PXD005912 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2019-03-12 |
AnnouncementXML | Submission_2019-03-11_20:33:26.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; deamidated residue; iodoacetamide derivatized residue; farnesylated residue; carbamoylated residue; amidated residue; L-homoarginine; morpholine-2-acetylated residue; formylated residue; monosodium salt; N6-lipoyl-L-lysine; carboxylated residue; palmitoylated residue; phosphorylated residue; geranylgeranylated residue; deaminated residue; N6-pyridoxal phosphate-L-lysine; iodoacetic acid derivatized residue; dihydroxylated residue; homoserine lactone; S-pyridylethyl-L-cysteine; S-carboxamidoethyl-L-cysteine; sulfated residue; (R)-5-oxo-1 4-tetrahydrothiazine-3-carboxylic acid; homoserine; monohydroxylated residue |
Instrument | LTQ Orbitrap |
Dataset History
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. |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Technical, Biological |
submitter keyword: TagGraph OpenSearch A375 melanoma |
Contact List
Joshua E. Elias |
contact affiliation | Department of Chemical & Systems Biology, Stanford University |
contact email | josh.elias@stanford.edu |
lab head | |
Joshua Elias |
contact affiliation | Chemical & Systems Biology |
contact email | josh.elias@stanford.edu |
dataset submitter | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD005912
- Label: PRIDE project
- Name: A375 melanoma cell line, Expanded database search comparisons