A robust and validated LC-MS/MS method for the quantification of ramucirumab in rat and human serum using direct enzymatic digestion without immunoassay

A new liquid chromatography tandem mass spectrometry (LC-MS/MS) method was established to quantify the anti-gastric cancer fully human monoclonal antibody (ramucirumab) in rat and human serum. The surrogate peptide (GPSVLPLAPSSK) for ramucirumab was generated by trypsin hydrolysis and quantified using the isotopically labeled peptide GPSVLPLAPSSK[13C6, 15N2]ST containing two more amino acids at the carboxyl end as an internal standard to correct for variations introduced during the enzymatic hydrolysis process and any mass spectrometry changes. Additionally, the oxidation and deamidation of unstable peptides (VVSVLTVLHQDWLNGK and NSLYLQMNSLR) were detected. The quantitative range of the proposed method was 1-1000 μg/mL, and complete methodological validation was performed. The precision, accuracy, matrix effect, sensitivity, stability, selectivity, carryover, and interference of the measurements met the required standards. The validated LC-MS/MS method was applied to pharmacokinetic studies in rats administered ramucirumab at 15 mg/kg intravenously. Overall, a robust, efficient, and cost-effective LC-MS/MS method was successfully developed for quantifying ramucirumab in rat and human serum.

Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques

Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.

Surrogate peptide selection and internal standardization for accurate quantification of endogenous proteins

Relative quantification techniques have dominated the field of proteomics. However, biomarker discovery, mathematical model development and studies on transporter-mediated drug disposition still need absolute quantification of proteins. The quality of data of trace-level protein quantification is solely dependent on the specific selection of surrogate peptides. Selection of surrogate peptides has a major impact on the accuracy of the method. In this article, the advanced approaches for selection of surrogate peptides, which can provide absolute quantification of the proteins are discussed. In addition, internal standardization, which accounts for variations in the quantitation process to achieve absolute protein quantification is discussed.

Proteomic analysis of Penicillin G acylases and resulting residues in semi-synthetic β-lactam antibiotics using liquid chromatography - tandem mass spectrometry

Penicillin G acylase (PGA), as a key enzyme, is increasingly used in the commercial production of semi-synthetic β-lactam antibiotics (SSBAs). With the substitution of conventional chemical synthesis by emerging bioconversion processes, more and more PGAs fermented from different types of strains such as Escherichia coli (E. coli, ATCC 11105), Achromobacter sp. CCM 4824 and Providencia rettgeri (ATCC 31052) have been used in this kind of enzymatic processes. As an intermediate reaction catalyst, PGA protein and its presence in the final products may cause a potential risk of human allergic reaction and bring challenges for both quality and process controls. To achieve qualitative and quantitative analysis of PGAs and their residues in SSBAs, a tryptic digestion coupled with liquid chromatography - tandem mass spectrometry (LC-MS/MS) method was developed and proposed because of advantages like high selectivity and sensitivity. A suitable filter aided sample preparation (FASP) method was also used to remove matrix interference and to enrich the target PGA retained in the ultrafiltration membrane for an efficient enzymatic hydrolysis and subsequent accurate MS detection. Finally, twelve batches of PGAs from eight companies were identified and categorized into two types of strains (E. coli and Achromobacter sp. CCM 4824) using proteomic analysis. In total nine batches of five types of SSBAs (amoxicillin, cephalexin, cefprozil, cefdinir and cefaclor) from eight manufacturers were selected for investigation. Trace levels of PGA residual proteins ranging from 0.01 to 0.44 ppm were detected in six batches of different SSBAs which were far lower than the safety limit of 35 ppm reported by DSM, a manufacturer with expertise in the production of SSBAs by enzymatic processes. The developed FASP with LC-MS/MS method is superior to traditional protein assays in terms of selectivity, sensitivity and accuracy. Moreover, it could provide in-depth analysis of amino acid sequences and signature peptides contributing to assignment of the strain sources of PGAs. This method could become a promising and powerful tool to monitor enzymatic process robustness and reliability of this kind of SSBAs manufacturing.

Development of an LC-MS/MS method to simultaneously quantify therapeutic mAbs and estimate hematocrit values in dried blood spot samples

Recently, monoclonal antibody (mAb) therapy has gained increasing attention in the medical field due to its high specificity. Dried blood spots (DBSs) have been used in various clinical fields due to their unique characteristics, such as easy transportation, low invasiveness, and home sampling. However, hematocrit (HCT)-associated issues may lead to inaccurate quantification; moreover, the HCT value is required for converting the drug concentration from DBS to plasma. To simultaneously measure HCT levels and quantify mAb concentrations in DBS samples, this study used volumetrically applied 15 μL DBS, and combined protein G purification and ethanol precipitation approaches as the sample preparation method. Sixty-two clinical samples were used to investigate the HCT estimation ability by using hemoglobin (Hb) peptides. Four mAbs, bevacizumab, trastuzumab, nivolumab and tocilizumab, were selected to demonstrate our method, and pembrolizumab was used as the internal standard. The optimized method could measure four mAbs and Hb peptides simultaneously within 11 min. Moreover, a correlation study revealed that the correlation coefficient for the Hb peptides and the HCT value was larger than 0.9. The HCT estimation results revealed that for over 90% of the real DBS samples the HCT could be obtained within ±20% estimation error acceptance criteria. The method was validated in terms of accuracy and precision for the four mAbs. The developed method was further applied to simultaneously quantify mAb concentrations and estimate HCT values in six patient DBS samples to demonstrate its clinical applicability. It is believed that this newly developed method could facilitate various clinical studies and provide benefits for mAb therapies in clinical fields.

