PXD003608

PXD003608 is an original dataset announced via ProteomeXchange.

Title	Latin Squares Spike-in Dataset for Comparisons of Statistical Methods
Description	21 proteins of three different size catgeories were purchased from a commercial supplier and used in different runs at different volumes. A yeast proteome background was present in every sample. This allows researchers to download the raw data, develop their own mathematical methods, and compare to others' methods when they upload their processed data to a Shiny application that calculates a range of performance measures. In the present study, different methods of summarising peptides to proteins and normalising between channels and between runs were compared.
HostingRepository	PRIDE
AnnounceDate	2017-06-12
AnnouncementXML	Submission_2017-06-12_04:25:01.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dario Strbenac
SpeciesList	scientific name: Bacillus licheniformis; NCBI TaxID: 1402; scientific name: Schistosoma japonicum (Blood fluke); NCBI TaxID: 6182; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iTRAQ8plex-116 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	QSTAR

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-10 02:12:30	ID requested
⏵ 1	2017-06-12 04:25:02	announced

Strbenac D, Zhong L, Raftery MJ, Wang P, Wilson SR, Armstrong NJ, Yang JYH, Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods. J Proteome Res, 16(7):2359-2369(2017) [pubmed]

curator keyword: Technical

submitter keyword: LC-MS/MS, Spike-in, iTRAQ, benchmarking, bias, variance

Professor Susan Wilson
contact affiliation	School of Mathematics and Statistics, Faculty of Science, University of New South Wales, Kensington, NSW, Australia
contact email	Sue.Wilson@unsw.edu.au
lab head
Dario Strbenac
contact affiliation	University of Sydney
contact email	dario.strbenac@sydney.edu.au
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/PXD003608

PRIDE project URI

• PRIDE
  1. PXD003608
     1. Label: PRIDE project
     2. Name: Latin Squares Spike-in Dataset for Comparisons of Statistical Methods