Evaluation of Plasma Protein Enrichment Methods for Mass Spectrometry Proteomics

Proteonano enrichment confidently identified 299 proteins with concentrations below 10^6 pg/L, while immunodepletion yielded the highest coverage of 660 proteins in the moderate abundance range. This dataset compares seven depletion and enrichment technologies for platelet-free plasma proteomics, assessed using an Orbitrap Astral instrument with data-independent acquisition. The data was published by Salem Al Siblani on figshare in 2026 under a CC-BY-NC-4.0 license.

Use Cases

• Benchmarking protein enrichment methods based on the comparison of seven technologies described.
• Analyzing the trade-off between proteomic depth and repeatability based on reported median coefficient of variation values.
• Investigating the impact of sample preparation on dynamic range reduction based on the combined ProteoMiner and immunodepletion results.
• Correlating quantitative protein profiles with neat plasma based on the 93% correlation reported for ENRICHplus.

Strengths

• Directly compares seven specific sample preparation methods: perchloric acid depletion, immunodepletion, ProteoMiner, MagNet-SAX, ENRICHplus, Proteonano, and a combination.
• Reports quantitative performance metrics, including 299 low-abundance protein identifications for Proteonano and a 93% correlation for ENRICHplus.
• Includes repeatability metrics, such as a median coefficient of variation of 13% for MagNet-SAX.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset is very small at 13.4 KB, indicating limited scope.

Provenance

Source

figshare

Collection Method

Experimental evaluation using an Orbitrap Astral instrument with data-independent acquisition (DIA) on platelet-free plasma.

Time Range

Experimental date range not specified.

Freshness

Last updated 2026-03-17 14:05:26; freshness should be verified.

Geography

Geographic coverage not specified.