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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%
12069166180.3%1115.4%1808.7%1175.7%
21285109385.1%685.3%826.4%423.3%
3108291084.1%434.0%797.3%504.6%
476863382.4%384.9%709.1%273.5%
587673784.1%485.5%525.9%394.5%
6111083074.8%1099.8%958.6%766.8%
798575176.2%616.2%11411.6%596.0%
870256480.3%365.1%588.3%446.3%
981063778.6%364.4%8110.0%566.9%
1075061782.3%344.5%597.9%405.3%
11133394570.9%665.0%23117.3%916.8%
12103387384.5%484.6%716.9%414.0%
1333427381.7%185.4%195.7%247.2%
1472756277.3%496.7%638.7%537.3%
1560449782.3%335.5%518.4%233.8%
1683971084.6%404.8%637.5%263.1%
17116996482.5%706.0%776.6%585.0%
1827623284.1%145.1%196.9%114.0%
191434119083.0%835.8%1067.4%553.8%
2055146083.5%305.4%305.4%315.6%
2125615660.9%2610.2%197.4%5521.5%
2249839679.5%306.0%5110.2%214.2%
X84864375.8%597.0%9811.6%485.7%
Y471021.3%1327.7%1429.8%1021.3%
MT151280.0%00.0%16.7%213.3%
?4125.0%125.0%250.0%00.0%

PEneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
1176941629392.1%6253.5%5693.2%2071.2%
2154870.5%40826.4%72546.8%40826.4%
351020.4%6913.5%28956.7%15029.4%
47111.4%79.9%1825.4%4563.4%
5576498.5%559.5%18431.9%28850.0%
1-4198231630382.2%11095.6%16018.1%8104.1%
Total203991635280.2%11645.7%17858.8%10985.4%

    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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