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Related:
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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%
12070161778.1%1105.3%1738.4%1708.2%
21276104982.2%866.7%876.8%544.2%
3108188982.2%474.3%726.7%736.8%
476861780.3%344.4%678.7%506.5%
587770580.4%546.2%586.6%606.8%
6111180872.7%1109.9%1019.1%928.3%
798373074.3%596.0%10510.7%899.1%
870255478.9%344.8%588.3%568.0%
981161876.2%425.2%789.6%739.0%
1075059879.7%415.5%516.8%608.0%
11133091368.6%614.6%18213.7%17413.1%
12103285082.4%525.0%676.5%636.1%
1333426378.7%154.5%226.6%3410.2%
1472054075.0%588.1%567.8%669.2%
1560447779.0%345.6%548.9%396.5%
1683969683.0%425.0%556.6%465.5%
17116993680.1%796.8%776.6%776.6%
1827622481.2%176.2%196.9%165.8%
191435116281.0%755.2%1027.1%966.7%
2055044781.3%397.1%213.8%437.8%
2125515661.2%155.9%228.6%6224.3%
2249838577.3%295.8%5611.2%285.6%
X84660371.3%718.4%9511.2%779.1%
Y47817.0%1429.8%1429.8%1123.4%
MT151280.0%16.7%00.0%213.3%
?4125.0%250.0%00.0%125.0%

PEneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
1174871581290.4%7034.0%6063.5%3662.1%
2172870.4%40123.2%69340.1%62736.3%
351520.4%5510.7%21541.7%24347.2%
47600.0%810.5%1519.7%5369.7%
5571335.8%539.3%16328.5%32256.4%
1-4198061582179.9%11675.9%15297.7%12896.5%
Total203771585477.8%12206.0%16928.3%16117.9%

    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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