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PXD008899

PXD008899 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRe-analysis of Hela phosphoproteome (PXD000612) with TagGraph
DescriptionThousands 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.
HostingRepositoryPRIDE
AnnounceDate2019-03-12
AnnouncementXMLSubmission_2019-04-04_00:02:33.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJoshua Elias
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-02-08 03:19:48ID requested
12019-03-11 20:53:45announced
22019-04-04 00:02:34announcedUpdated publication reference for PubMed record(s): 30936560.
Publication List
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]
Keyword List
curator keyword: Biological
submitter keyword: TagGraph, Hela, PTM, Posphorylation
Contact List
Joshua E Elias
contact affiliationDept of Chemical & Systems Biology, Stanford University, Stanford CA 94305
contact emailjosh.elias@stanford.edu
lab head
Joshua Elias
contact affiliationChemical & Systems Biology
contact emailjosh.elias@stanford.edu
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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