Bioanalytical method development and validation of highly selective and sensitive LC-MS/MS method for determination of teriparatide (parathyroid hormone fragment 1-34) in human serum through direct detection of intact teriparatide molecule

Teriparatide is a novel recombinant peptide fragment of the first 1-34 amino acids of human parathyroid recommended for treatment of osteoporosis. Therapeutic proteins and peptides are routinely estimated using ligand binding assay formats however LC-MS/MS technique which is routinely used in bioanalysis of small molecules has now gained importance in large molecule bioanalysis for the advantages it can offer over LBAs in terms of improved accuracy, selectivity and anti-body free method development. This paper presents a sensitive bioanalytical method for determination of teriparatide in human serum using ultra performance liquid chromatography aligned with tandem mass spectrometric detection. Teriparatide was isolated from human serum using solid phase extraction. The intact peptide was separated on a chromatograph and the multiply charged ion (+7) was detected using a mass spectrometer. The total run time was 4.0 min. The internal standard used was rat PTH 1-34 fragment. The mass transitions of m/z 589.3 > 656.3 for teriparatide and m/z 677.4 > 778.6 for internal standard were used for MS/MS detection. The sample extraction involved a solid phase extraction method followed by concentration of the eluent by evaporation and subsequent reconstitution. The non-specific binding effect caused by the adherence of the peptides/proteins to the vials/tube walls was significantly reduced by using BSA solution as blocking agent. The method has been validated over a linear range of 15.07-913.3 pg/mL with a correlation coefficient ≥ 0.99. The precision (%RSD) was 6.36 to 10.85 and accuracy was within 96.71% to 100.88%. A two-treatment, two-period, cross over study was conducted to establish bioequivalence between test and reference formulation (20 mcg/80 mL - solution for injection) and the method was successfully applied to quantify teriparatide in serum samples of this clinical study and about 1220 human serum samples were analyzed to determine teriparatide. This method is a promising anti-body free LC-MS/MS based methodology for estimation of teriparatide in human serum and may be applied as starting method for other such peptide molecules.

A generic sample preparation method for the multiplex analysis of seven therapeutic monoclonal antibodies in human plasma or serum with liquid chromatography-tandem mass spectrometry

Due to the increasing number of therapeutic monoclonal antibodies (mAbs) used in the clinic, there is an increasing need for robust analytical methods to quantify total mAb concentrations in human plasma for clinical studies and therapeutic drug monitoring. We developed an easy, rapid, and robust sample preparation method for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The method was validated for infliximab (IFX), rituximab (RTX), cetuximab (CTX), dupilumab (DPL), dinutuximab (DNX), vedolizumab (VDZ), and emicizumab (EMZ). Saturated ammonium sulfate (AS) was used to precipitate immunoglobulins in human plasma. After centrifugation, supernatant containing albumin was decanted, and the precipitated immunoglobulin fraction was re-dissolved in buffer containing 6M guanidine. This fraction was then completely denatured, reduced, alkylated, and trypsin digested. Finally, signature peptides from the seven mAbs were simultaneously quantified on LC-MS/MS together with their internal standards stable isotopically labeled peptide counterparts. The linear dynamic ranges (1 - 512 mg/L) of IFX, CTX, RTX, and EMZ showed excellent (R2 > 0.999) linearity and those of DPL, DNX, and VDZ showed good (R2 > 0.995) linearity. The method was validated in accordance with the EMA guidelines. EDTA plasma, sodium citrate plasma, heparin plasma, and serum yielded similar results. Prepared samples were stable at room temperature (20°C) and at 5°C for 3 days, and showed no decline in concentration for all tested mAbs. This described method, which has the advantage of an easy, rapid, and robust pre-analytical sample preparation, can be used as a template to quantify other mAbs in human plasma or serum.

Quantification of surrogate monoclonal antibodies in mouse serum using LC-MS/MS

Background: Surrogate monoclonal antibodies (mAbs) used in preclinical in vivo studies can be challenging to quantify due to lack of suitable immunoaffinity reagents or unavailability of the mAb protein sequence. Generic immunoaffinity reagents were evaluated to develop sensitive LC-MS/MS assays. Peptides of unknown sequence can be used for selective LC-MS quantification. Results: anti-mouse IgG1 was found to be an effective immunoaffinity reagent, enabling quantification of mouse IgG1 mAbs in mouse serum. Selective peptides of unknown sequence were applied for multiplex LC-MS quantification of two rat mAbs co-dosed in mouse. Conclusion: Generic anti-mouse IgG subtype-specific antibodies can be used to improve assay sensitivity and peptides of unknown sequence can be used to quantify surrogate mAbs when the mAb protein sequence in unavailable.

Method development and validation of LC-MS/MS-based assay for the simultaneous quantitation of trastuzumab and pertuzumab in cynomolgus monkey serum and its application in pharmacokinetic study

We present a simple and robust LC-MS/MS assay for the simultaneous quantitation of an antibody cocktail of trastuzumab and pertuzumab in monkey serum. The LC-MS/MS method saved costs, decreased the analysis time, and reduced quantitative times relative to the traditional ligand-binding assays. The serum samples were digested with trypsin at 50°C for 60 min after methanol precipitation, ammonium bicarbonate denaturation, dithiothreitol reduction, and iodoacetamide alkylation. The tryptic peptides were chromatographically separated using a C18 column (2.1 × 50 mm, 2.6 μm) with mobile phases of 0.1% formic acid in water and acetonitrile. The other monoclonal antibody, infliximab, was used as internal standards to minimize the variability during sample processing and detection. A unique peptide for each monoclonal antibody was simultaneously quantified using LC-MS/MS in the multiple reaction monitoring mode. Calibration curves were linear from 2.0 to 400 μg/mL. The intra- and inter-assay precision (%CV) was within 8.9 and 7.4% (except 10.4 and 15.1% for lower limit of quantitation), respectively, and the accuracy (%Dev) was within ±13.1%. The other validation parameters were evaluated, and all results met the acceptance criteria of the international guiding principles. Finally, the method was successfully applied to a pharmacokinetics study after a single-dose intravenous drip administration to cynomolgus monkeys.

