PXD000333

PXD000333 is an original dataset announced via ProteomeXchange.

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	Óscar 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

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-10 07:04:16	ID requested
⏵ 1	2014-09-16 06:08:00	announced

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]

curator keyword: Biomedical, Technical

submitter keyword: Human, LymPHOS, LC-MSMS, T-cells, phosphoproteomics, demo files

Óscar Gallardo Román
contact affiliation	LP-CSIC/UAB
contact email	ogallardo@proteored.org
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/2014/09/PXD000333

PRIDE project URI

• PRIDE
  1. PXD000333
     1. Label: PRIDE project
     2. Name: Human Primary T-cells Phospoproteomic WorkFlow