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PeptideAtlas and the Chromosome-Centric Human Proteome Project


In 2010, the Chromosome-centric Human Proteome Project was launched as a component of the Human Proteome Project (HPP) with the initial goal of characterizing a single protein form for each currently identified protein-coding gene. The Human PeptideAtlas builds are an essential resource for the project, combining data from over 1000 experiments, covering a wide variety of sample types, all processed through a uniform computational pipeline to yield a final protein list with a stringent, less than 1% FDR (false discovery rate).

PeptideAtlas vs C-HPP Summary Table

PeptideAtlas Builds :
ChromosomeneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
12068174184.2%1014.9%1426.9%844.1%
21295114188.1%564.3%665.1%322.5%
3107994787.8%363.3%585.4%383.5%
476765985.9%293.8%536.9%243.1%
587777788.6%374.2%323.6%313.5%
6102985783.3%494.8%615.9%615.9%
7102678576.5%494.8%10510.2%878.5%
870258983.9%213.0%578.1%355.0%
980965380.7%455.6%637.8%485.9%
1074863985.4%324.3%445.9%334.4%
11133198974.3%574.3%19114.4%947.1%
12103690987.7%373.6%545.2%363.5%
1333328786.2%133.9%133.9%206.0%
1473559581.0%446.0%506.8%456.1%
1560650683.5%325.3%467.6%223.6%
1684273086.7%394.6%455.3%283.3%
17117099985.4%554.7%726.2%443.8%
1827523886.5%82.9%196.9%103.6%
191437123385.8%543.8%976.8%533.7%
2054947586.5%264.7%234.2%254.6%
2125416765.7%187.1%207.9%4919.3%
2250541181.4%367.1%418.1%173.4%
X84767379.5%607.1%779.1%374.4%
Y471327.7%1225.5%1123.4%1123.4%
MT151386.7%00.0%00.0%213.3%
?4250.0%00.0%250.0%00.0%

PEneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
1183541690592.1%6303.4%6153.4%2011.1%
21266564.4%24519.4%56444.5%40131.7%
315021.3%85.3%8456.0%5637.3%
4900.0%111.1%00.0%888.9%
56016010.0%6210.3%17929.8%29949.8%
1-4197791696385.8%8844.5%12636.4%6663.4%
Total203801702383.5%9464.6%14427.1%9654.7%

ChromosomePE1PE2PE3 PE4PE5PE1-4
11859139212472021
212274631181277
310055160171062
47023311021746
5835262014863
6940544130999
78621076150976
8625345038664
9704614040769
10681470119729
111069168540401291
129595220231013
13311101011322
146327512214721
15536390031575
16772440125817
1710875730231147
1825581011264
1913187980321405
20504310014535
21204272021233
22454235023482
X765500032815
Y37300740
MT15000015
?220004

    Column description:
  1. nextProt entries: Number of entries in the quoted release of neXtProt for each chromosome
  2. Canonical - Proteins seen with 2 distinct, uniquely mapping peptides
  3. Uncertain - Proteins with some evidence that is not sufficient for canonical status
  4. Redundant - Protein that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
  5. Not Observed - No detections at all in PeptideAtlas above our very stringent threshold
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