Intact protein quantification in biological samples by liquid chromatography - high-resolution mass spectrometry: somatropin in rat plasma

The quantitative determination of intact proteins in biological samples by LC with high-resolution MS detection can be a useful alternative to ligand-binding assays or LC-MS-based quantification of a surrogate peptide after protein digestion. The 22-kDa biopharmaceutical protein somatropin (recombinant human growth hormone) was quantified down to 10 ng/mL (0.45 nM) in 75 μL of rat plasma by the combination of an immunocapture step using an anti-somatropin antibody and LC-MS on a quadrupole-time of flight instrument. Accuracy and precision of the method as well as its selectivity and sensitivity did not depend on the width of the mass extraction window nor on whether only one or a summation of multiple charge states of the protein analyte were used as the detection response. Quantification based on deconvoluted mass spectra showed equally acceptable method performance but with a less favorable lower limit of quantification of 30 ng/mL. Concentrations in plasma after dosing of somatropin to rats correlated well for the deconvolution approach and the quantification based on the summation of the response of the four most intense charge states (14⁺ to 17⁺) of somatropin.

Investigating surrogate cerebrospinal fluid matrix compositions for use in quantitative LC-MS analysis of therapeutic antibodies in the cerebrospinal fluid

As quantitative analysis of biotherapeutics in cerebrospinal fluid (CSF) with LC-MS becomes increasingly widespread, there is a need for method developments towards higher sensitivity. By using artificial CSF (aCSF) in the development phase, the consumption of costly and sparsely available CSF can be limited. The aCSF compositions tested here were made from various dilutions of bovine serum albumin (BSA) or rat plasma to mimic the total protein concentration found in CSF. Focusing on monoclonal antibodies, the aCSF was spiked with human immunoglobulin (hIgG) and prepared with the bottom-up analysis technique using LC-MS. Assuming that the composition of the aCSF would affect the digest, the response from aCSF matrices was compared with CSF from rat, monkey, and dog in terms of estimated sample concentration and matrix effects. The samples were spiked with hIgG in the range of 10 to 1000 ng/mL and volumes of 10 μL were transferred to sample preparation. The results indicate that BSA dilutions from 300 to 2000 μg/mL and rat plasma dilutions of 0.5–2% provide the most accurate concentration estimates when compared with rat CSF. 1000 μg/mL BSA did not produce significantly different concentration estimates for 500 ng/mL samples when compared with CSF from rat, monkey, and dog, and can therefore be used as aCSF for several different species.

Development and fit-for-purpose verification of an LC-MS method for quantitation of hemagglutinin and neuraminidase proteins in influenza virus-like particle vaccine candidates

Recombinant influenza Virus-Like Particle (VLP) vaccines are promising vaccine candidates to prevent influenza, contain two major viral antigenic glycoproteins, Hemagglutinin (HA) and Neuraminidase (NA), on the surface of recombinant VLPs. Accurate quantitation of the mass of these antigenic proteins is important to ensure the product quality and proper dosing. Currently, Single Radial Immunodiffusion (SRID) is a recognized assay for determination of the HA immuno-reactive concentration (potency) in vaccine products, based on immuno-reactivity of HA with strain-specific antisera. The SRID assay, however, requires availability of strain-specific and properly calibrated reagents, which can be time-consuming to generate and calibrate. In addition, the assay is not suitable for quantitation of low abundant proteins, such as NA. In order to accelerate the overall production cycle, we have developed and optimized a high-resolution (HR) LC-MS method for absolute quantitation of both HA and NA protein concentrations in influenza VLP vaccine candidates. In this work, we present the method development, optimization and verification of its suitability for the intended purpose, as a prerequisite for its potential application in Quality Control, by assessing specificity, precision and accuracy, detection characteristics, and dynamic linear range. The method can be also used for other HA/NA containing preparations including in-process samples, purified proteins, whole virus preparations, nano-particle and egg-based vaccine preparations, or for calibration of SRID reference antigens.

Development and validation of an LC-MS/MS method for simultaneous quantification of co-administered trastuzumab and pertuzumab

Given the increasing use of combination therapy with multiple monoclonal antibodies (mAbs), there is a clinical need for multiplexing assays. For the frequently co-administered anti-human epidermal growth factor receptor 2 (HER2) mAbs trastuzumab and pertuzumab, we developed a high-throughput and robust hybrid ligand-binding liquid chromatography-mass spectrometry (LC-MS)/MS quantitative assay. Nanomolar concentrations of trastuzumab and pertuzumab were determined in 10 µL serum samples after extraction by affinity purification through protein A beads, followed by on-bead reduction, alkylation, and trypsin digestion. After electrospray ionization, quantification was obtained by multiple reaction monitoring LC-MS/MS using SILuMab as an internal standard. The method was validated according to the current guidelines from the US Food and Drug Administration and the European Medicines Agency. Assay linearity was established in the ranges 0.250-250 μg/mL for trastuzumab and 0.500-500 μg/mL for pertuzumab. The method was accurate and selective for the simultaneous determination of trastuzumab and pertuzumab in clinical samples, thereby overcoming the limitation of ligand binding assays that cannot quantify mAbs targeting the same receptor. Furthermore, this method requires a small blood volume, which reduces blood collection time and stress for patients. The assay robustness was verified in a clinical trial where trastuzumab and pertuzumab concentrations were determined in 670 serum samples. As we used commercially available reagents and standards, the described generic bioanalytical strategy can easily be adapted to multiplex quantifications of other mAb combinations in non-clinical and clinical samples.

Protein quantification by LC–MS: a decade of progress through the pages of Bioanalysis

Over the past 10 years, there has been a remarkable increase in the use of LC–MS for the quantitative determination of proteins, and this technique can now be considered an established bioanalytical platform for the quantification of macromolecular drugs and biomarkers, next to the traditional ligand-binding assays. Many researchers have contributed to the field and helped improve both the technical possibilities of LC–MS-based workflows and our understanding of the meaning of the results that are obtained. As a tribute to Bioanalysis, which has published many important contributions, this report gives a high-level overview of the most important trends in the field of protein LC–MS, as published in this journal since its inauguration a decade ago. It describes the major technical developments with regard to sample handling, separation and MS detection of both digested and intact protein analysis. In addition, the relevance of the complex structure and in vivo behavior of proteins is discussed and the effect of protein–protein interactions, biotransformation and the occurrence of isoforms on the analytical result is addressed.

