PXD002800

PXD002800 is an original dataset announced via ProteomeXchange.

Title	Improved functional annotation of posttranslationally modified proteins
Description	Identification of posttranslational modifications (PTMs) by mass spectrometry is biased towards abundant proteins, skewing our understanding of PTMs towards readily detected proteins. To uncover specifically enriched Gene Ontology (GO) terms associated with PTMs, we developed a method to account for protein abundance bias when performing GO term enrichment analyses on PTM datasets. GO term enrichment analysis is frequently used to examine “-omics” datasets for overrepresented functional terms within a subset of the dataset, such as regulated genes or modified proteins. However, the identification of PTMs is biased to abundant proteins that are more readily detected in the mass spectrometer. Therefore, GO enrichment analyses comparing posttranslationally modified proteins (referred to here as modified proteins) to unmodified proteins are likely to reveal overrepresented GO terms associated with abundant proteins, rather than modified proteins specifically. The method we developed here provides more accurate GO term enrichment analysis of PTMs and identifies terms whose enrichment results from the bias to identify PTMs on abundant proteins.
HostingRepository	PRIDE
AnnounceDate	2020-07-01
AnnouncementXML	Submission_2020-07-01_15:20:55.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brian Weinert
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	ubiquitinylated lysine; phosphorylated residue; N6-succinyl-L-lysine; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-27 01:19:01	ID requested
⏵ 1	2020-07-01 15:20:55	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Yeast, HeLa, phosphorylation, acetylation, succinylation, ubiquitylation, di-gly

Brian Tate Weinert
contact affiliation	Chuna Choudahry University of Copenhagen Center for Protein Research Blegdamsvej 3B, 6.1 DK-2200 Copenhagen N Denmark
contact email	brtw@cpr.ku.dk
lab head
Brian Weinert
contact affiliation	Proteomics
contact email	brtw@cpr.ku.dk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/07/PXD002800

PRIDE project URI

• PRIDE
  1. PXD002800
     1. Label: PRIDE project
     2. Name: Improved functional annotation of posttranslationally modified proteins