PXD010296

PXD010296 is an original dataset announced via ProteomeXchange.

Title	ASSESSING AUTOMATED SAMPLE PREPARATION TECHNOLOGIES FOR HIGH-THROUGHPUT PROTEOMICS OF FROZEN WELL CHARACTERIZED TISSUES FROM SWEDISH BIOBANKS
Description	Large cohorts of carefully collected and stored clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such heterogeneous samples is labor intensive and requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors and low reproducibility, which limits the chances of making new Biomarker discoveries. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues from our biobank were assessed. The instruments evaluated included the Bioruptor for tissue disruption and protein extraction; the Barocycler, which is able to disrupt tissues and digest the proteins; and the Bravo AssayMAP, a micro-chromatography platform for protein denaturation, digestion, peptide desalting and fractionation. A wide variety of tissue samples from 1) rat spleen, 2) human melanoma tumor, 3) human pancreatic tumor and 4) pancreatic tumor xenografts were assessed. The three instruments displayed reproducible and consistent results, as was proven by the high correlation between the measurements and by low coefficients of variation for the protein intensities for the different tissue types. Furthermore, we found that there is a good correlation between the obtained protein amount from the respective tumor tissues and the surface area of the analyzed tissue. This is of particular importance as the applicability is favored even in heterogeneous tumors originating form malignant melanoma patients. The results from this study has allowed us to integrate these technologies into an automated sample preparation workflow for large-scale proteomic studies that are currently ongoing.
HostingRepository	PRIDE
AnnounceDate	2018-11-27
AnnouncementXML	Submission_2018-11-27_08:56:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Magdalena Kuras
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-03 05:38:24	ID requested
⏵ 1	2018-11-27 08:56:39	announced

Kuras M, Betancourt LH, Rezeli M, Rodriguez J, Szasz M, Zhou Q, Miliotis T, Andersson R, Marko-Varga G, Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks. J Proteome Res, 18(1):548-556(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: clinical proteomics, tissue, Bioruptor, Barocycler, Bravo AssayMAP, mass spectrometry

Gyorgy Marko-Varga
contact affiliation	Div. Clinical Protein Science & Imaging, Dept. of Clinical Sciences (Lund) and Dept. of Biomedical Engineering, Lund University, Lund, Sweden
contact email	gyorgymarkovarga@hotmail.com
lab head
Magdalena Kuras
contact affiliation	Lund University
contact email	magdalena.kuras@med.lu.se
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/2018/11/PXD010296

PRIDE project URI

• PRIDE
  1. PXD010296
     1. Label: PRIDE project
     2. Name: ASSESSING AUTOMATED SAMPLE PREPARATION TECHNOLOGIES FOR HIGH-THROUGHPUT PROTEOMICS OF FROZEN WELL CHARACTERIZED TISSUES FROM SWEDISH BIOBANKS