Perspectives on potentiating immunocapture-LC-MS for the bioanalysis of biotherapeutics and biomarkers

The integration of ligand-binding assay and LC-MS/MS (immunocapture-LC-MS) has unleashed the combined advantages of both powerful techniques for addressing the ever increasing bioanalytical challenges for biotherapeutics and biomarker assays. The highly specific, selective and sensitive characteristics of the immunocapture-LC-MS-based assays have enabled the determination of biotherapeutics and biomarkers in biomatrices with ease of method development, less requirements on key reagents as well as structural specificity for endogenous and engineered biomolecules. In addition, the versatile immunocapture-LC-MS technology has expanded into many challenging areas to enhance mechanistic studies of drug interactions with their targets. This paper intends to summarize our perspectives on enhancing the use of immunocapture-LC-MS in drug discovery and development for emerging new modalities.

Bioanalytical workflow for novel scaffold protein–drug conjugates: quantitation of total Centyrin protein, conjugated Centyrin and free payload for Centyrin–drug conjugate in plasma and tissue samples using liquid chromatography–tandem mass spectrometry

Aim: Alternative scaffold proteins have emerged as novel platforms for development of therapeutic applications. One such application is in protein–drug conjugates (PDCs), which are analogous to antibody–drug conjugates. Methodology: Liquid chromatography–mass spectrometry methods for quantitation of total protein, conjugate and free payload for a PDC based on Centyrin scaffold were developed. Tryptic peptides generated from a region of the Centyrin that does not contain a conjugation site, and another that has the conjugation site with the linker-payload attached were used as surrogates of the total and conjugated Centyrin, respectively. Conclusion: The methods were successfully applied to analysis of samples from mice to quantify the plasma and tissue concentrations. This same workflow can potentially be applied to other PDCs and site-specific antibody–drug conjugates.

Improving selectivity and sensitivity of protein quantitation by LC–HR–MS/MS: determination of somatropin in rat plasma

Aim: Protein quantitation by digestion of a biological sample followed by LC–MS analysis of a signature peptide can be a challenge because of the high complexity of the digested matrix. Results/methodology: The use of LC with high-resolution (quadrupole-TOF) MS detection allowed quantitation of the 22-kDa biopharmaceutical somatropin in 60 μl of rat plasma down to 25 ng/ml with minimal further sample treatment. Reducing the mass extraction window to 0.01 Da considerably decreased the interference of tryptic peptides, enhanced sensitivity and improved accuracy and precision. Analysis with LC–MS/MS resulted in a less favorable limit of quantitation of 100 ng/ml. Conclusion: HRMS is an interesting option for the quantitation of proteins after digestion and has the potential to improve sensitivity with minimal method development.

LC–HRMS quantitation of intact antibody drug conjugate trastuzumab emtansine from rat plasma

Aim: Compared with small molecules, LC–MS quantitation of larger biotherapeutic proteins such as antibodies and antibody–drug conjugates at the intact level presents many challenges in both LC and MS due to their higher molecular weight, bigger size, structural complexity and heterogeneity. Results & conclusion: In this study, quantitation of an intact lysine-linked antibody–drug conjugate, trastuzumab emtansine is presented. Trastuzumab emtansine was extracted from rat plasma using bead-based immunoaffinity capture; after elution from the beads, it was directly analyzed on a LC–HRMS system. Quantitation using both extracted ion chromatogram and deconvoluted mass peaks was evaluated. A limit of quantitation was approximately 20 ng on column with a linear dynamic range from 5 to 100 μg/ml. In addition, the reproducibility and distribution of the drug-to-antibody ratio at different trastuzumab emtansine concentrations were discussed.

Qualitative and quantitative characterization of protein biotherapeutics with liquid chromatography mass spectrometry

In the last decade, the advancement of liquid chromatography mass spectrometry (LC/MS) techniques has enabled their broad application in protein characterization, both quantitatively and qualitatively. Owing to certain important merits of LC/MS techniques (e.g., high selectivity, flexibility, and rapid method development), LC/MS assays are often deemed as preferable alternatives to conventional methods (e.g., ligand-binding assays) for the analysis of protein biotherapeutics. At the discovery and development stages, LC/MS is generally employed for two purposes absolute quantification of protein biotherapeutics in biological samples and qualitative characterization of proteins. For absolute quantification of a target protein in bio-matrices, recent work has led to improvements in the efficiency of LC/MS method development, sample treatment, enrichment and digestion, and high-performance low-flow-LC separation. These advances have enhanced analytical sensitivity, specificity, and robustness. As to qualitative analysis, a range of techniques have been developed to characterize intramolecular disulfide bonds, glycosylation, charge variants, primary sequence heterogeneity, and the drug-to-antibody ratio of antibody drug conjugate (ADC), which has enabled a refined ability to assess product quality. In this review, we will focus on the discussion of technical challenges and strategies of LC/MS-based quantification and characterization of biotherapeutics, with the emphasis on the analysis of antibody-based biotherapeutics such as monoclonal antibodies (mAbs) and ADCs. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:734-754, 2017.

Novel strategy using tryptic peptide immunoaffinity-based LC–MS/MS to quantify denosumab in monkey serum

Aim: Denosumab is a recombinant fully human IgG2 that has a high affinity and specificity for human RANKL. Commercially available RANKL labeled with an Fc fragment cannot be used to establish an indirect ELISA. To characterize denosumab pharmacokinetic a robust and accuracy method should be developed urgently. Results: In this study, an immunoaffinity enrichment method coupled with LC–MS/MS was established. The LC–MS/MS method acquired a linear range from 0.1 to 30 μg/ml. The intra- and inter-run precision (CV%) was within 11.5 and 10.5%, respectively. More importantly, the LC–MS/MS pharmacokinetic data were consistent with ELISA. Conclusion: This approach accelerated the quantification, reduced the costs and provided an alternative in case of lacking the special antigen to denosumab or a RANKL-biotinylated reagent.

