PXD003236

PXD003236 is an original dataset announced via ProteomeXchange.

Title	pyQms - partial labeled proteome gold standard
Description	" The novel mass spectrometry quantitation tool pyQms can calculate isotope patterns for molecules that have any isotope enrichment or combinations of, e.g. 13C or 15N and allows partially labeled molecules to be quantified as well, as observed in pulse or pulse-chase experiments where enrichment levels change dynamically. In order to test how pyQms performs on such a task, we created a gold standard (GS) data set of partially labeled proteomes, which allows evaluation of algorithms detecting partial labeld isotopologues against the ground truth against 5 mixed samples. Cultures of Chlamydomonas reinhardtii were grown on medium containing 20, 40, 60, 80 and 100% 15N. Since partially labeled peptides will not produce interpretable fragmentation spectra, each of the partially labeled proteomes were mixed with an unlabeled (14N) or fully labeled (15N) proteome, yielding 5 mixed samples (0|100, 20|100, 40|100, 0|60 and 0|80). " (Modified from manuscript)
HostingRepository	PRIDE
AnnounceDate	2017-08-15
AnnouncementXML	Submission_2017-08-15_00:30:31.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johannes Leufken
SpeciesList	scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-11-25 04:49:32	ID requested
1	2017-08-10 02:18:14	announced
⏵ 2	2017-08-15 00:30:32	announced	Updated project metadata.

Leufken J, Niehues A, Sarin LP, Wessel F, Hippler M, Leidel SA, Fufezan C, pyQms enables universal and accurate quantification of mass spectrometry data. Mol Cell Proteomics, 16(10):1736-1745(2017) [pubmed]

curator keyword: Technical

submitter keyword: LC-MS/MS, Gold standard dataset

Dr. Christian Fufezan
contact affiliation	Institute of Plant Biology and Biotechnology, University of Muenster, Germany
contact email	christian@fufezan.net
lab head
Johannes Leufken
contact affiliation	Max Planck Institute for Molecular Biomedicine RNA biology laboratory Von-Esmarch-Straße 54 48149 Münster Germany
contact email	johannes.leufken@uni-muenster.de
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/2017/08/PXD003236

PRIDE project URI

• PRIDE
  1. PXD003236
     1. Label: PRIDE project
     2. Name: pyQms - partial labeled proteome gold standard