PXD000991 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-05-20 08:14:00 | ID requested | |
⏵ 1 | 2015-01-05 07:28:34 | announced | |
Publication List
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] |
Keyword List
curator keyword: Technical |
submitter keyword: Saliva, proteoforms, proteogenomics |
Contact List
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 | |
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/2015/01/PXD000991 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000991
- Label: PRIDE project
- Name: Method to identify novel proteoform peptides from salivary supernatant.