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Special datasets

Rare samples

Capture of data from rare samples.

  1. Proteomic and terminomic study of human red blood cells by Lange, Huesgen et. al is available in ProteomeXchange with ID PXD000434 and the associated manuscript can be read and downloaded at JPR.
  2. Prudova, A., Serrano, K., Eckhard, U., Fortelny, N., Devine, D. V., Overall, C. M., TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage, e-Blood, 2014, 124(26):e49-e60.
  3. Lange, P.F., Huesgen, P.F., Nguyen, K., Overall, C. M., Annotating N Termini for the Human Proteome Project: N Termini and Nα-Acetylation Status Differentiate Stable Cleaved Protein Species from Degradation Remnants in the Human Erythrocyte Proteome, Journal of Proteome Research, 2014, 13, 2028−2044.
  4. Eckhard, U., Marino, G., Abbey, S. R., Tharmarajah, G., Matthew, I., Overall, C. M., The Human Dental Pulp Proteome and N‑Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues, Journal of Proteome Research, 2015, 14, 3568−3582.
  5. Eckhard, U., Marino, G., Abbey, S. R., Matthew, I., Overall, C. M., TAILSN-terminomic and proteomic datasets of healthy human dental pulp, Data in Brief, 2015, 5, 542–548.
  6. Abbey, S. R., Eckhard, U., Solis, N., Marino, G., Matthew, I., Overall, C. M., The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes, Journal of Dental Research, 2017.

Characterization of homologous proteins

Dataset for characterization of homologous members of protein families.

  1. Deep, high quality single data set from Lloyd Smith's group published in Mollecular & Cellular Proteomics identifying novel splice-junction peptides with combination of RNA-seq and DDA shotgup proteomics analysis of Jurkat cells. The GPMDB version is available here. The raw files can be found in PeptideAtlas. Letter of Young-Ki Paik, chair of C-HPP on this issue is available here.

Datasets targeting post-translational modifications

Datasets targeting specific classe(s) of post-translational modified proteins/ppetides.

  1. Comprehensive annotation of human lysine acetylation sites is provided at the Global Proteome Machine web site.
  2. Phosphorylation (pSYT) sites of Homo sapiens proteins in GPMDB is available at ftp://ftp.proteomecentral.org/modifications/phosphoryl/.
  3. The list of "Gold" phosphoproteins according to neXtProt is available here. The listed 6831 entries have at least 1 experimental phosphosite annotated as "GOLD" in the current neXtProt version (neXtProt release 2013-07-15). This list could be used as a starting point to consider PTMs in C-HPP.
  4. Study focussing on N-termini and N-terminal acetylation of human red blood cells by Lange, Huesgen et. al is available in ProteomeXchange with ID PXD000434 and the associated manuscript can be read and downloaded at JPR.

Others

  1. Ontology Collection, HS-CHR21 is available at http://gpmdb.thegpm.org/go/HS-CHR21.html.
  2. Report of chromosome 21 is available at ftp://ftp.nextprot.org/pub/current_release/chr_reports/nextprot_chromosome_21.txt (release of February 12, 2013).
  3. List of protein level evidence from GPM is available in GPM_Protein_Level_Evidence.xlsx.
  4. The proteomics LC-MS/MS dataset used in "Variation and genetic control of protein abundance in humans" published in Nature by the group of Michael Snyder is available in GPMDB and in Peptide Atlas.
  5. Frequently updated characterization status of proteins and the availability of MS data and Ab reagents is available for each chromosomes is available at NextProt.