PXD016957

PXD016957 is an original dataset announced via ProteomeXchange.

Title	Optimized MeOH/MTBE-based Protein Precipitation and Lipid Removal Enables High Enrichment of Low Molecular Weight Peptides and Proteins from Human Plasma
Description	Low molecular weight (LMW) peptides and proteins (LMWPs, < 30 kDa) in human plasma, serving as potential biomarkers or drug targets, are endowed with a wealth of biological and clinical research values. However, the extraction of LMW species is retarded by high-abundance proteins (HAPs) and therein large dynamic concentration ranges of proteins in plasma. Here we present an optimized MeOH/MTBE-based organic solvent precipitation approach that combining the efficient protein precipitation and effective delipidation (referred here as MeOH/MTBE) to enrich LMWPs from human plasma. The Tricine-SDS-PAGE analysis showed that MeOH/MTBE can not only maximally deplete HAPs but also effectively extract LMWPs from human plasma. By coupling with Top-Down Proteomics (TDP) strategy, MeOH/MTBE enabled the identification of 725 peptides derived from 158 proteins on average from human plasma, which should represent the largest number to our best knowledge with regard to TDP-based single LC-MS/MS acquisition. When combined with Bottom-Up Proteomics (BUP) strategy, MeOH/MTBE allowed for the identification of 376 proteins from human plasma. Notably, 155 out of 376 identified proteins (41.2%) were found to be with a molecular weight under 30 kDa, which further proved the efficient enrichment of LMWPs from human plasma by MeOH/MTBE approach. Moreover, concentrations of the identified proteins were found to span 5-6 orders of magnitude according to the PaxDb dataset. Additionally, many low abundant peptides including 25 neuropeptides and 19 smORF-encoded polypeptides (SEPs) derived from long noncoding RNAs (lncRNAs) were detected. Taken together, the MeOH/MTBE approach described here represents a simple, rapid and reproducible methodology for efficient and sensitive analysis of LMWPs and low abundant proteins from human plasma, which will greatly facilitate the selective identification and quantification of LMWPs from human plasma and accelerate the discovery rate of potential biomarkers and drug targets.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:08:39.656.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Na Li
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-06 05:12:13	ID requested
1	2020-07-07 06:39:03	announced
⏵ 2	2024-10-22 05:08:40	announced	2024-10-22: Updated project metadata.

Li N, Zhou Y, Wang J, Niu L, Zhang Q, Sun L, Ding X, Guo X, Xie Z, Zhu N, Zhang M, Chen X, Cai T, Yang F, Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma. J Proteome Res, 19(8):3340-3351(2020) [pubmed]

10.1021/acs.jproteome.0c00232;

curator keyword: Technical

submitter keyword: Human, plasma, LC-MS/MS

Fuquan Yang
contact affiliation	Institute of Biophysics, Chinese Academy of Sciences
contact email	fqyang@sun5.ibp.ac.cn
lab head
Na Li
contact affiliation	Institute of Biophysics， Chinese Academy of Sciences
contact email	mjades@ibp.ac.cn
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/2020/07/PXD016957

PRIDE project URI

• PRIDE
  1. PXD016957
     1. Label: PRIDE project
     2. Name: Optimized MeOH/MTBE-based Protein Precipitation and Lipid Removal Enables High Enrichment of Low Molecular Weight Peptides and Proteins from Human Plasma