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SOPs

SOPS for missing proteins

SOPs describing process for discovery of missing proteins and poorly identified protein.

  • Human Proteome Project Data Interpretation Guidelines (Version 2.1.0 - July 28, 2016) is available in docx word format here in pdf format here. Paper published in Journal of Proteome Research related to the guideline is available here.
  • Human Proteome Project Data Interpretation Guidelines (Version 2.0.1 - December 7, 2015) is available here. This guidleine provide check list for LC-MS/MS (DDA, SRM, DIA) data interpretation, management and guidelines for extraordinary detection claims (e.g., missing proteins, novel coding elements). The statement for establishing new HPP guidelines (Dec 7, 2015) is available here.

Targeted and shotgun proteomics

Standards for Targeted and shotgun proteomics.

Data sharing

ProteomeXchange

SOPs to describe process for data deposition in ProteomeXchange.
  1. Get informed on new datasets available at ProteomeXchange (Juan Antonio Vizcaíno on February 11, 2013).
  2. Document describing data submission procedure to ProteomeXchange (Juan Antonio Vizcaíno on March 15, 2013).
  3. Tutorial on submission of MS/MS datasets to ProteomeXchange via PRIDE is acceible in the document px_submission_tutorial2.pdf or can be accessible at ProteomeXchange site under the following link(external link) (version December 13, 2013). This document is an advanced tutorial, and contains the summary of steps that the Spanish C-HPP team has established to perform ProteomeXChange submissions. Some of the tools described in this tutorial are part of the Spanish C-HPP workflow, but the PRIDE team is not responsible for maintaining them. For contact on more information please email to Juan Antonio Vizcaíno. Added on Spetember 8, 2013 and modified on February 4, 2014.

Data integration

SOPs for integration multiple omics data.

Protein ID convertion to gene ID using Gene a la Cart(external link)

Power point slides showing protocol on how to convert list of Uniprot protein ID to gene ID.

Data browsers

Informatics resources to mine proteomics data grouped to chromosomes.

HPP Chromosome Browsers

  1. The Proteome Browser(external link) at Monash University. The Proteome Browser
  2. Chromosome-Assembled human Proteome browsER(external link) at BPRC(Beijing). CAPER
  3. GenomewidePDB(external link) at Yonsei University. GenomewidePDB
  4. H-InvDB(external link) at Biomedicinal Information Research Center (Japan). H-InvDB

Chromosome-specific knowledgebases

  1. Chromosome 18 Knowledgebase(external link) at Institute of Biomedical Chemistry (Andrey Lisitsa, Russia). Chromosome 18 Knowledgebase
  2. All of the phosphorylation site information in GPMDB for human proteins, annotating ENSEMBL v. 70 protein sequences is available at ftp://ftp.proteomecentral.org/modifications/phosphoryl/(external link). The README.txt explains the used file formats. Fairly strict set of conditions were used to make the list, therefore the list should be considered to be a "minimum" set of well-founded site assignments, rather than an attempt to find as many sites as possible. Any comments on this resource sould be addressed to Ron Beavis (University of British Columbia, Canada).

RNASeq integration

SOPs for integration of RNASeq with proteomic data.

RNASeq deposition

SOPS for RNASeq data set deposition.

Top down integration

SOPs for integration of top down with bottom up data sets.

Improved protocols

SOPs for improved proteomic experimental protocols.

Nomenclature of biological objects

Nomenclature of human biological "objects" is availabel in Nomenclature_issues_HPP.docx.