PXD000991

PXD000991 is an original dataset announced via ProteomeXchange.

Title	Method to identify novel proteoform peptides from salivary supernatant.
Description	We describe the use Galaxy framework to facilitate complete proteogenomic analysis for a representative salivary dataset. We demonstrate how Galaxy’s many features make it a unique and ideal solution for proteogenomic analysis. We highlight Galaxy’s flexibility by creating a modular workflow incorporating both established and customized software and processing steps that improve depth and quality of proteogenomic results. We demonstrate Galaxy’s accessibility, via the easy sharing of complete, and even complex (approximately 140 steps), proteogenomic workflows, which can be used and customized by others via a public instance of the framework (usegalaxyp.org). Our results provide a blueprint for the establishment of the Galaxy framework as an ideal solution for the emerging field of proteogenomics.
HostingRepository	PRIDE
AnnounceDate	2015-01-05
AnnouncementXML	Submission_2015-01-05_07:28:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pratik Jagtap
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-05-20 08:14:00	ID requested
⏵ 1	2015-01-05 07:28:34	announced

Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ, Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res, 13(12):5898-908(2014) [pubmed]

curator keyword: Technical

submitter keyword: Saliva, proteoforms, proteogenomics

Timothy Griffin
contact affiliation	Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA
contact email	tgriffin@umn.edu
lab head
Pratik Jagtap
contact affiliation	Center for Mass Spectrometry and Proteomics
contact email	pjagtap@umn.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/2015/01/PXD000991

PRIDE project URI

• PRIDE
  1. PXD000991
     1. Label: PRIDE project
     2. Name: Method to identify novel proteoform peptides from salivary supernatant.