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

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

Component Whole cell extract Nuclear extract
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
  1. #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.
  2. *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.