PXD005912

PXD005912 is an original dataset announced via ProteomeXchange.

Title	A375 melanoma cell line, Expanded database search comparisons
Description	Thousands of protein post-translational modifications (PTMs) dynamically impact nearly all cellular functions. Mass spectrometry is well suited to PTM identification, but proteome-scale analyses are biased towards PTMs with existing enrichment methods. To measure the full landscape of PTM regulation, 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 orders of magnitude faster than current approaches, and probabilistic validation model optimized for PTM assignments. When applied to a human proteome map, TagGraph tripled confident identifications while revealing thousands of modification types on nearly one million sites spanning the proteome. We expand known sites by orders of magnitude for highly abundant yet understudied PTMs such as proline hydroxylation, and derive tissue-specific insight into these PTMs’ roles. TagGraph expands our ability to survey the full landscape of PTM function and regulation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:35:40.002.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; flavin modified residue; dehydrated residue; biotinylated residue; S-(N-isopropylcarboxamidomethyl)-L-cysteine; O-phosphopantetheine-L-serine; myristoylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue; farnesylated residue; carbamoylated residue; L-homoarginine; amidated residue; morpholine-2-acetylated residue; N6-lipoyl-L-lysine; monosodium salt; formylated residue; (R)-5-oxo-1; carboxylated residue; palmitoylated residue; phosphorylated residue; geranylgeranylated residue; deaminated residue; N6-pyridoxal phosphate-L-lysine; iodoacetic acid derivatized residue; dihydroxylated residue; S-pyridylethyl-L-cysteine; homoserine lactone; S-carboxamidoethyl-L-cysteine; sulfated residue; homoserine; monohydroxylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-13 01:13:10	ID requested
1	2019-03-11 20:33:26	announced
2	2019-04-04 00:02:08	announced	Updated publication reference for PubMed record(s): 30936560.
⏵ 3	2024-10-22 04:35:40	announced	2024-10-22: Updated project metadata.

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]

10.1038/s41587-019-0067-5;

curator keyword: Technical, Biological

submitter keyword: TagGraph OpenSearch A375 melanoma

Joshua E. Elias
contact affiliation	Department of Chemical & Systems Biology, Stanford University
contact email	josh.elias@stanford.edu
lab head
Joshua Elias
contact affiliation	Chan Zuckerberg Biohub
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/PXD005912

PRIDE project URI

• PRIDE
  1. PXD005912
     1. Label: PRIDE project
     2. Name: A375 melanoma cell line, Expanded database search comparisons