PXD023648 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: small protein, low molecular weight protein, breast cacner cell line, serum, tumour, protein precipitation |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD023648
- Label: PRIDE project
- Name: A sub-optimal protein precipitation method to improve identification of low molecular weight less abundant proteins