PXD062785

PXD062785 is an original dataset announced via ProteomeXchange.

Title	Impact of Sample Preparation Strategies on The Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics
Description	Serum proteomics plays a crucial role in biomarker discovery and disease research, yet the selection of an optimal sample preparation method remains challenging. Evaluating the accuracy of protein quantitation is of major importance and a vital part of a benchmarking study in proteomics, since clinical studies are based on the differential expression of certain proteins that can be used as biomarkers or be indicative for a pathological state. In this study, we performed a direct comparison of 6 widely used serum proteomic sample preparation workflows: In-gel digestion (IGD), Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), Top 14 Abundant Protein Depletion (Top 14), Isopropanol/Trichloroacetic Acid (IPA/TCA) precipitation, PreOmics ENRICH-iST (PreOmics), and Seer Proteograph XT (Seer). Seer and PreOmics demonstrated superior quantitative accuracy especially for proteins with low abundance in serum while Seer enrichment approach provided the highest number of protein identifications (> 2000) as measured by an Orbitrap Exploris 480. All methods had median CVs close to or below 20%. This comparative analysis provides a comprehensive resource for selecting the most appropriate serum sample preparation strategy based on specific experimental needs, facilitating human serum proteomic profiling for biomedical research.
HostingRepository	PRIDE
AnnounceDate	2025-09-15
AnnouncementXML	Submission_2025-09-14_21:24:05.833.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Drosos Katsavelis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-09 10:11:38	ID requested
⏵ 1	2025-09-14 21:24:06	announced

10.1021/acs.jproteome.5c00572;

Katsavelis D, van der Hart MGC, Wolters JC, Permentier HP, Horvatovich P, Cremers TIFH, Impact of Sample Preparation Strategies on the Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics. J Proteome Res, 24(9):4792-4803(2025) [pubmed]

submitter keyword: reproducibility, quantitative accuracy,serum proteomics, depth of coverage

P.L. (Peter)
contact affiliation	Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
contact email	p.l.horvatovich@rug.nl
lab head
Drosos Katsavelis
contact affiliation	MSc
contact email	d.katsavelis@rug.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062785
     1. Label: PRIDE project
     2. Name: Impact of Sample Preparation Strategies on The Quantitative Accuracy of Low-Abundance Serum Proteins in Shotgun Proteomics