PXD010688-1

PXD010688 is an original dataset announced via ProteomeXchange.

Title	ABLE-SWATH
Description	Proteomic methods typically involve lengthy, multi-step sample preparation protocols (14-16 hrs), especially for the lysis and digestion of solid tissue samples or cells. We developed a streamlined proteomic sample preparation protocol termed Accelerated Barocycler Lysis and Extraction (ABLE), that substantially reduces the time and cost of tissue sample processing. ABLE is based on pressure cycling technology (PCT) for rapid tissue solubilisation and reliable, controlled proteolytic digestion. Here, the previously reported PCT protocol was optimised using 1-4 mg biopsy punches from rat kidney. The tissue denaturant urea was substituted with a combination of sodium deoxycholate (SDC) and N-propanol. ABLE produced comparable numbers of protein identifications in half the sample preparation time and with reduced cost, being ready for MS injection in 3 hrs (vs the conventional urea PCT method of 6 hrs). To validate the method, it was applied across a diverse range of rat tissues (kidney, lung, muscle, brain, testis), human HEK 293 cells and ovarian tumours by coupling PCT with SWATH-mass spectrometry (SWATH-MS). There were similar numbers of quantified proteins between ABLE-SWATH and PCT-SWATH methods, with greater than 70% overlap for all sample types, except muscle with 58% overlap. The ABLE tissue processing protocol offers a standardised, high-throughput, efficient and reproducible proteomic preparation method, accelerating sample throughput for any type of MS analysis. Coupled with SWATH-MS, ABLE has the potential to accelerate proteomics analysis towards a clinically relevant turn-around-time.
HostingRepository	PRIDE
AnnounceDate	2019-01-21
AnnouncementXML	Submission_2019-01-21_08:09:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Natasha Lucas
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-06 03:11:37	ID requested
⏵ 1	2019-01-21 08:09:49	announced

Peters S, Hains PG, Lucas N, Robinson PJ, Tully B, 810 Computational Analysis Runs. J Proteome Res, 18(3):1019-1031(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: SWATH, Sample Preparation, Barocycler, PCT, SDC, Urea, Clinical Proteomics

Phillip J Robinson
contact affiliation	Head of Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney Co-Director of ProCan - The ACRF International Centre for the Proteome of Human Cancer Co-Director of ACRF Centre for Kinomics
contact email	PRobinson@cmri.org.au
lab head
Natasha Lucas
contact affiliation	CMRI
contact email	nlucas@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/2019/01/PXD010688

PRIDE project URI

• PRIDE
  1. PXD010688
     1. Label: PRIDE project
     2. Name: ABLE-SWATH