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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%
12063161778.4%1095.3%1627.9%1758.5%
21273105182.6%846.6%856.7%534.2%
3107788982.5%474.4%686.3%736.8%
476261680.8%344.5%658.5%476.2%
587270580.8%546.2%576.5%566.4%
6111180872.7%1099.8%1009.0%948.5%
793972677.3%515.4%9910.5%636.7%
870355478.8%344.8%588.3%578.1%
980961876.4%404.9%779.5%749.1%
1075059879.7%415.5%516.8%608.0%
11132591368.9%574.3%17012.8%18514.0%
12103185082.4%525.0%656.3%646.2%
1332926279.6%154.6%216.4%319.4%
1467753779.3%456.6%497.2%466.8%
1560047679.3%355.8%508.3%396.5%
1683769583.0%425.0%546.5%465.5%
17116693580.2%786.7%766.5%776.6%
1827622481.2%176.2%196.9%165.8%
191433116281.1%755.2%1007.0%966.7%
2055044681.1%397.1%213.8%448.0%
2125215862.7%145.6%197.5%6124.2%
2249738577.5%295.8%5611.3%275.4%
X83860071.6%708.4%9110.9%779.2%
Y47817.0%1429.8%1429.8%1123.4%
MT151280.0%16.7%00.0%213.3%
?5120.0%240.0%00.0%240.0%

PEneXtProt entriesCanonical%Uncertain %Redundant%Not Observed%
1174701579890.4%7034.0%5863.4%3832.2%
2166070.4%38923.4%65639.5%60836.6%
345220.4%337.3%20645.6%21146.7%
47400.0%810.8%1418.9%5270.3%
5574345.9%549.4%16528.7%32155.9%
1-4196561580780.4%11335.8%14627.4%12546.4%
Total202301584178.3%11875.9%16278.0%15757.8%

    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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