44,000 Protein Forms Mapped in Plasma

DIA mass spectrometry maps extensive proteoform diversity in human plasma

October 19, 2026
3 min

The Analytical Scientist

Objective:

To map the diversity of protein forms (proteoforms) in human plasma and examine how proteoform diversity relates to measurements from affinity-based proteomic platforms.

Approach:

Sample preparation: Researchers depleted 14 highly abundant plasma proteins and separated intact proteins by size and electrical charge using three methods.
Proteomic analysis: They analyzed 3,114 fractions with data-independent mass spectrometry and computationally reconstructed peptide signals across fractions.
Confidence assessment: Proteoforms detected in at least three of four replicate gel experiments were classified as high confidence.

Key Findings:

The dataset contained 179,049 potential proteoforms across 5,077 protein groups; 44,083 proteoforms from 2,089 groups met the high-confidence criterion.
The median was 11 high-confidence proteoforms per protein.
Proteoform diversity was greatest among abundant proteins and proteins involved in nutrient transport, blood clotting, and the complement system.
The most abundant form accounted for less than half of a protein’s total measured peptide signal.
Olink and SomaScan measurements generally agreed more closely for relatively abundant proteins with low or moderate proteoform diversity. Poor agreement was most often associated with low protein concentrations.

Interpretation:

The authors note that assays targeting the same protein may recognize different proteoforms, potentially affecting comparisons between technologies and interpretation of results.

Limitations:

The atlas is an initial reference, not a complete account of the plasma proteome.
Most proteoforms were separated by physical properties but not fully identified at the molecular level.
Low-abundance and disease-associated forms may be underrepresented, and some results may represent groups of related proteoforms rather than individual molecules.
Some detected proteins may have resulted from cellular contamination.

Conclusion:

The authors state that further work using top-down mass spectrometry, clinical cohorts, and samples from different populations is needed to determine which proteoforms relate to normal biology or disease.