PXD004573

PXD004573 is an original dataset announced via ProteomeXchange.

Title	Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: PTM-SWATH-MS Gold Standard data set
Description	The PTM-SWATH MS Gold Standard data set consists of a previously published (Soste et al., 2014, PMID:25194849) set of 579 unpurified, synthetic, heavy-isotope labeled phosphopeptides (Thermo Scientific Biopolymers). These phosphopeptides represent biologically relevant sequences from S. cerevisiae proteins, which have been found altered in their phosphorylation status under various conditions. The complete peptide set contains a mixture of singly and doubly phosphorylated sequences with in average more than 3 modifiable residues per peptide (serines, threonines or tyrosins, often in close proximity to each other). All peptides were mixed with equal volumes (concentrations are unknown due to the unpurified status of the peptides) and the resulting peptide mix was either analyzed directly in DDA mode for assay library generation or spiked into a human cell line background proteome in a 13-step dilution series and analyzed in SWATH mode for the generation of the SWATH Gold Standard data set.
HostingRepository	PRIDE
AnnounceDate	2017-06-12
AnnouncementXML	Submission_2017-06-19_08:15:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	George Rosenberger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-07-14 03:01:23	ID requested
1	2017-06-12 01:26:47	announced
⏵ 2	2017-06-19 08:15:42	announced	Updated publication reference for PubMed record(s): 28604659.

Rosenberger G, Liu Y, R, ö, st HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmstr, ö, m L, Aebersold R, Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nat Biotechnol, 35(8):781-788(2017) [pubmed]

submitter keyword: yeast, human, synthetic phosphopeptides, gold standard data set, OpenSWATH, IPF

Ruedi Aebersold
contact affiliation	ETH Zurich Prof. Dr. Ruedi Aebersold Institute of Molecular Systems Biology Head of Department of Biology HPT E 78 Auguste-Piccard-Hof 1 CH-8093 Zurich Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
George Rosenberger
contact affiliation	Institute of Molecular Systems Biology ETH Zurich
contact email	rosenberger@imsb.biol.ethz.ch
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/2017/06/PXD004573

PRIDE project URI

• PRIDE
  1. PXD004573
     1. Label: PRIDE project
     2. Name: Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: PTM-SWATH-MS Gold Standard data set