A framework for quality control in quantitative proteomics

A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.

A Spike-Control Approach that Evaluates High Resolution Mass Spectrometry-Based Sequence Variant Analytical Method Performance for Therapeutic Proteins

An amino acid sequence variant (SV) is defined as an unintended amino acid substitution in protein drug products. SVs contribute to product heterogeneity and can potentially impact product quality, safety, immunogenicity, and efficacy. The analysis of biotherapeutics for SVs is important throughout the product life cycle including clone selection, development of nutrient feed strategies, commercial manufacturing process, and post-approval changes to monitor product quality. The proposed analytical procedure for SVs consists of both qualitative (identification of SVs) and quantitative (quantitation of identified SVs) components. The complexities of SV analysis and the variety of current procedures highlight the need for a systematic approach for assessing the capability of these methodologies to reliably identify and quantitate SVs in biotherapeutics. We described here a "spike-control" approach for evaluating SV analytical procedure. The concept was adopted from quality control samples routinely used in analytical procedure validation. One FDA approved monoclonal antibody (mAb) was spiked with accurate amounts of highly homologous mAb to create mAb samples containing low yet accurate levels of "artificial" SVs. Spike-control samples were denatured, reduced, alkylated, digested and then analyzed by high resolution Orbitrap mass spectrometry. In silico analysis revealed four single amino acid differences between the two mAbs that could be used to represent SVs in the spike-control samples. All four "artificial" SVs were reliably identified by the current workflow. Analytical range (0.01% to 2%), accuracy and precision of identified SVs have also been evaluated. Overall, spike-control sample(s) helped to demonstrate that the SV analytical procedure (i.e., sample preparation, LC separation, mass spectrometry determinations and bioinformatic software) was fit for purpose and suitable for the identification and quantitation of SVs at a pre-determined threshold.

Establishment of Ph. Eur. Somatropin/desamidosomatropin resolution mixture Chemical Reference Substance batch 2

The control of somatropin products according to the monographs of the European Pharmacopoeia (Ph. Eur.) requires a system suitability preparation for the test for related proteins by liquid chromatography. A preparation consisting in a mixture of somatropin and desamidosomatropin, such as the Ph. Eur. Somatropin/desamidosomatropin resolution mixture Chemical Reference Substance (CRS), is to be used to ascertain adequate resolution of the chromatographic setup. Due to low stocks, the Biological Standardisation Programme (BSP) of the Council of Europe and the European Union ran a study to establish a new batch of this system suitability CRS. A freeze-dried candidate batch (cCRS2) was produced and tested at the European Directorate for the Quality of Medicines and HealthCare (EDQM, Council of Europe). The resolution between the peaks due to somatropin and desamidosomatropin was 1.7 and the symmetry factor for the somatropin peak was 1.2. The mean percentage area of the desamidosomatropin peak was 14.6 %. These results showed that cCRS2 is suitable for its intended purpose. Based on these data, in May 2020 the Ph. Eur. Commission established the candidate batch as Ph. Eur. Soma-tropin/desamidosomatropin resolution mixture CRS batch 2.

Development of LC-MS/MS method and application to bioequivalence study of a light sensitive drug montelukast

OBJECTIVE

The aim of the study was to develop a simple, highthroughput and sensitive LC-MS/MS method and apply to a bioequivalence study of montelukast, a light sensitive drug.

METHOD

The effects of organic modifiers in mobile phase, protein precipitation agent to plasma sample ratio, and light on montelukast stability in unprocessed and processed human plasma, were evaluated. Validation was conducted in accordance with European Medicines Agency Guideline on bioanalytical method validation.

RESULTS

No interference peak was observed when acetonitrile was used as an organic modifier. Acetonitrile to plasma ratio of 4:1 produced clean plasma sample. Approximately 3 % of cis isomer was detected in unprocessed plasma samples while 21 % of cis isomer was detected in processed plasma samples after exposing to fluorescent light for 24h. The standard calibration curve was linear over 3.00-1200.00 ng/mL. All method validation parameters were within the acceptance criteria.

CONCLUSION

The validated method was successfully applied to a bioequivalence study of two montelukast formulations involving 24 healthy Malaysian volunteers. The light stability of a light sensitive drug in unprocessed and processed human plasma samples should be studied prior to pharmacokinetic/bioequivalence studies. Measures could then be taken to protect the analyte in human plasma from light degradation.

