Proteomic analysis of mismatch repair-mediated alkylating agent-induced DNA damage response

Cell & Bioscience

Table 1 Number of peptides and proteins identified and quantified in MNNG-treated cells

Component	Whole cell extract		Nuclear extract
Component	TK6	MT1	TK6	MT1
Unique phosphopeptides	1438 (FDR^# = 1.9%)	1654 (FDR^# = 1.6%)	1594 (FDR^# = 2.7%)	1348 (FDR^# = 2.3%)
Unique proteins	1792 (FDR^# = 4.9%)	1765 (FDR^# = 4.5%)	1238 (FDR^# = 4.5%)	1102 (FDR^# = 4.8%)
Phosphopeptides quantified	766	925	1108	901
Proteins quantified	1153	1198	794	724
Down-regulated phosphopeptides^*	13	13	127	37
Up-regulated phosphopeptides^*	15	16	76	74
Down-regulated proteins^*	30	20	23	16
Up-regulated proteins^*	26	29	51	178

^#The FDR (false-discovery rate) of phosphopeptides was calculated by searching query sequences against a randomized SwissProt human database with significance threshold p set to 0.05. The identified proteins were grouped by Scaffold (version 2_04_00) to eliminate redundancy and the FDR of proteins were also calculated by Scaffold software.
^*The cutoff threshold was set at 1.5-fold increase or decrease, that is, a light-to-heavy ratio (L/H) ≥ 1.5 or ≤ 0.66.

ISSN: 2045-3701