A sub-optimal protein precipitation method to improve identification of low molecular weight less abundant proteins

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture, Blood Serum

DISEASE(S): Breast Cancer

SUBMITTER: PARTHIBAN PERIASAMY  

LAB HEAD: Harsha Gowda

PROVIDER: PXD023648 | Pride | 2021-08-19

REPOSITORIES: Pride