Quantitative LC/ESI-SRM/MS of antibody biopharmaceuticals: use of a homologous antibody as an internal standard and three-step method development

Monoclonal antibody-based therapeutic agents (antibody drugs) have attracted considerable attention as a new type of drug. Concomitantly, the use of quantitative approaches for characterizing antibody drugs, such as liquid chromatography (LC)-mass spectrometry (MS), has increased. Generally, selective quantification of antibody drugs is done using unique peptides from variable regions (V _H and V _L) as surrogate peptides. Further, numerous internal standards (ISs) such as stable isotope-labeled (SIL)-intact proteins and SIL-surrogate peptides are used. However, developing LC-MS methodology for characterizing antibody drugs is time-consuming and costly. Therefore, LC-MS is difficult to apply for this purpose, particularly during the drug discovery stage when numerous candidates must be evaluated. Here, we demonstrate an efficient approach to developing a quantitative LC/electrospray ionization (ESI)-selected reaction monitoring (SRM)/MS method for characterizing antibody drugs. The approach consists of the following features: (i) standard peptides or SIL-IS are not required; (ii) a peptide from the homologous monoclonal antibody serves as an IS; (iii) method development is monitored using a spiked plasma sample and one quantitative MS analysis; and (iv) three predicted SRM assays are performed to optimize quantitative SRM conditions such as transition, collision energy, and declustering potential values. Using this strategy, we developed quantitative SRM methods for infliximab, alemtuzumab, and bevacizumab with sufficient precision (<20%)/accuracy (<±20%) for use in the drug discovery stage. We have also demonstrated that choosing a higher homologous peptide pair (from analyte mAb/IS mAb) is necessary to obtain the sufficient precision and accuracy. Graphical abstract ᅟ.

Reagent-free LC–MS/MS-based pharmacokinetic quantification of polyhistidine-tagged therapeutic proteins

Aim: Immobilized metal ion affinity chromatography is widely employed for purifying polyhistidine-tagged recombinant proteins from cell lysates. The technique can be applied for quantification of therapeutic proteins in biological matrices by LC–MS/MS. Results: A protein reagent-free workflow was developed for quantifying polyhistidine-tagged proteins by LC–MS/MS. The workflow includes target protein enrichment by immobilized metal ion affinity chromatography, on-bead trypsin digestion and quantification of signature peptides by LC–MS/MS. It was applied to quantify a 6×His-tagged protein in a mouse pharmacokinetic study with assay sensitivity of 10.0 ng/ml and linearity up to 10,000 ng/ml. Conclusion: The protein reagent-free workflow developed herein can overcome reagent limitation and serve as a viable approach for quantifying polyhistidine-tagged therapeutic proteins to support discovery pharmacokinetic and pharmacodynamic studies.

Evaluation of Gallium as a Tracer of Exogenous Hemoglobin-Haptoglobin Complexes for Targeted Drug Delivery Applications

Haptoglobin (Hp) is a plasma glycoprotein that generates significant interest in the drug delivery community because of its potential for delivery of antiretroviral medicines with high selectivity to macrophages and monocytes, the latent reservoirs of human immunodeficiency virus. As is the case with other therapies that exploit transport networks for targeted drug delivery, the success of the design and optimization of Hp-based therapies will critically depend on the ability to accurately localize and quantitate Hp-drug conjugates on the varying and unpredictable background of endogenous proteins having identical structure. In this work, we introduce a new strategy for detecting and quantitating exogenous Hp and Hp-based drugs with high sensitivity in complex biological samples using gallium as a tracer of this protein and inductively coupled plasma mass spectrometry (ICP MS) as a method of detection. Metal label is introduced by reconstituting hemoglobin (Hb) with gallium(III)-protoporphyrin IX followed by its complexation with Hp. Formation of the Hp/Hb assembly and its stability are evaluated with native electrospray ionization mass spectrometry. Both stable isotopes of Ga give rise to an abundant signal in ICP MS of a human plasma sample spiked with the metal-labeled Hp/Hb complex. The metal label signal exceeds the spectral interferences' contributions by more than an order of magnitude even with the concentration of the exogenous protein below 10 nM, the level that is more than adequate for the planned pharmacokinetic studies of Hp-based therapeutics. Graphical Abstract ᅟ.

LC–MS/MS strategies for therapeutic antibodies and investigation into the quantitative impact of antidrug-antibodies

Aim: We aimed to establish novel, high-throughput LC–MS/MS strategies for quantification of monoclonal antibodies in human serum and examine the potential impact of antidrug antibodies. Methodology: We present two strategies using a thermally stable immobilized trypsin. The first strategy uses whole serum digestion and the second introduces Protein G enrichment to improve the selectivity. The impact of anti-trastuzumab antibodies on the methods was tested. Conclusion: Whole serum digestion has been validated for trastuzumab (LLOQ 0.25 µg/ml). Protein G enrichment has been validated for trastuzumab (LLOQ 0.1 µg/ml), bevacizumab (LLOQ 0.1 µg/ml) and adalimumab (LLOQ 0.25 µg/ml). We have shown the potential for anti-drug antibodies to impact on the quantification and we have subsequently established a strategy to overcome this impact where total quantification is desired.

A whole-molecule immunocapture LC–MS approach for the in vivo quantitation of biotherapeutics

Aim: Large-molecule biotherapeutic quantitation in vivo by LC–MS has traditionally relied on enzymatic digestion followed by quantitation of a ‘surrogate peptide’ to infer whole-molecule concentration. MS methods presented here measure the whole molecule and provide a platform to better understand the various circulating drug forms by allowing for variant quantitation. Results: An immunocapture LC–MS method for quantitation of a biotherapeutic monoclonal antibody from human plasma is presented. Sensitivity, precision and accuracy for each molecular portion are presented along with an example of glycoform variant quantitation. Conclusion: The method is presented as a basic platform to be further developed for Good Practice (GxP) applications, critical quality attribute analysis or general understanding of molecular forms present as required for the wide range of drug development processes.

