PXD020801

PXD020801 is an original dataset announced via ProteomeXchange.

Title	HUPO HPP Phosphopeptide Challenge
Description	The Phosphopeptide Challenge of the MS Resource Pillar of the Human Proteome Project (HPP) provides a unique opportunity for the HUPO membership to evaluate and compare methods for peptide sequence analysis by mass spectrometry, phosphosite localization, phosphopeptide enrichment, and data processing. Each participant is to apply their own methods and chosen bioinformatic pipeline to fully characterize the provided Phosphopeptide Challenge samples. As a result of this collaborative endeavor, multiple purification schemes, analytical protocols and data processing strategies will be evaluated, making it possible to determine the approach(es) that provide the highest coverage of the phosphopeptides in the mixture. Each participating laboratory will receive two sample vials. The vial labeled 'Phosphopeptide' contains a set of synthesized phosphorylated (Ser, Thr, or Tyr) peptides of human sequence origin at various concentrations, mixed with their non-phosphorylated counterparts. For some peptides, there is more than one phosphorylated form. The peptide sequences are included in the attached Excel file. The second vial labeled 'Phosphopeptide-Yeast' contains the same peptides in a background matrix consisting of 6 ug of trypsin-digested yeast lysate. Each vial is provided dry. Resuspension in 100 uL will result in synthetic peptide concentrations of 3 fmol/uL to 30 fmol/uL. The goal for the study is for you to provide your best method(s) to: 1. Identify the peptide sequences in the vial and determine the number and location of phosphorylation sites on each peptide (Phosphopeptide). 2. Determine the relative abundance of phosphorylation at each modified site by comparison with its non-phosphorylated counterpart (Phosphopeptide). 3. Enrich for phosphorylated peptides from the sample containing the yeast background matrix and re-analyze by MS (Phosphopeptide-Yeast).
HostingRepository	MassIVE
AnnounceDate	2020-08-11
AnnouncementXML	Submission_2020-08-11_17:23:54.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	HPP MS Resouce Pillar Phosphopeptide Challenge 2018
SpeciesList	scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl; Phospho
Instrument	Orbitrap Fusion; Q Exactive HF; instrument model; amaZon ETD; impact; maXis; TripleTOF 5600; LTQ Orbitrap XL; Orbitrap Fusion Lumos; Q Exactive; Q Exactive Plus; instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-08 15:08:34	ID requested
⏵ 1	2020-08-11 17:23:54	announced

no publication

submitter keyword: HUPO, HPP, Phosphopeptide, Challenge, Phosphorylated peptides, phospho site localization, phosphopeptide enrichment, false identification rate, Human Proteome Project, mass spectrometry

Michael Hoopmann
contact affiliation	Institute for Systems Biology
contact email	michael.hoopmann@isbscience.org
lab head
Susan Weintraub
contact affiliation	UT Health San Antonio
contact email	Weintraub@uthscsa.edu
lab head
HPP MS Resouce Pillar Phosphopeptide Challenge 2018
contact affiliation	HUPO HPP
contact email	weintraub@uthscsa.edu
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000085932/