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Zhang X, Qi Y, Zhang Q, Liu W. Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy. Biomed Pharmacother 2019; 120:109542. [PMID: 31629254 DOI: 10.1016/j.biopha.2019.109542] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
One of the challenges for cancer vaccine and adoptive T-cell-based immunotherapy is to identify the major histocompatibility complex (MHC)-associated non-self neoantigens recognized by T cells. T cell epitope in silico prediction algorithms have been widely used for neoantigen prediction; nonetheless, this platform lacks the experimental evidence of directly identification of the presented epitopes on cell surface. Currently, mass spectrometry (MS)-based proteomics is an advanced analytical technology for large-scale peptide sequencing, which has become a powerful tool for directly profiling the immunopeptidome presented by MHC molecules. Integrating with next-generation sequencing, proteogenomic analysis provides the "gold standard" for neoantigen identification at protein level. This method discovers the tumor-specific neoantigens derived from somatic mutations, proteasome splicing, noncoding RNA, and post-translational modified antigens. Herein, we review basis of antigen processing and presentation, tumor antigen classification, existing approaches for neoantigen discovery, quantitative proteomics, epitope prediction programs, and advantages and drawbacks of proteomics workflow for MHC immunopeptidome profiling. Furthermore, we summarize 40 recently published reports addressing the fundamental theory, breakthrough and most advanced updates for the mass spectrometry-based neoantigen discovery for cancer immunotherapy.
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Affiliation(s)
- Xiaomei Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Yue Qi
- Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA
| | - Qi Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA.
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202
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Attenuation of Equine Lentivirus Alters Mitochondrial Protein Expression Profile from Inflammation to Apoptosis. J Virol 2019; 93:JVI.00653-19. [PMID: 31391270 DOI: 10.1128/jvi.00653-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/23/2019] [Indexed: 12/18/2022] Open
Abstract
Equine infectious anemia virus (EIAV) is an equine lentivirus similar to HIV-1, targets host immune cells, and causes a life-long infection in horses. The Chinese live EIAV vaccine is attenuated from long-term passaging of a highly virulent strain in vitro The parent pathogenic strain (EIAVDLV34) induces a host inflammatory storm to cause severe pathological injury of animals. However, the vaccine strain (EIAVDLV121) induces a high level of apoptosis to eliminate infected cells. To investigate how these processes are regulated, we performed a comparative proteomics analysis and functional study in equine monocyte-derived macrophages (eMDMs) and found that the divergent mitochondrial protein expression profiles caused by EIAV strains with different virulence led to disparate mitochondrial function, morphology, and metabolism. This in turn promoted the distinct transformation of macrophage inflammatory polarization and intrinsic apoptosis. In EIAVDLV34-infected cells, a high level of glycolysis and increased mitochondrial fragmentation were induced, resulting in the M1-polarized proinflammatory-type transformation of macrophages and the subsequent production of a strong inflammatory response. Following infection with EIAVDLV121, the infected cells were transformed into M2-polarized anti-inflammatory macrophages by inhibition of glycolysis. In this case, a decrease in the mitochondrial membrane potential and impairment of the electron transport chain led to increased levels of apoptosis and reactive oxygen species. These results correlated with viral pathogenicity loss and may help provide an understanding of the key mechanism of lentiviral attenuation.IMPORTANCE Following viral infection, the working pattern and function of the cell can be transformed through the impact on mitochondria. It still unknown how the mitochondrial response changes in cells infected with viruses in the process of virulence attenuation. EIAVDLV121 is the only effective lentiviral vaccine for large-scale use in the world. EIAVDLV34 is the parent pathogenic strain. Unlike EIAVDLV34-induced inflammation storms, EIAVDLV121 can induce high levels of apoptosis. For the first time, we found that, after the mitochondrial protein expression profile is altered, EIAVDLV34-infected cells are transformed into M1-polarized-type macrophages and cause inflammatory injury and that the intrinsic apoptosis pathway is activated in EIAVDLV121-infected cells. These studies shed light on how the mitochondrial protein expression profile changes between cells infected by pathogenic lentivirus strains and cells infected by attenuated lentivirus strains to drive different cellular responses, especially from inflammation to apoptosis.
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203
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Garofalo R, Wohlgemuth I, Pearson M, Lenz C, Urlaub H, Rodnina MV. Broad range of missense error frequencies in cellular proteins. Nucleic Acids Res 2019; 47:2932-2945. [PMID: 30649420 PMCID: PMC6451103 DOI: 10.1093/nar/gky1319] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 12/25/2022] Open
Abstract
Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with missense amino acid substitutions. By analyzing incorporation of near- and non-cognate amino acids in a model protein EF-Tu, we show that most of missense errors are too rare to detect by conventional methods, such as DDA, and are estimated to be between <10−7–10-5 by QRAS. We also observe error hotspots of up to 10−3 for some types of mismatches, including the G-U mismatch. The error frequency depends on the expression level of EF-Tu and, surprisingly, the amino acid position in the protein. QRAS is not restricted to any particular miscoding event, organism, strain or model protein and is a reliable tool to analyze very rare proteogenomic events.