A workflow for absolute quantitation of large therapeutic proteins in biological samples at intact level using LC-HRMS

Aim: The commonly used LC–MS workflow to quantify protein therapeutics in biological samples is ‘bottom-up’ approach. In this study, the aim is to establish ‘top-down’ approach for absolute quantitation of therapeutic antibodies or proteins of similar sizes in biological samples at intact level. Materials & methods: Using a recombinant human monoclonal antibody as the model molecule, we present a workflow to measure large therapeutic proteins in plasma at intact level based on deconvoluted high-resolution MS (HRMS) peaks. A novel MultiQuant™ software function was developed to automatically deconvolute the peaks and process the data. Results & conclusion: The workflow showed satisfying performance. This is a proof of concept study demonstrating the feasibility of bioanalysis of large therapeutic proteins at intact level using LC-HRMS.

Utilizing enzymatic digestion procedures in the bioanalytical laboratory

In recent years, the use of LC–MS technologies in the bioanlytical laboratory for quantitation of peptide/protein biomarkers and biotherapeutics has increased dramatically. The increased interest is due to the improvement in sensitivity of MS instruments over the last 5–10 years, as well as its proven ability to overcome some common issues associated with immunoassay, namely selectivity and reagent availability. However, large proteins (>10 kDa) chromatograph and ionize poorly. To overcome this challenge, LC–MS/MS workflows for proteins larger than 10 kDa utilize enzymatic digestion procedures with subsequent quantitation of one or more of these enzymatically derived peptides to act as a surrogate for the intact protein. Here, recommendations of digestion technique and potential internal standards are summarized.

LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications

Bioanalytical LC–MS for protein quantification is traditionally based on enzymatic digestion of the target protein followed by absolute quantification of a specific signature peptide relative to a stable-isotope labeled analog. The enzymatic digestion, nonetheless, limits rapid method development, sample throughput and turnaround time, and, moreover, makes that essential information regarding the biological function of the intact protein is lost. The recent advancements in high-resolution MS instrumentation and improved sample preparation techniques dedicated to protein clean-up raise the question to what extent LC–MS can be applied for quantitative bioanalysis of intact proteins. This review provides an overview of current and potential applications of LC–MS for intact protein quantification as well as the main limitations and challenges for broad application.

Application of high-resolution MS in the quantification of a therapeutic monoclonal antibody in human plasma

BACKGROUND

Monoclonal antibodies are the fastest growing class of protein therapeutics. Ligand-binding assays have been the technique of choice for the quantification of these large proteins; however, LC-MS and more recently LC-HRMS have been gaining momentum as robust alternatives for the bioanalysis of antibodies in biological matrices.

RESULTS

Optimization of sample preparation and LC-HRMS analysis in MRM(HR) mode has allowed us to develop a highly specific dual-peptide targeted assay for the quantification of Rituximab, in human plasma. The linearity of the assay was established from 1.0 to 200 µg/ml for both light and heavy chain surrogate peptides, with accuracy and precision within 15%.

CONCLUSION

LC-HRMS can be an effective tool for the quantification of monoclonal antibodies in regulated bioanalysis.

A multiplexed hybrid LC-MS/MS pharmacokinetic assay to measure two co-administered monoclonal antibodies in a clinical study

BACKGROUND

Combination therapies with monoclonal antibodies (mAbs) enhance therapeutic activity and may circumvent drug resistance. However, these studies present bioanalytical challenges for ligand-binding assays (LBAs). Recent MS-based protein quantification offers an alternative for bioanalysis.

RESULTS

A hybrid LC-MS/MS assay was developed to simultaneously measure human serum concentrations of two mAbs. Anti-idiotypic reagents that did not work in LBAs were successfully used for mAb affinity capture enrichment. Stable isotope-labeled peptide internal standards were employed. The mAb quantification involved measuring a signature CDR peptide derived from each mAb as a surrogate. Selected clinical samples were successfully analyzed.

CONCLUSION

The multiplexed LC-MS/MS method provided a powerful quantitative tool for clinical PK assessment of co-administered mAbs without the requirement for stringent affinity capture reagents.

Bioanalytical method validation considerations for LC–MS/MS assays of therapeutic proteins

This paper highlights the recommendations of a group of industry scientists in validating regulated bioanalytical LC–MS/MS methods for protein therapeutics in a 2015 AAPSJ White Paper. This group recommends that most of the same precision and accuracy validation criteria used for ligand-binding assays (LBAs) be applied to LC–MS/MS-based assays where proteins are quantified using the LC–MS/MS signal from a surrogate peptide after proteolytic digestion (PrD-LCMS methods). PrD-LCMS methods are generally more complex than small molecule LC–MS/MS assays and may often include LBA procedures, leading to the recommendation for a combination of chromatographic and LBA validation strategies and appropriate acceptance criteria. Several key aspects of this bioanalytical approach that are discussed in the White Paper are treated here in additional detail. These topics include selectivity/specificity, matrix effect, digestion efficiency, stability and critical reagent considerations.

Surfactant-aided precipitation/on-pellet-digestion (SOD) procedure provides robust and rapid sample preparation for reproducible, accurate and sensitive LC/MS quantification of therapeutic protein in plasma and tissues

For targeted protein quantification by liquid chromatography mass spectrometry (LC/MS), an optimal approach for efficient, robust and hi-throughput sample preparation is critical, but often remains elusive. Here we describe a straightforward surfactant-aided-precipitation/on-pellet-digestion (SOD) strategy that provides effective sample cleanup and enables high and constant peptide yields in various matrices, allowing reproducible, accurate and sensitive protein quantification. This strategy was developed using quantification of monocolnocal antibody in tissues and plasma as the model system. Surfactant treatment before precipitation substantially increased peptide recovery and reproducibility from plasma/tissue, likely because surfactant permits extensive denaturation/reduction/alkylation of proteins and inactivation of endogenous protease inhibitors, and facilitates removal of matrix components. The subsequent precipitation procedure effectively eliminates the surfactant and nonprotein matrix components, and the thorough denaturation by both surfactant and precipitation enabled very rapid on-pellet-digestion (45 min at 37 °C) with high peptide recovery. The performance of SOD was systematically compared against in-solution-digestion, in-gel-digestion and filter-aided-sample-preparation (FASP) in plasma/tissues, and then examined in a full pharmacokinetic study in rats. SOD achieved the best peptide recovery (∼21.0-700% higher than the other three methods across various matrices), reproducibility (3.75-10.9%) and sensitivity (28-30 ng/g across plasma and tissue matrices), and its performance was independent of matrix types. Finally, in validation and pharmacokinetic studies in rats, SOD outperformed other methods and provided highly accurate and precise quantification in all plasma samples without using stable isotope labeled (SIL)-protein internal standard (I.S.). In summary, the SOD method has proven to be highly robust, efficient and rapid, making it readily adaptable to large-scale clinical and pharmaceutical quantification of biomarkers or biotherapeutics.

