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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%
12056157976.8%1135.5%1808.8%1848.9%
21267100078.9%715.6%876.9%1098.6%
3107386480.5%413.8%878.1%817.5%
476160179.0%334.3%699.1%587.6%
587068378.5%617.0%637.2%637.2%
6110879571.8%1109.9%988.8%1059.5%
793570475.3%646.8%9810.5%697.4%
870154177.2%355.0%608.6%659.3%
980760474.8%435.3%8210.2%789.7%
1075259579.1%374.9%597.8%618.1%
11132389467.6%675.1%16112.2%20115.2%
12103083581.1%565.4%727.0%676.5%
1332825678.0%164.9%247.3%329.8%
1466149474.7%233.5%507.6%9414.2%
1560046878.0%437.2%467.7%437.2%
1683668081.3%364.3%698.3%516.1%
17116692579.3%756.4%806.9%867.4%
1827521879.3%155.5%217.6%217.6%
191428100570.4%1359.5%18112.7%1077.5%
2054943579.2%376.7%264.7%519.3%
2125215260.3%166.3%218.3%6325.0%
2249334970.8%275.5%5210.5%6513.2%
X82958470.4%688.2%10212.3%759.0%
Y48714.6%1429.2%1633.3%1122.9%
MT151280.0%00.0%00.0%320.0%
?5120.0%00.0%240.0%240.0%

PEneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
1170081520689.4%6894.1%6183.6%4952.9%
21939271.4%42021.7%79741.1%69535.8%
356350.9%6511.5%22339.6%27048.0%
47700.0%1114.3%1316.9%5368.8%
5572356.1%518.9%15527.1%33157.9%
1-4195871523877.8%11856.0%16518.4%15137.7%
Total201591527375.8%12366.1%18069.0%18449.1%

    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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