Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic

Strategies to verify equimolar peptide release in mass spectrometry-based protein quantification exemplified for apolipoprotein(a)

OBJECTIVES

Quantitative protein mass spectrometry (MS) is ideally suited for precision diagnostics and for reference standardization of protein analytes. At the Leiden Apolipoprotein Reference Laboratory we apply MS strategies to obtain detailed insight into the protein-to-peptide conversion in order to verify that quantifier peptides are not partly concealed in miscleaved protein backbone.

METHODS

Apolipoprotein(a) (apo(a)) was digested in a non-optimal manner to enhance the number of miscleaved peptides that were identified by high resolution liquid chromatography tandem-MS measurements. The protein-to-peptide conversion was carefully mapped with specific attention for miscleaved peptides that contain an apo(a) quantifier peptide. Four different isotopologues of each apo(a)-quantifier peptide were applied to evaluate linearity of internal peptide standards during measurement of specific real-life samples.

RESULTS

Two apo(a) quantifier peptides that were concealed in two different miscleaved peptides were included into a multiple reaction monitoring list in our targeted MS-based apo(a) quantifications to alert for potential protein digestion discrepancies. The presence of miscleaved peptides could be ruled out when applying our candidate reference measurement procedure (RMP) for apo(a) quantification.

CONCLUSIONS

These data further corroborate the validity of our apo(a) candidate RMP as higher order method for certification of commercial Lp(a) tests that is endorsed by the International Federation of Clinical Chemistry and Laboratory Medicine. MS-based molecular detection and quantification of heterogeneous apo(a) proteoforms will allow manufacturers' transitioning from confounded lipoprotein(a) [Lp(a)] mass levels into accurate molar apo(a) levels.

Reproducible protein quantitation of 270 human proteins at increased depth using nanoparticle-based fractionation and multiple reaction monitoring mass spectrometry with stable isotope-labelled internal standards

Here we show that when using a mix of 274 light synthetic peptide standards (NAT) as surrogates for 270 human plasma proteins, as well as stable isotope-labelled standards (SIS) as normalizers (both from MRM Proteomics Inc.) for targeted quantitative analysis by liquid chromatography multiple reaction monitoring mass spectrometry (LC/MRM-MS), the Seer Proteograph™ platform allowed for the enrichment and absolute quantitation of up to an additional 62 targets (median) compared to two standard proteomic workflows without enrichment, representing an increase of 44%. The nanoparticle-based fractionation workflow resulted in improved reproducibility compared to a traditional proteomic workflow with no fractionation (median 8.3% vs. 13.1% CV). As expected, the protein concentrations in nanoparticle coronas were higher and had more compressed dynamic range in comparison to the concentrations determined either by a 3-hour Trypsin/LysC or overnight tryptic digestion methods. As the nanoparticle-based fractionation technology gains popularity, additional steps such as establishing technique-specific protein reference ranges across plasma samples and comparisons to well-established protein quantitation methods like enzyme-linked immunosorbent assay (ELISA) and LC/MRM-MS may be explored to enable absolute quantification of plasma proteins based on nanoparticle-based fractionation data.

Coomassie Brilliant Blue G for Smart Colorimetric Determination of the Ionic Surfactants in Triton X-100 Solutions

The conditions for the smart colorimetric determination of cetylpyridinium chloride and sodium dodecyl sulfate by reaction with Coomassie brilliant blue G (CBBG) have been proposed. The nature of the absorption and fluorescence spectra of aqueous solutions of CBBG as a function of acidity has been investigated. A variety of reagent forms and associations with ionic surfactants have been demonstrated. The composition of the associates formed in the CBBG-cationic surfactant system has been established. The increase in the analytical signal of the cationic surfactant and the stabilization of the colloid-chemical state of the system during reactions in the organized medium of the nonionic surfactant Triton X-100 has been demonstrated. These effects are realized through association in premicellar solutions and as a result of the solubilization of components in Triton X-100 micellar solutions. The addition of long-chain cationic surfactants to the reagent occurs with the replacement of the heteroatom proton. The absorption of CBBG-cationic surfactant associates solutions increases with the length of the cationic surfactant hydrocarbon chain. Ethanol additives decrease the aggregation of CBBG. The technique of cationic surfactant determination has been tested in the analysis of the pharmaceutical. The results show that the simplicity of analytical signal registration with satisfactory correctness and acceptably high sensitivity of determination is an advantage of the developed technique.

