Dataset Information

Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies.

ABSTRACT: For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. To support clinical trials based on HLA-presented tumor-associated antigens, in this study the sensitive LC-MS/MS HLA class I antigen identification pipeline was fully validated for our technical equipment according to the current US Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines.The immunopeptidomes of JY cells with or without spiked-in, isotope labeled peptides, of peripheral blood mononuclear cells of healthy volunteers as well as a chronic lymphocytic leukemia and a bladder cancer sample were reliably identified using a data-dependent acquisition method. As the LC-MS/MS pipeline is used for identification purposes, the validation parameters include accuracy, precision, specificity, limit of detection and robustness.

SUBMITTER: Ghosh M

PROVIDER: S-EPMC7050110 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies.

Ghosh Michael M Gauger Marion M Marcu Ana A Nelde Annika A Denk Monika M Schuster Heiko H Rammensee Hans-Georg HG Stevanović Stefan S

Molecular & cellular proteomics : MCP 20200114 3

For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails ...[more]

PMID: 31937595

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Project description:The occurrence of antibiotics in the environment from discharges of wastewater treatment plants (WWTPs) and from the land application of antibiotic-laden manure from animal agriculture is a critical global issue because these residues have been associated with the increased emergence of antibiotic resistance in the environment. In addition, other classes of pharmaceuticals and personal care products (PPCPs) have been found in effluents of municipal WWTPs, many of which persist in the receiving environments. Analysis of antibiotics by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in samples from different countries presents unique challenges that should be considered, from ion suppression due to matrix effects, to lack of available stable isotopically labeled standards for accurate quantification. Understanding the caveats of LC-MS/MS is important for assessing samples with varying matrix complexity. Ion ratios between quantifying and qualifying ions have been used for quality assurance purposes; however, there is limited information regarding the significance of setting criteria for acceptable variabilities in their values in the literature. Upon investigation of 30 pharmaceuticals in WWTP influent and effluent samples, and in receiving surface water samples downstream and upstream of the WWTP, it was found that ion ratios have higher variabilities at lower concentrations in highly complex matrices, and the extent of variability may be exacerbated by the physicochemical properties of the analytes. In setting the acceptable ion ratio criterion, the overall mean, which was obtained by taking the average of the ion ratios at all concentrations (1.56 to 100 ppb), was used. Then, for many of the target analytes included in this study, the tolerance range was set at 40% for WWTP influent samples and 30% for WWTP effluent, upstream, and downstream samples. A separate tolerance range of 80% was set for tetracyclines and quinolones, which showed higher variations in the ion ratios compared to the other analytes.

Project description:Mass spectrometry (MS) is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across human leukocyte antigen (HLA) allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery driven. Hence, data-dependent tandem MS (MS/MS) acquisition (DDA) is widely used, as it generates high-quality references of peptide fingerprints. However, DDA suffers from the stochastic selection of abundant ions that impairs sensitivity and reproducibility. In contrast, in data-independent acquisition (DIA), the systematic fragmentation and acquisition of all fragment ions within given isolation m/z windows yield a comprehensive map for a given sample. However, many DIA approaches commonly require generating comprehensive DDA-based spectrum libraries, which can become impractical for studying noncanonical and personalized neoantigens. Because the amount of HLA peptides eluted from biological samples such as small tissue biopsies is typically not sufficient for acquiring both meaningful DDA data necessary for generating comprehensive spectral libraries and DIA MS measurements, the implementation of DIA in the immunopeptidomics translational research domain has remained limited. We implemented a DIA immunopeptidomics workflow and assessed its sensitivity and accuracy by matching DIA data against libraries with growing complexity-from sample-specific libraries to libraries combining 2 to 40 different immunopeptidomics samples. Analyzing DIA immunopeptidomics data against a complex multi-HLA spectral library resulted in a two-fold increase in peptide identification compared with sample-specific library and in a three-fold increase compared with DDA measurements, yet with no detrimental effect on the specificity. Furthermore, we demonstrated the implementation of DIA for sensitive personalized neoantigen discovery through the analysis of DIA data with predicted MS/MS spectra of clinically relevant HLA ligands. We conclude that a comprehensive multi-HLA library for DIA approach in combination with MS/MS prediction is highly advantageous for clinical immunopeptidomics, especially when low amounts of biological samples are available.

Dataset Information

Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies.

Publications

Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies.

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