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Makey DM, Ruotolo BT. Liquid-phase separations coupled with ion mobility-mass spectrometry for next-generation biopharmaceutical analysis. Expert Rev Proteomics 2024:1-12. [PMID: 38934922 DOI: 10.1080/14789450.2024.2373707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION The pharmaceutical industry continues to expand its search for innovative biotherapeutics. The comprehensive characterization of such therapeutics requires many analytical techniques to fully evaluate critical quality attributes, making analysis a bottleneck in discovery and development timelines. While thorough characterization is crucial for ensuring the safety and efficacy of biotherapeutics, there is a need to further streamline analytical characterization and expedite the overall timeline from discovery to market. AREAS COVERED This review focuses on recent developments in liquid-phase separations coupled with ion mobility-mass spectrometry (IM-MS) for the development and characterization of biotherapeutics. We cover uses of IM-MS to improve the characterization of monoclonal antibodies, antibody-drug conjugates, host cell proteins, glycans, and nucleic acids. This discussion is based on an extensive literature search using Web of Science, Google Scholar, and SciFinder. EXPERT OPINION IM-MS has the potential to enhance the depth and efficiency of biotherapeutic characterization by providing additional insights into conformational changes, post-translational modifications, and impurity profiles. The rapid timescale of IM-MS positions it well to enhance the information content of existing assays through its facile integration with standard liquid-phase separation techniques that are commonly used for biopharmaceutical analysis.
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Affiliation(s)
- Devin M Makey
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics. Mol Cell Proteomics 2024:100800. [PMID: 38880244 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-based proteomics over the past few years. DIA stands out for its ability to systematically sample all peptides in a given mass-to-charge range, allowing an unbiased acquisition of proteomics data. This greatly mitigates the issue of missing values and significantly enhances quantitative accuracy, precision, and reproducibility compared to many traditional methods. This review focuses on the critical role of DIA analysis software tools, primarily focusing on their capabilities and the challenges they address in proteomic research. Advances in MS technology, such as trapped ion mobility spectrometry, or high field asymmetric waveform ion mobility spectrometry require sophisticated analysis software capable of handling the increased data complexity and exploiting the full potential of DIA. We identify and critically evaluate leading software tools in the DIA landscape, discussing their unique features, and the reliability of their quantitative and qualitative outputs. We present the biological and clinical relevance of DIA-MS and discuss crucial publications that paved the way for in-depth proteomic characterization in patient-derived specimens. Furthermore, we provide a perspective on emerging trends in clinical applications and present upcoming challenges including standardization and certification of MS-based acquisition strategies in molecular diagnostics. While we emphasize the need for continuous development of software tools to keep pace with evolving technologies, we advise researchers against uncritically accepting the results from DIA software tools. Each tool may have its own biases, and some may not be as sensitive or reliable as others. Our overarching recommendation for both researchers and clinicians is to employ multiple DIA analysis tools, utilizing orthogonal analysis approaches to enhance the robustness and reliability of their findings.
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Affiliation(s)
- Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Eva Brombacher
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Adrianna Seredynska
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Maximilian Maldacker
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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Welch N, Mishra S, Bellar A, Kannan P, Gopan A, Goudarzi M, King J, Luknis M, Musich R, Agrawal V, Bena J, Koch CJ, Li L, Willard B, Shah YM, Dasarathy S. Differential impact of sex on regulation of skeletal muscle mitochondrial function and protein homeostasis by hypoxia-inducible factor-1α in normoxia. J Physiol 2024; 602:2763-2806. [PMID: 38761133 PMCID: PMC11178475 DOI: 10.1113/jp285339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
Hypoxia-inducible factor (HIF)-1α is continuously synthesized and degraded in normoxia. During hypoxia, HIF1α stabilization restricts cellular/mitochondrial oxygen utilization. Cellular stressors can stabilize HIF1α even during normoxia. However, less is known about HIF1α function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1α function at baseline during normoxia in skeletal muscle. Untargeted multiomics data analyses were followed by experimental validation in differentiated murine myotubes with loss/gain of function and skeletal muscle from mice without/with post-natal muscle-specific Hif1a deletion (Hif1amsd). Mitochondrial oxygen consumption studies using substrate, uncoupler, inhibitor, titration protocols; targeted metabolite quantification by gas chromatography-mass spectrometry; and post-mitotic senescence markers using biochemical assays were performed. Multiomics analyses showed enrichment in mitochondrial and cell cycle regulatory pathways in Hif1a deleted cells/tissue. Experimentally, mitochondrial oxidative functions and ATP content were higher with less mitochondrial free radical generation with Hif1a deletion. Deletion of Hif1a also resulted in higher concentrations of TCA cycle intermediates and HIF2α proteins in myotubes. Overall responses to Hif1amsd were similar in male and female mice, but changes in complex II function, maximum respiration, Sirt3 and HIF1β protein expression and muscle fibre diameter were sex-dependent. Adaptive responses to hypoxia are mediated by stabilization of constantly synthesized HIF1α. Despite rapid degradation, the presence of HIF1α during normoxia contributes to lower mitochondrial oxidative efficiency and greater post-mitotic senescence in skeletal muscle. In vivo responses to HIF1α in skeletal muscle were differentially impacted by sex. KEY POINTS: Hypoxia-inducible factor -1α (HIF1α), a critical transcription factor, undergoes continuous synthesis and proteolysis, enabling rapid adaptive responses to hypoxia by reducing mitochondrial oxygen consumption. In mammals, skeletal muscle is the largest protein store which is determined by a balance between protein synthesis and breakdown and is sensitive to mitochondrial oxidative function. To investigate the functional consequences of transient HIF1α expression during normoxia in the basal state, myotubes and skeletal muscle from male and female mice with HIF1α knockout were studied using complementary multiomics, biochemical and metabolite assays. HIF1α knockout altered the electron transport chain, mitochondrial oxidative function, signalling molecules for protein homeostasis, and post-mitotic senescence markers, some of which were differentially impacted by sex. The cost of rapid adaptive responses mediated by HIF1α is lower mitochondrial oxidative efficiency and post-mitotic senescence during normoxia.