ELISA microplate: a viable immunocapture platform over magnetic beads for immunoaffinity-LC–MS/MS quantitation of protein therapeutics?

Aim: Evaluate the performance of ELISA microplates versus commonly used magnetic beads for biological sample cleanup and/or enrichment in immunoaffinity-LC–MS/MS to reduce tedious beads washing procedures and a relatively high assay cost. Materials & Methods: ELISA microplates were used as immunicapture platform and compared with magnetic beads for sample cleanup for LC–MS/MS quantitation of protein therapeutics. Results: One unmodified and two surface-activated microplates provided comparable linear ranges and sensitivities for a therapeutic protein (mass 78 kDa) using a human serum sample of 100 µl with 1:1 dilution compared with Tosylactivated magnetic beads using 200 µl of human serum without sample dilution. The assays’ precision and accuracy were all within acceptable ranges. No nonspecific binding or other selectivity issues were observed. Conclusion: The results suggested an ELISA microplate could be a viable immunocapture platform for immunoaffinity-LC–MS/MS quantitation of protein therapeutics.

High-sensitivity quantitation of a Nanobody® in plasma by single-cartridge multidimensional SPE and ultra-performance LC–MS/MS

Background: A major challenge in protein quantitation based on enzymatic digestion of complex biological samples and subsequent LC–MS/MS analysis of a signature peptide is dealing with the high complexity of the matrix after digestion, which can reduce sensitivity considerably. Results: Using single cartridge multidimensional SPE, sufficient selectivity was introduced to allow quantitation in 50 µl of plasma down to 10.0 ng/ml (˜0.3 nM). An inhouse prepared 18O-labeled signature peptide was used as the internal standard. The procedure was validated for human and rabbit plasma. Conclusion: The developed SPE procedure allowed the sensitive and selective LC–MS/MS quantitation of the Nanobody® without the use of antibodies. When appropriate precautions are taken, the 18O-labeled peptide is a practical and economical alternative to custom synthesis.

A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry

A new sample preparation method for target proteome absolute quantitation using ¹⁸O labeling-MRM MS.

Introduction of a routine quan/qual approach into research DMPK: experiences and evolving strategies

After graduating with an Oceanography degree from Swansea University, Lloyd has spent over 20 years in the field of bioanalysis and metabolite profiling. He started his career in large pharma at Wyeth UK, where he was involved in setting up the first GC and LC–MS/MS systems for both QC and early DMPK assays, employing EI/CI, thermospray, and the then new electrospray ionization techniques. Lloyd then joined Celltech, now UCB, where he is primarily tasked with metabolite profiling by LC–MS and NMR to support both early research projects and late-stage clinical studies.

The application of liquid chromatography high-resolution mass spectrometry for simultaneous quantitative and qualitative (quan/qual) analysis has gained momentum across a range of different scientific arenas in recent years. The ability to acquire high quality quantitative data, whilst also capturing qualitative data for either parallel or retrospective analysis, is a powerful resource, especially in view of ever-reducing cycle times, laboratory space and budgets. The quan/qual approach employing a Q-Exactive™ Orbitrap high-resolution mass spectrometer has been successfully introduced into UCB's research DMPK department. This article describes our experiences in introducing quan/qual, issues that we discovered in establishing this new working paradigm, the evolution of the strategy and its future potential.

Guanidinated protein internal standard for immunoaffinity-liquid chromatography/tandem mass spectrometry quantitation of protein therapeutics

RATIONALE

A protein internal standard (IS) is essential and superior to a peptide IS to achieve reproducible results in the quantitation of protein therapeutics using immunoaffinity-liquid chromatography/tandem mass spectrometry (LC/MS/MS). Guanidination has been used as a protein post-modification technique for more than half a century. A decade ago, the modification was applied to lysine-ending peptides to enhance their MALDI responses and peptide sequencing coverage. However, rarely has tryptic digestion of guanidinated proteins been investigated, likely due to the early conclusion that trypsin did not hydrolyze peptide bonds involving homoarginine in guanidinated proteins. In this study, the opposite was observed. Guanidinated lysine residues of proteins did not hinder the access of trypsin allowing for proteolytic digestion. Based on this observation, a new concept of internal standard, named Guanidinated Protein Internal Standard (GP-IS), was proposed for LC/MS/MS quantitation of protein therapeutics.

METHODS

The GP-IS is prepared by treating a portion of the therapeutic protein (analyte) with guanidine to convert arginine residues in the protein into homoarginine residues. After tryptic digestion, the GP-IS produces a series of homoarginine-ending peptides plus another series of arginine-ending peptides. One of the homoarginine-ending peptides, which corresponds to the analyte surrogate (lysine-ending) peptide, was chosen as a peptide internal standard (GP-PIS) for LC/MS/MS quantitation.

RESULTS

Using this GP-IS approach, a sensitive and robust immunoaffinity-LC/MS/MS assay was developed and fully validated with a linearity range from 10 to 1000 ng/mL using 200 μL of human serum for the quantitation of an Astellas protein drug in clinical development.

CONCLUSIONS

The proposed strategy allows LC/MS/MS to play an ever-increasing role in bioanalytical support for protein therapeutics development because of its capability of completely tracking all variations from the beginning to the end of sample analysis, easier preparation compared to isotope-labeled protein-IS, and greater flexibility for changing to alternate analyte surrogate peptides.