A Python-Based Pipeline for Preprocessing LC-MS Data for Untargeted Metabolomics Workflows

Preprocessing data in a reproducible and robust way is one of the current challenges in untargeted metabolomics workflows. Data curation in liquid chromatography–mass spectrometry (LC–MS) involves the removal of biologically non-relevant features (retention time, m/z pairs) to retain only high-quality data for subsequent analysis and interpretation. The present work introduces TidyMS, a package for the Python programming language for preprocessing LC–MS data for quality control (QC) procedures in untargeted metabolomics workflows. It is a versatile strategy that can be customized or fit for purpose according to the specific metabolomics application. It allows performing quality control procedures to ensure accuracy and reliability in LC–MS measurements, and it allows preprocessing metabolomics data to obtain cleaned matrices for subsequent statistical analysis. The capabilities of the package are shown with pipelines for an LC–MS system suitability check, system conditioning, signal drift evaluation, and data curation. These applications were implemented to preprocess data corresponding to a new suite of candidate plasma reference materials developed by the National Institute of Standards and Technology (NIST; hypertriglyceridemic, diabetic, and African-American plasma pools) to be used in untargeted metabolomics studies in addition to NIST SRM 1950 Metabolites in Frozen Human Plasma. The package offers a rapid and reproducible workflow that can be used in an automated or semi-automated fashion, and it is an open and free tool available to all users.

Establishment of an erythropoietin CRS with stable measurable dimer content for SEC system suitability qualification

The European Pharmacopoeia (Ph. Eur.) monograph 1316 'Erythropoietin concentrated solution' prescribes that the dimer content of therapeutic erythropoietin (EPO) preparations must not exceed 2% as determined by Size-Exclusion Chromatography (SEC). This report describes the evaluation of a candidate Chemical Reference Substance (cCRS) to serve as system suitability reference material for the qualification of SEC systems used to assess dimer and oligomer content in EPO solutions. The study organised by the European Directorate for the Quality of Medicines & HealthCare (EDQM) was performed with the participation of six European laboratories which tested the candidate material and the EPO for physicochemical tests CRS batch 1. The candidate material was shown to be a suitable reference material for the determination of the resolving capability of the SEC system for separation of dimer and higher oligomers from monomeric EPO. The cCRS was adopted by the Ph. Eur. Commission as Erythropoietin for SEC system suitability CRS batch 1 following consideration of the report. The importance of the resolving capability of the SEC system, as defined by the peak ratios or the peak-to-valley resolution, together with the asymmetry of the peaks eluted, and the linear response of the UV detector were all seen as critical parameters. Therefore, the monograph Erythropoietin concentrated solution (1316) was revised concomitantly to take account of the CRS and to set acceptance criteria for these critical parameters..

An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments

We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC-MS/MS runs are automatically imported into Skyline and multiple identification-free metrics are extracted from targeted peptides. These data are then uploaded to the Panorama Skyline document repository where metrics can be viewed in a web-based interface using powerful process control techniques, including Levey-Jennings and Pareto plots. The interface is versatile and takes user input, which allows the user significant control over the visualization of the data. The pipeline is vendor and instrument-type neutral, supports multiple acquisition techniques (e.g., MS 1 filtering, data-independent acquisition, parallel reaction monitoring, and selected reaction monitoring), can track performance of multiple instruments, and requires no manual intervention aside from initial setup. Data can be viewed from any computer with Internet access and a web browser, facilitating sharing of QC data between researchers. Herein, we describe the use of this pipeline, termed Panorama AutoQC, to evaluate LC-MS/MS performance in a range of scenarios including identification of suboptimal instrument performance, evaluation of ultrahigh pressure chromatography, and identification of the major sources of variation throughout years of peptide data collection.

Performance metrics for evaluating system suitability in liquid chromatography--Mass spectrometry peptide mass mapping of protein therapeutics and monoclonal antibodies

The use of liquid chromatography--mass spectrometry (LC-MS) for the characterization of proteins can provide a plethora of information related to their structure, including amino acid sequence determination and analysis of posttranslational modifications. The variety of LC-MS based applications has led to the use of LC-MS characterization of therapeutic proteins and monoclonal antibodies as an integral part of the regulatory approval process. However, the improper use of an LC-MS system, related to intrinsic instrument limitations, improper tuning parameters, or poorly optimized methods may result in the production of low quality data. Improper system performance may arise from subtle changes in operating conditions that limit the ability to detect low abundance species. To address this issue, we systematically evaluated LC-MS/MS operating parameters to identify a set of metrics that can be used in a workflow to determine if a system is suitable for its intended purpose. Development of this workflow utilized a bovine serum albumin (BSA) digest standard spiked with synthetic peptides present at 0.1% to 100% of the BSA digest peptide concentration to simulate the detection of low abundance species using a traditional bottom-up workflow and data-dependent MS(2) acquisition. BSA sequence coverage, a commonly used indicator for instrument performance did not effectively identify settings that led to limited dynamic range or poorer absolute mass accuracy on 2 separate LC-MS systems. Additional metrics focusing on the detection limit and sensitivity for peptide identification were determined to be necessary to establish system suitability for protein therapeutic characterization by LC-MS.