PXD020727-1

PXD020727 is an original dataset announced via ProteomeXchange.

Title	Affinity capture enrichment versus Affinity depletion: A comparison of strategies for increasing coverage of low abundant human plasma proteins
Description	present study, we evaluated four small molecule affinity-based probes based on agarose-immobilized benzamidine (ABA), O-Phospho-L-Tyrosine (pTYR), 8-Amino-hexyl-cAMP (cAMP), or 8-Amino-hexyl-ATP (ATP) for their ability to remove high-abundant proteins such as serum albumin from plasma samples thereby enabling the detection of medium-to-low abundant proteins in plasma samples by mass spectrometry-based proteomics. We compared their performance with the commonly used immunodepletion method, the Multi Affinity Removal System Human 14 (MARS14) targeting the top 14 most abundant plasma proteins and also the ProteoMiner protein equalization method by label-free quantitative LC-MSMS analysis. The affinity-based probes demonstrated high reproducibility for low abundant plasma proteins, down to picomol per ml levels, compared to the MARS14 and the Proteominer methods, and also demonstrated a superior removal of the majority of the high abundant plasma proteins. The ABA-based affinity probe and the Proteominer protein equalization method performed superior compared to all other methods in terms of the number of analyzed proteins. All the tested methods were highly reproducible for both high-abundant plasma proteins and low abundant proteins as measured by correlation analysis of six replicate experiments. In conclusion, our results demonstrated that small-molecule based affinity-based probes are excellent alternatives to the commonly used immune-depletion methods for proteomic biomarker discovery studies in plasma.
HostingRepository	PRIDE
AnnounceDate	2020-08-27
AnnouncementXML	Submission_2020-08-27_00:48:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hans Christian Beck
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-05 01:19:35	ID requested
⏵ 1	2020-08-27 00:48:03	announced

Palstr, ø, m NB, Rasmussen LM, Beck HC, Affinity Capture Enrichment versus Affinity Depletion: A Comparison of Strategies for Increasing Coverage of Low-Abundant Human Plasma Proteins. Int J Mol Sci, 21(16):(2020) [pubmed]

submitter keyword: human plasma, depletion, affinity enrichment

Hans Christian Beck
contact affiliation	Centre for Clinical Proteomics, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Denmark
contact email	hans.christian.beck@rsyd.dk
lab head
Hans Christian Beck
contact affiliation	Odense University Hospital, Odense, Denmark
contact email	hans.christian.beck@rsyd.dk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020727
     1. Label: PRIDE project
     2. Name: Affinity capture enrichment versus Affinity depletion: A comparison of strategies for increasing coverage of low abundant human plasma proteins