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Special datasets

Deeper studies

Datasets of deeper proteomics exploration studies.
  1. In-depth membrane proteomic study of breast cancer tissues acquired by Satoshi Muraoka is available in ProteomeXchange with ID PXD000066(external link) and the results associated with this dataset can be found in GPMDB(external link).
  2. Two Nature papers on the human proteome project have been published recently by Akhilesh Pandely(external link) (Chr 22 PI) and Bernhard Kuster (Munich)(external link). Letter of Young-Ki Paik, Chair fo C-HPP on this issue is available here.

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(external link) and the associated manuscript can be read and downloaded at JPR(external link).

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(external link) identifying novel splice-junction peptides with combination of RNA-seq and DDA shotgup proteomics analysis of Jurkat cells. The GPMDB version is available here(external link). The raw files can be found in PeptideAtlas(external link). 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(external link).
  2. Phosphorylation (pSYT) sites of Homo sapiens proteins in GPMDB is available at ftp://ftp.proteomecentral.org/modifications/phosphoryl/(external link).
  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(external link) and the associated manuscript can be read and downloaded at JPR(external link).

Others

  1. Ontology Collection, HS-CHR21 is available at http://gpmdb.thegpm.org/go/HS-CHR21.html(external link).
  2. Report of chromosome 21 is available at ftp://ftp.nextprot.org/pub/current_release/chr_reports/nextprot_chromosome_21.txt(external link) (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(external link) by the group of Michael Snyder is available in GPMDB(external link) and in Peptide Atlas(external link).
  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(external link).