Table 1

Distribution of unique tryptic peptides and tryptic peptides containing the N-X-T/S motif over subcellular classes of proteins in the human protein (IPI) database

Tryptic peptidesa

Peptides containing N-X-T/S


Number of peptidesa

Number of proteins

Number of peptidesa

Number of proteins


Intracellular

510,685(68.2%b)

26,721(66.6%c)

32,770(4.4%b)

17,475(43.6%c)

Secreted

80,069(10.7%)

3,772(9.4%)

7,195(1.0%b)

2,772(6.9%c)

Transmembrane

114,282(15.3%)

6,375(15.9%)

10,359(1.4%)

4,645(11.6%)

Cell surface

70,126(9.4%)

3,242(8.1%)

5,138(0.7%)

2,166(5.4%)

All extracellular

264,477(35.5%)

13,389(33.4%)

22,692(3.0%)

9,583(23.9%)

Total protein

749,163(100%)

40,110(100%)

52,442(7.0%)

27,058(67.5%)


The human International Protein Index (IPI) database (version 2.28) contains a total of 40,110 protein entries. aTryptic peptides are defined as peptide sequences that end with Arg or Lys, are not followed by proline, and fall within the mass range from 500 to 5000 Da. bThe percentage represents the fraction of total tryptic peptides from the human database (749,163). cThe percentage represents the fraction of total proteins from the human database (40,110).

Zhang et al. Genome Biology 2006 7:R73   doi:10.1186/gb-2006-7-8-r73

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