTM sites were localized in each of the three replicates with a localization probability of >0.75. The sample consisted of SILAC-labeled Jurkat cells stimulated for 4 h with 1 μM bortezomib, a proteasome inhibitor. pS, pT and pY indicate phosphorylation on serine, threonine and tyrosine residues, respectively; K(GG) indicates ubiquitination, and K(Ac) indicates acetylation, on lysine residues. Every mass spectrometry run required 2.5 h of measurement time.