PXD032908

PXD032908 is an original dataset announced via ProteomeXchange.

Title	Validating pyAscore, A Python Package for the Localization of Protein Modifications
Description	The submitted dataset contains results of validation experiments for pyAscore, an efficient and versatile implementation of the Ascore algorithm in Python for scoring the localization of user defined PTMs in data dependent mass spectrometry. In order to test the versatility of the package, three samples from three pride accessions were re-analyzed: label-free phosphoprotome samples were downloaded from PXD007740, TMT-labeled phosphoproteome samples were downloaded from PXD007145, and label free acetylome samples were downloaded from MSV000079068. We also wanted to evaluate the performance of pyAscore's PTM localizations on data where the modification site of peptides was known. Thus, we downloaded and re-analyzed synthetic phosphopeptide samples which were analyzed with 3 different fragmentation approaches: HCD and ETD synthetic phosphopeptide data were downloaded from PXD000138 and CID data were downloaded from PXD000759.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:58:51.998.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anthony Barente
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Velos; Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-02 10:59:12	ID requested
1	2022-11-01 08:28:10	announced
⏵ 2	2023-11-14 08:58:52	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Human,Synthetic,Phosphorylation,PTM,Acetylation

Judit Villén
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
contact email	jvillen@uw.edu
lab head
Anthony Barente
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
contact email	valenta4@uw.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/2022/10/PXD032908

PRIDE project URI

• PRIDE
  1. PXD032908
     1. Label: PRIDE project
     2. Name: Validating pyAscore, A Python Package for the Localization of Protein Modifications