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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%
12067170782.6%1065.1%1668.0%884.3%
21295112086.5%695.3%675.2%393.0%
3107993786.8%312.9%726.7%393.6%
476965685.3%303.9%658.5%182.3%
587777388.1%394.4%364.1%293.3%
6102984582.1%555.3%676.5%626.0%
7102576874.9%515.0%11411.1%929.0%
870258182.8%253.6%598.4%375.3%
980964479.6%556.8%627.7%485.9%
1074862884.0%314.1%557.4%344.5%
11133197072.9%564.2%21716.3%886.6%
12103689386.2%444.2%595.7%403.9%
1333328385.0%144.2%154.5%216.3%
1473557978.8%557.5%516.9%506.8%
1560650082.5%345.6%498.1%233.8%
1684371885.2%475.6%495.8%293.4%
17116997983.7%706.0%746.3%463.9%
1827523685.8%93.3%196.9%114.0%
191436121984.9%664.6%1057.3%463.2%
2054946985.4%254.6%295.3%264.7%
2125416163.4%197.5%249.4%5019.7%
2250540680.4%285.5%5310.5%183.6%
X84766378.3%617.2%829.7%414.8%
Y471225.5%1327.7%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%
1183571669991.0%7253.9%6953.8%2381.3%
2126530.2%24219.1%62349.2%39731.4%
314700.0%96.1%9463.9%4429.9%
4900.0%111.1%00.0%888.9%
5601559.2%569.3%19031.6%30049.9%
1-4197781670284.4%9774.9%14127.1%6873.5%
Total203791675782.2%10335.1%16027.9%9874.8%

ChromosomePE1PE2PE3 PE4PE5PE1-4
11859139212462021
212284531181277
310055250171062
47013511022747
5835262014863
6940544130999
78631056150975
8625345038664
9706584041768
10681470119729
111069169530401291
129595220231013
13311101011322
146327512214721
15535400031575
16773440125818
1710875530241145
1825590011264
1913187980311405
20504310014535
21204272021233
22455235022483
X764510032815
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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