PXD023648

PXD023648 is an original dataset announced via ProteomeXchange.

Title	A sub-optimal protein precipitation method to improve identification of low molecular weight less abundant proteins
Description	Mass spectrometry-based proteomics studies have enabled identification and quantification of thousands of proteins from biological samples. High molecular weight abundant proteins are readily sampled in global proteomics studies compared to low molecular weight less abundant proteins. Although extensive fractionation can facilitate identification of low molecular weight less abundant proteins, it requires additional infrastructure, mass spectrometry time and labour. There is a need for a simple method that can deplete high molecular weight proteins and enrich for low molecular weight proteins to improve their coverage in proteomics studies. We developed a simple method that depletes high molecular weight proteins from various biological samples including cell lines, tissues, and serum. Using this strategy, we demonstrate identification of proteins that are often underrepresented in proteomics datasets. This approach also enabled identification of low abundant serum proteins that are often not detected using immunodepletion strategy. We also identified several novel proteins encoded by annotated non-coding regions in the human genome including lncRNAs and UTRs. Our approach can complement existing proteomics workflows to increase detection and coverage of low molecular weight less abundant proteins.
HostingRepository	PRIDE
AnnounceDate	2021-08-19
AnnouncementXML	Submission_2021-08-19_21:26:18.627.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	PARTHIBAN PERIASAMY
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-18 00:08:33	ID requested
1	2021-08-19 03:12:49	announced
⏵ 2	2021-08-19 21:26:19	announced	2021-08-20: Updated publication reference for PubMed record(s): 34390184.

Periasamy P, Rajandran S, Ziegman R, Casey M, Nakamura K, Kore H, Datta K, Gowda H, A simple organic solvent precipitation method to improve detection of low molecular weight proteins. Proteomics, 21(19):e2100152(2021) [pubmed]

submitter keyword: small protein, low molecular weight protein, breast cacner cell line, serum, tumour, protein precipitation

Harsha Gowda
contact affiliation	Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
contact email	Harsha.Gowda@qimrberghofer.edu.au
lab head
PARTHIBAN PERIASAMY
contact affiliation	Faculty of Medicine, The University of Queensland, Brisbane, Australia
contact email	parthiban.periasamy@uq.net.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/2021/08/PXD023648

PRIDE project URI

• PRIDE
  1. PXD023648
     1. Label: PRIDE project
     2. Name: A sub-optimal protein precipitation method to improve identification of low molecular weight less abundant proteins