PXD015912

PXD015912 is an original dataset announced via ProteomeXchange.

Title	Strategies to enable large-scale proteomics for reproducible research.
Description	An experiment was designed to assess the reproducibility of SWATH-MS measurements collected from different mass spectrometers in a single facility over a period spanning approximately four months. Data were acquired with 90-minute gradient lengths at the Australian Cancer Research Foundation International Centre for the Proteome of Human Cancer (ProCan) on six SCIEX TripleTOF 6600 QTOF mass spectrometers. Multiple replicate aliquots were prepared for eight samples. These comprised a dilution series of ovarian cancer tissue (0%, 3.125%, 6.25%, 12.5%, 25% and 50%) offset by yeast and a fixed proportion (50%) of prostate cancer tissue (Samples 1-6), a 1:1 mix of ovarian cancer tissue and yeast cells (Sample 7), and a human cell line (HEK293T; Sample 8). On each mass spectrometer, sets of 20 replicate aliquots (three aliquots of Samples 2-5, and two aliquots of Samples 1, 6-8) were run during each of thirteen 48-hour periods. Experimental data were acquired in 48-hour time periods on each instrument continuously for eight days (with sets of 20 replicates commencing on days 1, 3, 5 and 7), once per week for the remainder of the month (commencing on days 14, 21 and 28), and then once per month for the remainder of the first three months (commencing on days 56 and 84). After each instrument underwent a major clean, the sets of 20 replicates were again run continuously for a further eight days (commencing on days 101, 103, 105 and 107). Data were therefore acquired during a total of thirteen 48-hour periods over approximately four months, during which time the mass spectrometry facility was fully operational. Mass spectrometer maintenance schedules varied according to each individual instrument's performance, and each instrument commenced data acquisition asynchronously within 28 days from the experiment start.
HostingRepository	PRIDE
AnnounceDate	2020-07-20
AnnouncementXML	Submission_2020-08-02_22:29:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rebecca Poulos
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-18 09:03:08	ID requested
1	2020-07-20 03:04:00	announced
⏵ 2	2020-08-02 22:29:15	announced	2020-08-03: Updated publication reference for PubMed record(s): 32732981.

Poulos RC, Hains PG, Shah R, Lucas N, Xavier D, Manda SS, Anees A, Koh JMS, Mahboob S, Wittman M, Williams SG, Sykes EK, Hecker M, Dausmann M, Wouters MA, Ashman K, Yang J, Wild PJ, deFazio A, Balleine RL, Tully B, Aebersold R, Speed TP, Liu Y, Reddel RR, Robinson PJ, Zhong Q, Strategies to enable large-scale proteomics for reproducible research. Nat Commun, 11(1):3793(2020) [pubmed]

submitter keyword: SWATH

DIA

Mass spectrometry

Reproducibility

ProCan

Qing Zhong
contact affiliation	Head, Cancer Data Science (ProCan) Children's Medical Research Institute University of Sydney Westmead, NSW, Australia
contact email	qzhong@cmri.org.au
lab head
Rebecca Poulos
contact affiliation	Children's Medical Research Institute, University of Sydney
contact email	rpoulos@cmri.org.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/2020/07/PXD015912

PRIDE project URI

• PRIDE
  1. PXD015912
     1. Label: PRIDE project
     2. Name: Strategies to enable large-scale proteomics for reproducible research.