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Affiliation(s)
- Raffaella Garofalo
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Michael Pearson
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany.,Department of Clinical Chemistry, Bioanalytics, University Medical Center Goettingen, Robert-Koch-Straße 40, 37075 Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany.,Department of Clinical Chemistry, Bioanalytics, University Medical Center Goettingen, Robert-Koch-Straße 40, 37075 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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204
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Heller NC, Garrett AM, Merkley ED, Cendrowski SR, Melville AM, Arce JS, Jenson SC, Wahl KL, Jarman KH. Probabilistic Limit of Detection for Ricin Identification Using a Shotgun Proteomics Assay. Anal Chem 2019; 91:12399-12406. [PMID: 31490662 DOI: 10.1021/acs.analchem.9b02721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Robust and highly specific methods for the detection of the protein toxin ricin are of interest to the law enforcement community. In previous studies, methods based on liquid chromatography-tandem mass spectrometry shotgun proteomics have been proposed. The successful implementation of this approach relies on specific data evaluation criteria addressing (1) the quality of the mass spectrometric data, (2) the confidence of peptide identifications (peptide-spectrum matches), and (3) the number and sequence specificity of peptides detected. We present such data evaluation criteria and use a novel approach to establish the limit of detection for this ricin assay. Specifically, we use logistic regression to determine the probability of detection for individual ricin peptides at different concentrations. We then apply basic rules from probability theory, combining these individual peptide probabilities into an overall assay limit of detection. This procedure yields an assay limit of detection for ricin at 42.5 ng on column or 21.25 ng/μL for a 2-μL injection. We also show that, despite the conventional wisdom that detergents are deleterious to mass spectrometric analyses, the presence of Tween-20 did not prevent detection of ricin peptides, and indeed assays performed in buffers that included Tween-20 gave better results than assays performed using other buffer formulations with or without detergent removal.
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Affiliation(s)
| | - Alaine M Garrett
- National Biodefense Analysis and Countermeasures Center , Operated by BNBI for the U.S. Department of Homeland Security Science and Technology Directorate , Frederick , Maryland , United States
| | | | - Stephen R Cendrowski
- National Biodefense Analysis and Countermeasures Center , Operated by BNBI for the U.S. Department of Homeland Security Science and Technology Directorate , Frederick , Maryland , United States
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205
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206
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Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:389-400. [PMID: 31347060 DOI: 10.1007/978-3-030-15950-4_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proteomics is a mass spectrometry-based discipline that aims to analyze proteomes and their functions. Many proteomic studies require well-developed protein databases for reference. However, most proteomes are not well-annotated, aside from model organisms. Techniques like six-frame translation, ab initio gene prediction, and EST databases can aid in maximizing the amount of proteins identified in proteomics experiments, however, each of these has its downfalls. Proteogenomics is a term used to describe the union of proteomics, genomics and transcriptomics to assist in the identification of peptides which would help build better annotated proteome databases. Here, current proteomic and proteogenomic methods will be reviewed, and an example of a comparative proteomics method using lake trout liver samples will be described.
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207
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Abstract
Castration-resistant prostate cancer (CRPC) remains incurable despite the approval of several new treatments. Identification of new biomarkers and therapeutic targets to enable personalization of CRPC therapy, with the aim of maximizing therapeutic responses and minimizing toxicity in patients, is urgently needed. Prostate cancer progression and therapeutic resistance are frequently driven by aberrantly activated kinase signalling pathways that are amenable to pharmacological inhibition. Personalized phosphoproteomics, which enables the analysis of signalling networks in individual tumours, is a promising approach to advance personalized therapy by discovering biomarkers of pathway activity and clinically actionable targets. Several technologies for global and targeted phosphoproteomic analysis exist, each with its own strengths and shortcomings. Global discovery phosphoproteomics is predominantly conducted using liquid chromatography-tandem mass spectrometry coupled with data-dependent or data-independent acquisition technologies. Multiplexed targeted phosphoproteomics can be divided into platforms based on mass spectrometry or antibodies, including selected or parallel reaction monitoring and triggered by offset, multiplexed, accurate mass, high-resolution, absolute quantification (known as TOMAHAQ) or forward-phase or reverse-phase protein arrays, respectively. Several obstacles still need to be overcome before the full potential of phosphoproteomics can be realized in routine clinical practice, but a future phosphoproteomics-centric trans-omic profiling approach should enable optimized personalized CRPC management through improved biomarkers and targeted treatments.
