PXD000333 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Human Primary T-cells Phospoproteomic WorkFlow |
Description | LymPHOS workflow: a collection of open source tools for mass spectrometric data mining in phosphoproteomic studies. We present several bioinformatics applications designed as a part of a workflow for the identification and quantification of phosphoproteome components by mass spectrometry. This workflow includes a front-end graphical user interface which combines several RAW to MGF extractors (EasierMgf), two graphical user interfaces for the well-known search engines Omssa and Sequest (OmssaGui and SequestGui) and three applications, one for FASTA database management (FastaTools), other for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in the analysis of proteomic and phosphoproteomic data and integrated in the workflow for the processing and feeding of data into our LymPHOS database . Applications are designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all Open Source Software under a GNU license, and can be freely downloaded from our software repository hosted at GoogleCode. |
HostingRepository | PRIDE |
AnnounceDate | 2014-09-16 |
AnnouncementXML | Submission_2014-09-16_06:07:59.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Ãscar Gallardo Román |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; dehydrated residue; iodoacetamide derivatized residue; phosphorylated residue; TMT6plex-126 reporter+balance reagent acylated residue |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2013-07-10 07:04:16 | ID requested | |
⏵ 1 | 2014-09-16 06:08:00 | announced | |
Publication List
Gallardo Ó, Ovelleiro D, Gay M, Carrascal M, Abian J, A collection of open source applications for mass spectrometry data mining. Proteomics, 14(20):2275-9(2014) [pubmed] |
Keyword List
curator keyword: Biomedical, Technical |
submitter keyword: Human, LymPHOS, LC-MSMS, T-cells, phosphoproteomics, demo files |
Contact List
Ãscar Gallardo Román |
contact affiliation | LP-CSIC/UAB |
contact email | ogallardo@proteored.org |
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/2014/09/PXD000333 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000333
- Label: PRIDE project
- Name: Human Primary T-cells Phospoproteomic WorkFlow