PXD003472

PXD003472 is an original dataset announced via ProteomeXchange.

Title	S. cerevisiae DDA orbitrap-based benchmark datasets. C4PR_LIV
Description	In this study, label free peptide intensities from a well quantitatively characterised yeast cell lysate were acquired on two orbitrap mass spectrometers (LTQ-Velos and Q Exactive HF). Additionally, samples containing Universal Proteomics Standard and the Proteomics Dynamic range Standard (http://www.sigmaaldrich.com/life-science/proteomics/mass-spectrometry/ups1-and-ups2-proteomic.html) in a yeast background were also acquired. The absolute abundances of over 340 proteins present in that yeast lysate (determined in a parallel SRM-based study) were then used in order to determine the flyability (or detectability) of thousands of peptides. The flyability scores, termed the ‘F-factors’, reflect how well a peptide ionises in a complex chromatographically separated sample. Specifically, F-factors are calculated by normalising peptide precursor ion intensity by the absolute abundance of its parent protein. Based on the analysis of the six datasets deposited here (reflecting different gradients and instrument platforms) the study found that physicochemical properties including peptide length, charge and hydrophobicity are predictors of peptide detectability. Furthermore, it was established that hydrophobicity has a non-linear relationship with detectability and that coelution with competing ions significantly affects peptide detectability. The analysis based on the data deposited here suggests that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex chromatographically-separated peptide mixtures. The concept of F-factors will also undoubtedly assist in better surrogate selection in targeted mass spectrometry studies and allow more accurate calibration of peptide ion signal in label-free workflows.
HostingRepository	PRIDE
AnnounceDate	2018-02-24
AnnouncementXML	Submission_2018-02-24_00:31:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Jarnuczak
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-01-18 01:46:32	ID requested
1	2017-01-30 04:11:10	announced
2	2017-08-10 00:30:45	announced	Updated project metadata.
⏵ 3	2018-02-24 00:31:17	announced	Updated project metadata.

Jarnuczak AF, Lee DC, Lawless C, Holman SW, Eyers CE, Hubbard SJ, Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics. J Proteome Res, 15(9):2945-59(2016) [pubmed]

ProteomeXchange project tag: Reference

curator keyword: Technical

submitter keyword: benchmark dataset, peptide ionization, peptide detectability, hydrophobicity, coelution

Professor Simon Hubbard
contact affiliation	University of Manchester, Faculty of Life Sciences,B1072 Michael Smith Building, Oxford Road, Manchester, M13 9PT
contact email	simon.hubbard@manchester.ac.uk
lab head
Andrew Jarnuczak
contact affiliation	University of Manchester
contact email	andrew.jarnuczak@manchester.ac.uk
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/PXD003472

PRIDE project URI

• PRIDE
  1. PXD003472
     1. Label: PRIDE project
     2. Name: S. cerevisiae DDA orbitrap-based benchmark datasets. C4PR_LIV