Peptides that were identified, in collaboration, by Spanish National Cancer Research Centre (CNIO) and Centro Nacional de Investigaciones Cardiovasculares (CNIC).
We interrogate peptides from eight large-scale human proteomics experiments and databases, irrespective of tissue or cell type, for the vast majority of the protein-coding genes in these experiments. The peptide has to be included in at least 2 experiments.
We collected the peptides for the analysis from eight distinct large-scale proteomics data sets: the PeptideAtlas and NIST databases and six published large-scale experiments.[3-8]. For the Wilhelm analysis, we only included the peptides from the publically available Cellzome experiments on human tissues.
The eight studies covered a huge range of tissues and cell types: the peptides from the PeptideAtlas database cover 51 different tissues, cell types, and developmental stages, whereas the Geiger study interrogated 11 different cell types. The spectra from the PeptideAtlas database were only part of the NIST database and the Ezkurdia analyses. The Kim and Wilhelm analyses peptides were generated from 30 and 35 distinct tissues types (51 tissues in total).
The following table describes the annotations of PROTEO tracks:
|Item||GVSEAAVLKPSEELPAEATSSVEPEK||string||Peptide found in 8 large-scale human proteomics experiments and databases|
|Score||2||int range [2-8]||Number experiments where the peptide were found. The peptide has to be included in at least 2 experiments|
|List of Ensembl transcript ID||ENST00000399804;ENST00000286835||string||List of variants (Ensembl transcript ID) that contains the peptide|
The data was generated by Spanish National Cancer Research Centre (CNIO), Centro Nacional de Investigaciones Cardiovasculares (CNIC) and Spanish Institute of Bioinformatics using a computational pipeline developed by Michael Tress, Iakes Ezkurdia and Jose Manuel Rodriguez.
If you have questions or comments, please write to:
All data is freely available to the public.
 Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vazquez J, Valencia A, Tress ML.
Most highly expressed protein-coding genes have a single dominant isoform.
J Proteome Res. 2015 Apr 3;14(4):1880-7. doi: 10.1021/pr501286b. Epub 2015 Mar 11. PubMed PMID: 25732134.
Note: The bold title corresponds to the main paper that provides the collected peptides.