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Affiliation(s)
- Nicole Welch
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Saurabh Mishra
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Annette Bellar
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Pugazhendhi Kannan
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Amrit Gopan
- KEM Hospital, Seth GS Medical College, Mumbai, India
| | - Maryam Goudarzi
- Respiratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jasmine King
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Mathew Luknis
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Ryan Musich
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Vandana Agrawal
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - James Bena
- Quantitative Health, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Ling Li
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Belinda Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Srinivasan Dasarathy
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
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Li K, Teo GC, Yang KL, Yu F, Nesvizhskii AI. diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595875. [PMID: 38854051 PMCID: PMC11160675 DOI: 10.1101/2024.05.25.595875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-MS/MS" spectra, facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass offset searches.
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Affiliation(s)
- Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kevin L. Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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Guo Z, Fan Y, Yu C, Lu H, Zhang Z. GCMSFormer: A Fully Automatic Method for the Resolution of Overlapping Peaks in Gas Chromatography-Mass Spectrometry. Anal Chem 2024; 96:5878-5886. [PMID: 38560891 DOI: 10.1021/acs.analchem.3c05772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Gas chromatography-mass spectrometry (GC-MS) is one of the most important instruments for analyzing volatile organic compounds. However, the complexity of real samples and the limitations of chromatographic separation capabilities lead to coeluting compounds without ideal separation. In this study, a Transformer-based automatic resolution method (GCMSFormer) is proposed to resolve mass spectra from GC-MS peaks in an end-to-end manner, predicting the mass spectra of components directly from the raw overlapping peaks data. Furthermore, orthogonal projection resolution (OPR) was integrated into GCMSFormer to resolve minor components. The GCMSFormer model was trained, validated, and tested using 100,000 augmented data. It achieves 99.88% of the bilingual evaluation understudy (BLEU) value on the test set, significantly higher than the 97.68% BLEU value of the baseline sequence-to-sequence model long short-term memory (LSTM). GCMSFormer was also compared with two nondeep learning resolution tools (MZmine and AMDIS) and two deep learning resolution tools (PARAFAC2 with DL and MSHub/GNPS) on a real plant essential oil GC-MS data set. Their resolution results were compared on evaluation metrics, including the number of compounds resolved, mass spectral match score, correlation coefficient, explained variance, and resolution speed. The results demonstrate that GCMSFormer has better resolution performance, higher automation, and faster resolution speed. In summary, GCMSFormer is an end-to-end, fast, fully automatic, and accurate method for analyzing GC-MS data of complex samples.
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Affiliation(s)
- Zixuan Guo
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, China
| | - Yingjie Fan
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, China
| | - Chuanxiu Yu
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, China
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, China
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Lorca C, Fernández-Rhodes M, Sánchez Milán JA, Mulet M, Elortza F, Ramos-Miguel A, Callado LF, Meana JJ, Mur M, Batalla I, Vilella E, Serra A, Gallart-Palau X. Next-Generation Proteomics of Brain Extracellular Vesicles in Schizophrenia Provide New Clues on the Altered Molecular Connectome. Biomedicines 2024; 12:129. [PMID: 38255234 PMCID: PMC10812948 DOI: 10.3390/biomedicines12010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Extracellular vesicles (EVs) are tiny membranous structures that mediate intercellular communication. The role(s) of these vesicles have been widely investigated in the context of neurological diseases; however, their potential implications in the neuropathology subjacent to human psychiatric disorders remain mostly unknown. Here, by using next-generation discovery-driven proteomics, we investigate the potential role(s) of brain EVs (bEVs) in schizophrenia (SZ) by analyzing these vesicles from the three post-mortem anatomical brain regions: the prefrontal cortex (PFC), hippocampus (HC), and caudate (CAU). The results obtained indicate that bEVs from SZ-affected brains contain region-specific proteins that are associated with abnormal GABAergic and glutamatergic transmission. Similarly, these vesicles from the analyzed regions were implicated in synaptic decay, abnormal brain immunity, neuron structural imbalances, and impaired cell homeostasis. Our findings also provide evidence, for the first time, that networks of molecular exchange (involving the PFC, HC, and CAU) are potentially active and mediated by EVs in non-diseased brains. Additionally, these bEV-mediated networks seem to have become partially reversed and largely disrupted in the brains of subjects affected by SZ. Taken as a whole, these results open the door to the uncovering of new biological markers and therapeutic targets, based on the compositions of bEVs, for the benefit of patients affected by SZ and related psychotic disorders.
