PXD009101

PXD009101 is an original dataset announced via ProteomeXchange.

Title	GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment
Description	This study shows the efficacy of a new tandem mass spectrometry peak finding software, GAGfinder. GAGfinder works by iterating through all potential fragments of a given precursor composition and comparing a theoretical isotopic distribution to the peak heights found in a tandem mass spectrum. We used ten synthetic heparan sulfate oligosaccharide to test the effectiveness of the method and compare GAGfinder's performance to that of an averagine-based algorithm.
HostingRepository	PRIDE
AnnounceDate	2018-04-09
AnnouncementXML	Submission_2018-04-09_01:36:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	John Hogan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	sulfated residue; acetylated residue
Instrument	solariX

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-02 06:15:33	ID requested
⏵ 1	2018-04-09 01:36:04	announced

Hogan JD, Klein JA, Wu J, Chopra P, Boons GJ, Carvalho L, Lin C, Zaia J, Software for Peak Finding and Elemental Composition Assignment for Glycosaminoglycan Tandem Mass Spectra. Mol Cell Proteomics, 17(7):1448-1456(2018) [pubmed]

curator keyword: Technical

submitter keyword: glycosaminoglycans, bioinformatics, heparan sulfate, chondroitin sulfate, keratan sulfate

Joseph Zaia
contact affiliation	Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
contact email	jzaia@bu.edu
lab head
John Hogan
contact affiliation	Boston University
contact email	jdhogan@bu.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/2018/04/PXD009101

PRIDE project URI

• PRIDE
  1. PXD009101
     1. Label: PRIDE project
     2. Name: GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment