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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%
21250100080.0%715.7%877.0%927.4%
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%
11132489467.5%675.1%16112.2%20215.3%
12103083581.1%565.4%727.0%676.5%
1332825678.0%164.9%247.3%329.8%
1464149477.1%233.6%507.8%7411.5%
1560146978.0%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%
2125315360.5%166.3%218.3%6324.9%
2247634973.3%275.7%5210.9%4810.1%
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%
1166181487489.5%6854.1%6063.6%4532.7%
2224731614.1%42418.9%80735.9%70031.2%
3573305.2%6511.3%22539.3%25344.2%
4961818.8%1111.5%1313.5%5456.2%
5574376.4%518.9%15527.0%33157.7%
1-4195341523878.0%11856.1%16518.5%14607.5%
Total201081527576.0%12366.1%18069.0%17918.9%

    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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