Blood Matrices and Sample Preparation Influence Blood Marker Discovery.

While plasma and serum are widely used in high-throughput proteomics, the impact of different blood matrix types remains underexplored. Routine diagnostics most commonly use serum or Li-heparin plasma, while the proteomics community primarily focuses on advancing analytical depth in EDTA plasma. Here, we systematically investigated the LC-MS/MS proteomic profiles of pooled blood samples from three healthy, voluntary probands including serum (with/without separation gel) and plasma anticoagulated with EDTA, citrate, or Li-heparin. Sample preparation was conducted with the commercially available iST and ENRICH-iST kits, strong-anion exchange (SAX) beads, the TFA-based approach SPEED, and perchloric acid (perCA) precipitation. Mass-spectrometric measurements were performed on a Q Exactive HF-X and a timsTOF HT in data-independent acquisition mode (DIA). Protein identifications varied considerably across matrix types with EDTA plasma and serum outperforming citrate plasma. Sample preparation methods with SAX beads, ENRICH-iST, and perCA yielded the highest identification numbers but also showed increased variability. Across all samples, 181 protein groups overlapped for timsTOF HT data. Subsets of protein groups were specific for the matrix and preparation. This study shows a systematic approach to determining suitable sample preparation and matrix parameters for the robust identification of individual body fluid marker proteins by mass spectrometry.