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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%
12056157276.5%1065.2%1919.3%1879.1%
21267101079.7%846.6%1028.1%715.6%
3107385980.1%454.2%878.1%827.6%
476159478.1%344.5%749.7%597.8%
587068178.3%576.6%687.8%647.4%
6110878871.1%1039.3%11110.0%1069.6%
793569774.5%576.1%11111.9%707.5%
870153576.3%375.3%659.3%649.1%
980760174.5%425.2%8510.5%799.8%
1075258778.1%395.2%658.6%618.1%
11132389467.6%554.2%16712.6%20715.6%
12103082480.0%575.5%817.9%686.6%
1332825678.0%154.6%257.6%329.8%
1466151978.5%304.5%558.3%578.6%
1560046577.5%396.5%528.7%447.3%
1683667580.7%404.8%698.3%526.2%
17116691378.3%827.0%827.0%897.6%
1827521778.9%114.0%259.1%228.0%
19142899669.7%1278.9%19713.8%1087.6%
2054943178.5%366.6%315.6%519.3%
2125214959.1%187.1%218.3%6425.4%
2249336574.0%408.1%5511.2%336.7%
X82957669.5%748.9%10312.4%769.2%
Y48612.5%1531.2%1633.3%1122.9%
MT151173.3%16.7%00.0%320.0%
?5120.0%00.0%240.0%240.0%

PEneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
1170081517389.2%7474.4%6713.9%4172.5%
2193970.4%38820.0%84043.3%70436.3%
356371.2%5710.1%24443.3%25545.3%
47700.0%1114.3%1215.6%5470.1%
5572274.7%417.2%17330.2%33157.9%
1-4195871518777.5%12036.1%17679.0%14307.3%
Total201591521475.5%12446.2%19409.6%17618.7%

    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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