Development of a highly sensitive liquid chromatography/tandem mass spectrometry method to quantify total and free levels of a target protein, interferon-gamma-inducible protein-10, at picomolar levels in human serum

RATIONALE

Liquid chromatography/tandem mass spectrometry (LC/MS/MS) assays are increasingly being used for absolute quantitation of proteins due to high specificity and low cost. However, the major challenge for the LC/MS method is insufficient sensitivity. This paper details the strategies developed to maximize the sensitivity from aspects of chromatography, mass spectrometry, and sample preparation to achieve a highly sensitive LC/MS method.

METHODS

The method is based on the LC/MS/MS measurement of a surrogate peptide generated from trypsin digestion of interferon-gamma-inducible protein-10 (IP-10). The sample preparation strategy involved selectively extracting IP-10 and removing high-abundance serum proteins through acidified protein precipitation (PPT). It was revealed in this work that these high-abundance serum proteins, if not separated from the protein of interest, could cause significant ionization saturation and high background noise in selected reaction monitoring (SRM), leading to a 100-fold higher lower limit of quantification (LLOQ).

RESULTS

Our method demonstrated that the acidified PPT could be optimized to selectively extract the protein of interest with full recovery of 97% to 103%, while the high-abundance serum proteins could be effectively removed with minimal matrix effect of 90% to 93%. For the first time, a highly sensitive LC/MS method with a LLOQ of 31.62 pM for the quantitation of IP-10 has been achieved, which is a 100-fold improvement over the generic method.

CONCLUSIONS

The described method offers excellent sensitivity with advantages of being antibody reagent independent and leads to significant cost and time savings. It has been successfully employed to determine both total and free IP-10 levels in human serum samples. This method development strategy may also be applied to other small proteins.

Advances in the quantitation of therapeutic insulin analogues by LC-MS/MS

Insulin analogues represent a major and growing class of biotherapeutics, and their quantitation is an important focus of commercial and public effort across a number of different fields. As LC-MS has developed, it has become an increasingly practicable and desirable alternative to ligand-binding-based approaches for quantitation of this class of compounds. The sensitivity challenge of measuring trace levels of this large peptide molecule in a protein-containing matrix is considerable; however, different approaches to detection, extraction and separation are described to overcome this challenge, including immunoaffinity capture, SPE and low-flow HPLC. Considerations such as bioanalytical assay acceptance criteria and antidrug antibody effects during drug development are included, alongside descriptions of recent sports doping and clinical applications. Factors affecting the correlation and agreement of MS with biological ligand-binding methods are discussed, with ways to anticipate and appreciate differences between the values derived from each technique. The 'future perspective' section discusses the likely trend towards MS-based analysis for these compounds and the impact of HRMS. A high degree of scientific creativity, combined with science-defined regulatory approaches that define suitable validation criteria, will be needed to meet the demanding requirements for high-throughput analysis of insulin by LC-MS.

Quantification of human mAbs in mouse tissues using generic affinity enrichment procedures and LC–MS detection

Background: The disease state can modulate the penetration of large antibody-sized therapeutic molecules into affected tissues. Suitable bioanalytical methods are required for the quantitative analysis of drug tissue levels to enable a better understanding of the parameters influencing drug penetration and target engagement. Results: Described is a sensitive and selective LC–MS/MS assay for the quantification of human mAb molecules in mouse tissues. By homogenizing tissues directly into serum, a common serum calibration curve can be used for multiple tissues. A generic procedure was used for affinity enrichment. An analytical range of 20 – 20,000 ng/ml was achieved in serum. Conclusion: The method described here can be applied for the quantitative analysis of mAb and Fc-fusion therapeutic molecules in a variety of animal tissue matrices.

Feasibility assessment of a novel selective peptide derivatization strategy for sensitivity enhancement for the liquid chromatography/tandem mass spectrometry bioanalysis of protein therapeutics in serum

RATIONALE

Sensitivity is one major challenge limiting the application of liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods for bioanalysis of proteins. A novel selective peptide derivatization (SPD) strategy was proposed to improve assay sensitivity. The main concept of the SPD strategy is to selectively derivatize surrogate peptides of the target protein in the digests, while not derivatizing the abundant background peptides, thereby improving the separation of target peptides during sample extraction and chromatography, and increasing the sensitivity. Additional benefits may help improve sensitivity include (1) increased ionization efficiency; (2) improved fragmentation pattern; and (3) increased sample extraction recovery of target peptides.

METHODS

Feasibility assessment of the SPD strategy was conducted using BMS-986012, a monoclonal antibody, as the model protein, and with malondialdehyde (MDA) to selectively derivatize the arginine-containing surrogate peptide SLIY in tryptic-digested monkey serum samples.

RESULTS

The decreased polarity and basicity of the MDA-derivatized peptide SLIY (MDA-SLIY) helped improve its separation from the background peptides during solid-phase extraction (SPE) and chromatography. The recovery of MDA-SLIY was 36.1-44.2%, which was ~3-fold higher than the recovery of peptide SLIY (11.9-16.1%). There was no significant ion suppression for MDA-SLIY. Overall, SPD improved the sensitivity ~5-fold. SPD methodology was then successfully applied to the development of a sensitive LC/MS/MS assay for BMS-986012 in monkey serum.

CONCLUSIONS

This work demonstrates the feasibility of the SPD strategy for sensitivity enhancement. SPD can provide a simple, cost-efficient, and antibody-free sample preparation approach to improve sensitivity.

Application and challenges in using LC–MS assays for absolute quantitative analysis of therapeutic proteins in drug discovery

As more protein therapeutics enter the drug-discovery pipeline, the traditional ligand-binding assay (LBA) faces additional challenges to meet the rapid and diverse bioanalytical needs in the early drug-discovery stage. The high specificity and sensitivity afforded by LC–MS, along with its rapid method development, is proving invaluable for the analysis of protein therapeutics in support of drug discovery. LC–MS not only serves as a quantitative tool to complement LBA in drug discovery, it also provides structural details at a molecular level, which are used to address issues that cannot be resolved using LBA alone. This review will describe the key benefits and applications, as well as the techniques and challenges for applying LC–MS to support protein quantification in drug discovery.