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Pre-analytical Sample Quality Determines Performance of Plasma Proteomics Workflows for Biomarker Discovery

ABSTRACT: This dataset contains mass spectrometry-based proteomic analyses of human plasma samples processed through five distinct proteomics workflows: neat plasma, perchloric acid precipitation with neutralization (PCA-N), and three bead-based enrichment methods (SAX magnetic beads, Sera Sil 700 magnetic beads, and non-magnetic beads). The study systematically evaluates how sample quality affects proteome coverage and quantification performance across these workflows through controlled spike-in experiments. We performed spike-in series of platelets, erythrocytes, and peripheral blood mononuclear cells (PBMCs) to assess workflow-specific susceptibilities to cellular contamination. Additional experiments include yeast protein spike-ins to evaluate detection of low-abundance proteins, buffer-bead combination screening, freeze-thaw cycle effects, and centrifugation condition comparisons. The dataset provides comprehensive evidence for how pre-analytical variables impact plasma proteome characterization and establishes quantitative benchmarks for assessing plasma sample quality in biomarker discovery studies.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Mario Oroshi

LAB HEAD: Mario Oroshi

PROVIDER: PXD063572 | Pride | 2025-08-21

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20230606_Human_SwissProt_Isoforms_FASTA.fasta	Fasta
	20230628_Human_SwissProt_Isoforms_FASTA_DIANN_speclib_Ox_AcN_standart_182beta.predicted.speclib	Other
	Rescue_Neat_raw_files.zip	Other
	Rescue_Nonmagnetic_raw_files.zip	Other
	Rescue_PCAN_raw_files.zip	Other

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