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Affiliation(s)
- Cristina Lorca
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), Neuroscience Area, +Pec Proteomics Research Group (+PPRG), University Hospital Arnau de Vilanova (HUAV), 80 Av. Rovira Roure, 25198 Lleida, Spain; (C.L.); (M.F.-R.); (J.A.S.M.); (M.M.)
- Department of Medical Basic Sciences, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), University of Lleida (UdL), 25198 Lleida, Spain
| | - María Fernández-Rhodes
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), Neuroscience Area, +Pec Proteomics Research Group (+PPRG), University Hospital Arnau de Vilanova (HUAV), 80 Av. Rovira Roure, 25198 Lleida, Spain; (C.L.); (M.F.-R.); (J.A.S.M.); (M.M.)
- Department of Medical Basic Sciences, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), University of Lleida (UdL), 25198 Lleida, Spain
| | - Jose Antonio Sánchez Milán
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), Neuroscience Area, +Pec Proteomics Research Group (+PPRG), University Hospital Arnau de Vilanova (HUAV), 80 Av. Rovira Roure, 25198 Lleida, Spain; (C.L.); (M.F.-R.); (J.A.S.M.); (M.M.)
- Department of Medical Basic Sciences, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), University of Lleida (UdL), 25198 Lleida, Spain
| | - María Mulet
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), Neuroscience Area, +Pec Proteomics Research Group (+PPRG), University Hospital Arnau de Vilanova (HUAV), 80 Av. Rovira Roure, 25198 Lleida, Spain; (C.L.); (M.F.-R.); (J.A.S.M.); (M.M.)
- Department of Medical Basic Sciences, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), University of Lleida (UdL), 25198 Lleida, Spain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, Science and Technology Park of Bizkaia, 48160 Derio, Spain;
| | - Alfredo Ramos-Miguel
- Department of Pharmacology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.R.-M.); (L.F.C.); (J.J.M.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Centro de Investigación Biomédica en Red en Salud Mental CIBERSAM, Instituto de Salud Carlos III, 43206 Reus, Spain
| | - Luis F. Callado
- Department of Pharmacology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.R.-M.); (L.F.C.); (J.J.M.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Centro de Investigación Biomédica en Red en Salud Mental CIBERSAM, Instituto de Salud Carlos III, 43206 Reus, Spain
| | - J. Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, 48940 Leioa, Spain; (A.R.-M.); (L.F.C.); (J.J.M.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Centro de Investigación Biomédica en Red en Salud Mental CIBERSAM, Instituto de Salud Carlos III, 43206 Reus, Spain
| | - Maria Mur
- Psychiatry Department, Hospital Universitari Santa Maria, Medicine Department, Universitat de Lleida (UdL), 25198 Lleida, Spain; (M.M.); (I.B.)
| | - Iolanda Batalla
- Psychiatry Department, Hospital Universitari Santa Maria, Medicine Department, Universitat de Lleida (UdL), 25198 Lleida, Spain; (M.M.); (I.B.)
| | - Elisabet Vilella
- Centro de Investigación Biomédica en Red en Salud Mental CIBERSAM, Instituto de Salud Carlos III, 43206 Reus, Spain
- Hospital Universitari Institut Pere Mata, Institut Investigació Sanitària Pere Virgili (IISPV)-CERCA, Universitat Rovira i Virgili, 43206 Reus, Spain
| | - Aida Serra
- Department of Medical Basic Sciences, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), +Pec Proteomics Research Group (+PPRG), University of Lleida (UdL), 25198 Lleida, Spain
| | - Xavier Gallart-Palau
- Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA), Neuroscience Area, +Pec Proteomics Research Group (+PPRG), University Hospital Arnau de Vilanova (HUAV), 80 Av. Rovira Roure, 25198 Lleida, Spain; (C.L.); (M.F.-R.); (J.A.S.M.); (M.M.)
- Department of Psychology, University of Lleida (UdL), 25001 Lleida, Spain
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