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PXD003236

PXD003236 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlepyQms - 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)
HostingRepositoryPRIDE
AnnounceDate2017-08-15
AnnouncementXMLSubmission_2017-08-15_00:30:31.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJohannes Leufken
SpeciesList scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055;
ModificationListmonohydroxylated residue; acetylated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-11-25 04:49:32ID requested
12017-08-10 02:18:14announced
22017-08-15 00:30:32announcedUpdated project metadata.
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: LC-MS/MS, Gold standard dataset
Contact List
Dr. Christian Fufezan
contact affiliationInstitute of Plant Biology and Biotechnology, University of Muenster, Germany
contact emailchristian@fufezan.net
lab head
Johannes Leufken
contact affiliationMax Planck Institute for Molecular Biomedicine RNA biology laboratory Von-Esmarch-Straße 54 48149 Münster Germany
contact emailjohannes.leufken@uni-muenster.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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