. Author manuscript; available in PMC: 2014 Mar 5.

Published in final edited form as: Nat Methods. 2013 Jun 9;10(7):634–637. doi: 10.1038/nmeth.2518

Table 1.

Relationship among depth of proteome and PTM-ome coverage, input amount of protein lysate, degree of fractionation and mass spectrometry instrument time

Coverage and input amount	Average number of proteins and site-localized PTMs quantified per replicate; no. of fractions and mass spectrometry runs
Coverage and input amount	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.