PXD006625

PXD006625 is an original dataset announced via ProteomeXchange.

Title	Considerations for peptide and protein error rate control in large-scale targeted DIA analyses: plasma analysis
Description	Liquid chromatography coupled to tandem mass spectrometry has become the main method for high-throughput identification and quantification of peptides and the inferred proteins. Discovery proteomics commonly employs data-dependent acquisition in combination with spectrum-centric analysis. The accumulation of data generated from thousands of samples by this method has approached saturation coverage of different proteomes. Recently, as a result of technological advances, methods based on data acquisition strategies compatible with peptide-centric scoring have also reached similar proteome coverage in individual runs, and scalability. This is exemplified by SWATH-MS, which combines data-independent acquisition (DIA) with targeted data extraction of groups of transitions uniquely detecting a peptide. As the data matrices generated by these experiments continue to grow with respect to both the number of peptides identified per sample and the number of samples analyzed per study, challenges for error rate control have emerged. Here, we discuss the adaptation of statistical concepts developed for discovery proteomics based on spectrum-centric scoring to large-scale DIA experiments analyzed with peptide-centric scoring strategies, and provide some guidance on their application. We propose that, in order to increase the quality and reproducibility of published proteomic results, well-established confidence criteria should be reported at each level as we progress from spectral evidence to identified or detected peptides and inferred proteins. These confidence criteria should equally be applied to proteomic analyses based on spectrum- and peptide-centric scoring strategies.
HostingRepository	PRIDE
AnnounceDate	2017-08-03
AnnouncementXML	Submission_2017-08-28_02:48:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Isabell Bludau
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-30 05:30:48	ID requested
1	2017-08-03 03:00:51	announced
⏵ 2	2017-08-28 02:48:51	announced	Updated publication reference for PubMed record(s): 28825704, 25652787.

Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, R, ö, st HL, Tate S, Ting YS, Collins BC, Aebersold R, Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat Methods, 14(9):921-927(2017) [pubmed]

Liu Y, Buil A, Collins BC, Gillet LC, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R, Quantitative variability of 342 plasma proteins in a human twin population. Mol Syst Biol, 11(1):786(2015) [pubmed]

curator keyword: Technical

submitter keyword: DIA, SWATH-MS, error rate control, plasma

Ruedi Aebersold
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland. Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Isabell Bludau
contact affiliation	ETH Zurich
contact email	bludau@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/2017/08/PXD006625

PRIDE project URI

• PRIDE
  1. PXD006625
     1. Label: PRIDE project
     2. Name: Considerations for peptide and protein error rate control in large-scale targeted DIA analyses: plasma analysis