Antibody based affinity capture LC-MS/MS in quantitative determination of proteins in biological matrices

Fiber-optic immunosensor based on a Fabry-Perot interferometer for single-molecule detection of biomarkers

Immunosensors capable of ultralow-concentration and single-molecule detection of biomarkers are garnering attention for the early diagnosis of cancer. Herein, a fiber-optic Fabry-Perot interferometer (FPI)-based immunosensor was used for the first time for single-molecule detection of progastrin-releasing peptide (ProGRP). The cascaded FPI structure of the immunosensor introduces a high-order harmonic Vernier effect (HVE). A piece of a side-polished D-shaped hollow-core photonic crystal fiber (HCPCF) was used as a sensing FPI, on which the biomarker was deposited to detect ProGRP. Compared with traditional FPIs with open-cavity structures, this structure provided a larger contact area and improved the sensitivity of the immunosensor. The polished side surface of the D-shaped HCPCF was modified using a gold nanoparticle-graphene oxide (AuNP@GO) nanointerface to enhance refractive index (RI) modulation via antigen-antibody binding and achieve selective energy enhancement of the binding site. The antigen binding changes the RI of the D-shaped HCPCF and the effective RI of the transmitted light in the sensing FPI, thereby changing the spectrum of the immunosensor. Experimental results showed that the high-order HVE and AuNP@GO nanointerface considerably improved the immunosensor sensitivity, exhibiting a liquid RI sensitivity of 583,000 nm/RIU. After functionalization with an anti-ProGRP antibody, the limit of detection of the immunosensor for ProGRP reached 17.1 ag/mL; moreover, the immunosensor could perform detection at the single-molecule level. The proposed novel immunosensor overcomes the sensitivity limitations of optical devices and achieves single-molecule detection of a protein.

Absolute protein quantification based on calibrated particle counting using electrospray-differential mobility analysis

The traceability of in vitro diagnostics or drug products is based on the accurate quantification of proteins. In this study, we developed an absolute quantification approach for proteins. This method is based on calibrated particle counting using electrospray-differential mobility analysis (ES-DMA) coupled with a condensation particle counter (CPC). The absolute concentration of proteins was quantified with the observed protein particle number measured with ES-DMA-CPC, and the detection efficiency was determined by calibrators. The measurement performance and quantitative level were verified using two certificated reference materials, BSA and NIMCmAb. The linear regression fit for the detection efficiency values of three reference materials and one highly purified protein (myoglobin, BSA, NIMCmAb and fibrinogen) indicated that the detection efficiency and the particle size distribution of these proteins exhibited a linear relationship. Moreover, to explore the suitability of the detection efficiency-particle size curve for protein quantification, the concentrations of three typical proteinaceous particles, including two high molecular weight proteins (NIST reference material 8671 and D-dimer) and one protein complex (glutathione S-transferase dimer), were determined. This work suggests that this calibrated particle counting method is an efficient approach for nondestructive, rapid and accurate quantification of proteins, especially for measuring proteinaceous particles with tremendous size and without reference standards.

Concise review on the combined use of immunocapture, mass spectrometry and liquid chromatography for clinical applications

Immunocapture is now a well-established method for sample preparation prior to quantitation of peptides and proteins in complex matrices. This short review will give an overview of some clinical applications of immunocapture methods, as well as protocols with and without enzymatic digestion in a clinical context. The advantages and limitations of both approaches are discussed in detail. Challenges related to the choice of mass spectrometer are also discussed. Top-down, middle-down, and bottom-up approaches are discussed. Even though immunocapture has its limitations, its main advantage is that it provides an additional dimension of separation and/or isolation when working with peptides and proteins. Overall, this short review demonstrates the potential of such techniques in the field of proteomics-based clinical medicine and paves the way for better personalized medicine.

The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis

Selective and efficient sample clean-up is important in mass spectrometric protein- and proteomics analyses from biological matrices. Molecularly imprinted polymers (MIPs), polymers prepared to have tailor-made cavities for capture of target analytes may by such represent an interesting alternative for selective clean-up. The present review aims to give an overview of the utility of MIPs for protein capture from biological matrices prior to mass spectrometry (MS) analysis. The application of MIPs in depletion of abundant proteins, in protein and proteotypic peptide capture as well as in capture of post-translational modifications (PTMs) is described and discussed. In addition, an overview of available MIP formats and their advantages and challenges is given, together with an overview of the mass spectrometric techniques used in protein analysis after MIP capture. Overall, the present literature demonstrates that for many applications MIPs for sample clean-up in mass spectrometric protein and proteomics analysis from biological matrices is still not fully matured. MIPs for proteotypic peptide capture is the most mature approach and a method for routine use may be available within the next few years.

Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS

The COVID-19 pandemic has necessitated exploration of alternative testing methods for detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) to ensure clinical laboratories can continue to provide critical testing results. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is established in many clinical laboratories due its high specificity and sensitivity, making it a logical alternative methodology. However, matching the sensitivity of quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains challenging, which forced utilization of antibody-based enrichment prior to targeted LC-MS/MS analysis. When utilizing antibody purification techniques, investigators must decide whether to enrich the target protein or peptides, but there are few studies comparing the two approaches to assist in this decision-making process. In this work, we present a comparison of intact protein and peptide antibody-based purification for LC-MS/MS based detection of SARS-CoV-2. We have found that protein purification yields more intense LC-MS/MS signals, but is also less specific, yielding higher noise and more background when compared to peptide purification techniques. Therefore, when using traditional data analysis techniques, the enrichment technique that provides superior sensitivity varies for individual peptides and no definitive overall conclusion can be made. These observations are corroborated when using a novel machine learning approach to determine positive/negative test results, which yielded superior sensitivity when using protein purification, but better specificity and area under the ROC curve when performing peptide purification.

Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part I-Development

The process of method development for a diagnostic assay based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) involves several disparate technologies and specialties. Additionally, method development details are typically not disclosed in journal publications. Method developers may need to search widely for pertinent information on their assay(s). This review summarizes the current practices and procedures in method development. Additionally, it probes aspects of method development that are generally not discussed, such as how exactly to calibrate an assay or where to place quality controls, using examples from the literature. This review intends to provide a comprehensive resource and induce critical thinking around the experiments for and execution of developing a clinically meaningful LC-MS/MS assay.

Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers

Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.

Sample Preparation Strategies for Antibody-Free Quantitative Analysis of High Mobility Group Box 1 Protein

Sickness behavior and fatigue are induced by cerebral mechanisms involving inflammatory cytokines. High mobility group box 1 (HMGB1) is an alarmin, and a potential key player in this process. Reliable quantification methods for total HMGB1 and its redox variants must be established in order to clearly understand how it functions. Current methods pose significant challenges due to interference from other plasma proteins and autoantibodies. We aimed to develop an antibody-free sample preparation method followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to measure HMGB1 in human plasma. Different methods were applied for the removal of interfering proteins and the enrichment of HMGB1 from spiked human plasma samples. A comparison of methods showed an overall low extraction recovery (<40%), probably due to the stickiness of HMGB1. Reversed-phase liquid chromatography separation of intact proteins in diluted plasma yielded the most promising results. The method produced an even higher degree of HMGB1 purification than that observed with immunoaffinity extraction. Detection sensitivity needs to be further improved for the measurement of HMGB1 in patient samples. Nevertheless, it has been demonstrated that a versatile and fully antibody-free sample preparation method is possible, which could be of great use in further investigations.

Immunocapture sample clean-up in determination of low abundant protein biomarkers – a feasibility study of peptide capture by anti-protein antibodies

Immunocapture in mass spectrometry based targeted protein analysis using a bottom-up workflow is nowadays mainly performed by target protein extraction using anti-protein antibodies followed by tryptic digestion. Already available monoclonal antibodies (mAbs) which were developed against intact target proteins (anti-protein antibodies) can capture proteotypic epitope containing peptides after tryptic digestion of the sample. In the present paper considerations when developing a method for targeted protein quantitation through capture of epitope containing peptides are discussed and a method applying peptide capture by anti-protein antibodies is compared with conventional immunocapture MS. The model protein used for this purpose was progastrin releasing peptide (ProGRP), a validated low abundant biomarker for Small Cell Lung Cancer with reference values in serum in the pg mL⁻¹ range. A set of mAbs which bind linear epitopes of ProGRP are available, and after a theoretical consideration, three mAbs (E146, E149 and M18) were evaluated for extraction of proteotypic epitope peptides from a complex sample. M18 was the best performing mAb for peptide capture by anti-protein antibodies, matching the LOD (54 pg mL⁻¹) and LOQ (181 pg mL⁻¹) of the existing conventional immunocapture LC-MS/MS method for determination of ProGRP. Peptide and protein capture using the same mAb were also compared with respect to sample clean-up, and the peptide capture workflow yielded cleaner extracts and therewith less complex chromatograms. Analysis of five patient samples demonstrated that peptide capture by anti-protein antibodies can be used for the determination of various levels of endogenously present ProGRP.

Targeted protein biomarker determination by immunocapture LC-MS/MS: comparison of peptide and protein capture using anti-protein antibodies.