PXD008902

PXD008902 is an original dataset announced via ProteomeXchange.

Title	TagGraph re-analysis of a lung proteome (Peptide Atlas PAe001771), which was a component of the Wilhelm et al human proteome map
Description	Thousands of protein post-translational modifications (PTMs) dynamically impact nearly all cellular functions. Although mass spectrometry is suited to PTM identification, it has historically been biased towards a few with established enrichment procedures. To measure all possible PTMs across diverse proteomes, software must overcome two fundamental challenges: intractably large search spaces and difficulty distinguishing correct from incorrect identifications. Here, we describe TagGraph, software that overcomes both challenges with a string-based search method that is orders of magnitude faster than current approaches, and a probabilistic validation model optimized for PTM assignments. When applied to a human proteome map, TagGraph triples confident identifications while revealing thousands of modification types spanning nearly one million sites across the proteome. We show new contexts for highly abundant yet understudied PTMs such as proline hydroxylation. TagGraph expands our ability to survey the full proteomic landscape of PTMs, shedding new light on their tissue-specific functions.
HostingRepository	PRIDE
AnnounceDate	2019-03-12
AnnouncementXML	Submission_2019-04-04_00:02:57.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joshua Elias
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; carboxylated residue; dehydrated residue; biotinylated residue; phosphorylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue; dihydroxylated residue; carbamoylated residue; amidated residue; formylated residue; monohydroxylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-08 03:48:17	ID requested
1	2019-03-11 22:07:40	announced
⏵ 2	2019-04-04 00:02:58	announced	Updated publication reference for PubMed record(s): 30936560.

Devabhaktuni A, Lin S, Zhang L, Swaminathan K, Gonzalez CG, Olsson N, Pearlman SM, Rawson K, Elias JE, TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nat Biotechnol, 37(4):469-479(2019) [pubmed]

curator keyword: Biological

submitter keyword: TagGraph, Lung, PTM

Joshua E Elias
contact affiliation	Dept of Chemcial & Systems Biology, Stanford University, Stanford CA 94305
contact email	josh.elias@stanford.edu
lab head
Joshua Elias
contact affiliation	Chemical & Systems Biology
contact email	josh.elias@stanford.edu
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/2019/03/PXD008902

PRIDE project URI

• PRIDE
  1. PXD008902
     1. Label: PRIDE project
     2. Name: TagGraph re-analysis of a lung proteome (Peptide Atlas PAe001771), which was a component of the Wilhelm et al human proteome map