Peculiarities of Hemostasis and Proteomics in Patients With Acute Myocardial Infarction and Healthy Volunteers After SARS-CоV-2 Infection

AIM

To identify the features of plasma, platelet hemostasis, and proteomic composition of the blood plasma in patients with acute myocardial infarction (AMI) and healthy volunteers after COVID-19.

MATERIAL AND METHODS

The study included patients with AMI who have recently had COVID-19 (AMI-post-COVID, n=56) and patients with AMI who have not recently had COVID-19 (AMI-control, n=141). Healthy volunteers constituted the control groups and were also divided into control-post-COVID (n=32) and control-control (n=71) groups. Previous SARS-CoV-2 infection was determined by anti-N IgG in the blood serum, the level of which persists for 6-10 months after the disease. Hemostasis was evaluated by thromboelastometry (on whole blood), thrombodynamics (on platelet-poor plasma), fibrinolysis, impedance aggregometry, and proteomic analysis.

RESULTS

The AMI-post-COVID and AMI-control groups had higher values of thrombus growth rate, size and density based on the data of thromboelastometry and thrombodynamics, as well as increased concentrations of the complement system components, proteins regulating the state of the endothelium, and a number of acute-phase and procoagulant proteins compared to the control groups. Furthermore, in the AMI-post-COVID group, compared to the AMI-control group, the thrombus density was lower, and its lysis rates were higher when measured by the thrombodynamics method on platelet-poor plasma, while the platelet aggregation induced by ADP and thrombin was higher. Also, in the control-post-COVID group, compared to the control-control group, the thrombus formation rate was lower, whereas, in contrast, the thrombus size as measured by the thrombodynamics method and the platelet aggregation induced by arachidonic acid and thrombin were higher. In addition, in the AMI-post-COVID group, compared to the AMI-control group, the concentrations of proteins involved in inflammation and hemostasis were lower.

CONCLUSION

Patients with AMI who have recently had COVID-19 are characterized by a less pronounced activation of the immune response compared to patients with AMI who have not had COVID-19. This may be due to long-term chronic inflammation and depletion of components of the immune activation system after SARS-CoV-2 infection. Long-term activation of the hemostasis system in both patients with AMI and healthy volunteers after COVID-19 is primarily due to the platelet component of hemostasis.

Targeted proteomic approach for quantification of collagen type I and type III in formalin-fixed paraffin-embedded tissue

Collagen is the most abundant protein in mammals and a major structural component of the extracellular matrix (ECM). Changes to ECM composition occur as a result of numerous physiological and pathophysiological causes, and a common means to evaluate these changes is the collagen 3 (Col3) to collagen 1 (Col1) ratio. Current methods to measure the Col3/1 ratio suffer from a lack of specificity and often under- or over-estimate collagen composition and quantity. This manuscript presents a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) method for quantification of Col3 and Col1 in FFPE tissues. Using surrogate peptides to generate calibration curves, Col3 and Col1 are readily quantified in FFPE tissue sections with high accuracy and precision. The method is applied to several tissue types from both human and reindeer sources, demonstrating its generalizability. In addition, the targeted LC-MS/MS method permits quantitation of the hydroxyprolinated form of Col3, which has significant implications for understanding not only the quantity of Col3 in tissue, but also understanding of the pathophysiology underlying many causes of ECM changes. This manuscript presents a straightforward, accurate, precise, and generalizable method for quantifying the Col3/1 ratio in a variety of tissue types and organisms.

Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum

Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%-19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.

Targeted Blood Plasma Proteomics and Hemostasis Assessment of Post COVID-19 Patients with Acute Myocardial Infarction

The molecular mechanisms underlying cardiovascular complications after the SARS-CoV-2 infection remain unknown. The goal of our study was to analyze the features of blood coagulation, platelet aggregation, and plasma proteomics in COVID-19 convalescents with AMI. The study included 66 AMI patients and 58 healthy volunteers. The groups were divided according to the anti-N IgG levels (AMI post-COVID (n = 44), AMI control (n = 22), control post-COVID (n = 31), and control (n = 27)). All participants underwent rotational thromboelastometry, thrombodynamics, impedance aggregometry, and blood plasma proteomics analysis. Both AMI groups of patients demonstrated higher values of clot growth rates, thrombus size and density, as well as the elevated levels of components of the complement system, proteins modifying the state of endothelium, acute-phase and procoagulant proteins. In comparison with AMI control, AMI post-COVID patients demonstrated decreased levels of proteins connected to inflammation and hemostasis (lipopolysaccharide-binding protein, C4b-binding protein alpha-chain, plasma protease C1 inhibitor, fibrinogen beta-chain, vitamin K-dependent protein S), and altered correlations between inflammation and fibrinolysis. A new finding is that AMI post-COVID patients opposite the AMI control group, are characterized by a less noticeable growth of acute-phase proteins and hemostatic markers that could be explained by prolonged immune system alteration after COVID-19.

Intra-Individual Variation in Disease-Specific IgG Fc Glycoform Ratios to Monitor the Disease Progression of Lung Cancer

Aberrant protein glycosylation is an active pathological alteration related to the progression of cancers. The speed of progression varies among individuals, increasing the difficulties of prognosis assessment. Hence, evaluating variation in glycosylation using patients themselves as their own controls is a potential way to reduce the impact of individual differences on progression monitoring. Here, following a longitudinal follow-up study involving 125 lung cancer (LC) patients with progressive disease, we isolated disease-specific IgG from serum using polyacrylamide gel electrophoresis, obtained IgG glycoform ratios using mass spectrometry, and then set a fold-change cutoff of 1.5 to utilize the intra-individual variation in IgG glycosylation to monitor PD. We found that the serial monitoring of 15 types of glycoform ratios provided an effective way for monitoring LC progression. Over 1.5-fold changes in glycoform ratios relative to the first observed value were detected in 117 of 125 LC patients (93.6%). Our established method predicted LC progression 55.8 (IQR 31.1-90.1) weeks earlier than imaging examination did. In summary, intra-individual variation in IgG glycoform ratios is useful to monitor LC progression, expanding our knowledge about the relationship between IgG glycosylation and cancer prognosis. The raw data files are available via the ProteomeXchange Consortium with the identifier PXD037541.

Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning

The recent surge of coronavirus disease 2019 (COVID-19) hospitalizations severely challenges healthcare systems around the globe and has increased the demand for reliable tests predictive of disease severity and mortality. Using multiplexed targeted mass spectrometry assays on a robust triple quadrupole MS setup which is available in many clinical laboratories, we determined the precise concentrations of hundreds of proteins and metabolites in plasma from hospitalized COVID-19 patients. We observed a clear distinction between COVID-19 patients and controls and, strikingly, a significant difference between survivors and nonsurvivors. With increasing length of hospitalization, the survivors' samples showed a trend toward normal concentrations, indicating a potential sensitive readout of treatment success. Building a machine learning multi-omic model that considers the concentrations of 10 proteins and five metabolites, we could predict patient survival with 92% accuracy (area under the receiver operating characteristic curve: 0.97) on the day of hospitalization. Hence, our standardized assays represent a unique opportunity for the early stratification of hospitalized COVID-19 patients.