Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies

Abstract

Plasma and serum are rich sources of information regarding an individual's health state and protein tests inform medical decision making. Despite major investments, few new biomarkers have reached the clinic. Mass spectrometry (MS)-based proteomics now allows highly specific and quantitative read-out of the plasma proteome. Here we employ Plasma Proteome Profiling to define contamination marker panels to assess plasma samples and the likelihood that suggested biomarkers are instead artifacts related to sample handling and processing. We acquire deep reference proteomes of erythrocytes, platelets, plasma and whole blood of 20 individuals (>6000 proteins), and compare serum and plasma proteomes. Based on spike-in experiments we determine contamination-associated proteins, many of which have been reported as biomarker candidates as revealed by a comprehensive literature survey. We provide sample preparation guidelines and an online resource (www.plasmaproteomeprofiling.org) to assess overall sample-related bias in clinical studies and to prevent costly miss-assignment of biomarker candidates.

Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids

“…More than half of all clinical decisions are currently based on blood biomarker analysis 31 . To extend our analysis to the plasma proteome we made use of a recently established high throughput plasma proteomics workflow [31][32][33] (Fig. 6a), and generated plasma proteomes from two independent cohorts of ILD patients (Munich, n=30 and Hannover, n=81; healthy age matched controls, n=30; see Table S10 for clinical characteristics and Table S11 for plasma protein quantifications).…”

Urinary proteome profiling for stratifying patients with familial Parkinson’s disease

“…Pre-analytical variation caused by inconsistent sample processing and contaminations during sample collection can have a strong impact on the results and may cause the reporting of incorrect biomarkers [34]. To ensure that the observed proteome changes are not caused by artifacts related to sample handling and processing, we assessed each sample for potential quality issues.…”

“…Our group has recently employed state-ofthe-art MS-based proteomics to obtain proteome profiles of the two body fluids, plasma and CSF, in multiple disease conditions [31][32][33][34][35]. Here, we extend this technology to urinary proteome profiling and provide first evidence that this approach can be used for PD biomarker discovery.…”

Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis

“…We used a Multiple Affinity Removal System (MARS) Hu-14 spin cartridge (Agilent, 5188-6560), which contains a bulk of immobilized antibodies against the 14 most abundant proteins (albumin, IgG, antitrypsin, IgA, transferrin, haptoglobin, fibrinogen, alpha-2-macroglobulin, alpha-1-acid glycoprotein, IgM, apolipoprotein A1, apolipoprotein A2, complement C3 and transthyretin), which are known to occupy about 95% of plasma proteome [20], enabling immunodepletion of such abundant proteins in SF. The 0.22 μm membrane filter (Agilent) was used to remove particulates from the fluid samples by centrifugation at 100 x g for 1.5 min.…”