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208
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Drabovich AP, Saraon P, Drabovich M, Karakosta TD, Dimitromanolakis A, Hyndman ME, Jarvi K, Diamandis EP. Multi-omics Biomarker Pipeline Reveals Elevated Levels of Protein-glutamine Gamma-glutamyltransferase 4 in Seminal Plasma of Prostate Cancer Patients. Mol Cell Proteomics 2019; 18:1807-1823. [PMID: 31249104 PMCID: PMC6731075 DOI: 10.1074/mcp.ra119.001612] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Indexed: 11/06/2022] Open
Abstract
Seminal plasma, because of its proximity to prostate, is a promising fluid for biomarker discovery and noninvasive diagnostics. In this study, we investigated if seminal plasma proteins could increase diagnostic specificity of detecting primary prostate cancer and discriminate between high- and low-grade cancers. To select 147 most promising biomarker candidates, we combined proteins identified through five independent experimental or data mining approaches: tissue transcriptomics, seminal plasma proteomics, cell line secretomics, tissue specificity, and androgen regulation. A rigorous biomarker development pipeline based on selected reaction monitoring assays was designed to evaluate the most promising candidates. As a result, we qualified 76, and verified 19 proteins in seminal plasma of 67 negative biopsy and 152 prostate cancer patients. Verification revealed a prostate-specific, secreted and androgen-regulated protein-glutamine gamma-glutamyltransferase 4 (TGM4), which predicted prostate cancer on biopsy and outperformed age and serum Prostate-Specific Antigen (PSA). A machine-learning approach for data analysis provided improved multi-marker combinations for diagnosis and prognosis. In the independent verification set measured by an in-house immunoassay, TGM4 protein was upregulated 3.7-fold (p = 0.006) and revealed AUC = 0.66 for detecting prostate cancer on biopsy for patients with serum PSA ≥4 ng/ml and age ≥50. Very low levels of TGM4 (120 pg/ml) were detected in blood serum. Collectively, our study demonstrated rigorous evaluation of one of the remaining and not well-explored prostate-specific proteins within the medium-abundance proteome of seminal plasma. Performance of TGM4 warrants its further investigation within the distinct genomic subtypes and evaluation for the inclusion into emerging multi-biomarker panels.
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Affiliation(s)
- Andrei P Drabovich
- ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5T 3L9 Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, M5T 3L9 Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada.
| | - Punit Saraon
- ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5T 3L9 Canada
| | | | - Theano D Karakosta
- §Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, M5T 3L9 Canada
| | | | - M Eric Hyndman
- **Department of Surgery, Division of Urology, Southern Alberta Institute of Urology, University of Calgary, Calgary, AB T2V 1P9, Canada
| | - Keith Jarvi
- ‡‡Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada; §§Department of Surgery, Division of Urology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, M5T 3L9 Canada.
| | - Eleftherios P Diamandis
- ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5T 3L9 Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, M5T 3L9 Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada; ‡‡Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5T 3L9 Canada.
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209
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Liu W, Song Q, Cao Y, Zhao Y, Huo H, Wang Y, Song Y, Li J, Tu P. Advanced liquid chromatography-mass spectrometry enables merging widely targeted metabolomics and proteomics. Anal Chim Acta 2019; 1069:89-97. [DOI: 10.1016/j.aca.2019.04.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
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210
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Cao WQ, Jiang BY, Huang JM, Zhang L, Liu MQ, Yao J, Wu MX, Zhang LJ, Kong SY, Wang Y, Yang PY. Straightforward and Highly Efficient Strategy for Hepatocellular Carcinoma Glycoprotein Biomarker Discovery Using a Nonglycopeptide-Based Mass Spectrometry Pipeline. Anal Chem 2019; 91:12435-12443. [DOI: 10.1021/acs.analchem.9b03074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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211
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Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR). Methods Mol Biol 2019. [PMID: 31432427 DOI: 10.1007/978-1-4939-9706-0_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Every year, a large number of published studies present biomarkers for various neurological disorders. Many of these studies are based on mass spectrometry proteomics data and describe comparison of the abundance of proteins in cerebrospinal fluid between two or more disease groups. As the number of such studies is growing, it is no longer straightforward to obtain an overview of which specific proteins are increased or decreased between the numerous relevant diseases and their many subcategories, or to see the larger picture or trends between related diseases. To alleviate this situation, we therefore mined the literature for mass spectrometry-based proteomics studies including quantitative protein data from cerebrospinal fluid of patients with multiple sclerosis, Alzheimer's disease, and Parkinson's disease and organized the extracted data in the Cerebrospinal Fluid Proteome Resource (CSF-PR). CSF-PR is freely available online at http://probe.uib.no/csf-pr , is highly interactive, and allows for easy navigation, visualization, and export of the published scientific data. This chapter will guide the user through some of the most important features of the tool and show examples of the suggested use cases.
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212
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Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FHT. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat Methods 2019; 16:743-749. [PMID: 31363225 PMCID: PMC6837886 DOI: 10.1038/s41592-019-0495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Cellular behavior is controlled by the interplay of diverse biomolecules. Most experimental methods, however, can only monitor a single molecule class or reaction type at a time. We developed an in vitro nuclear magnetic resonance spectroscopy (NMR) approach, which permitted dynamic quantification of an entire 'heterotypic' network-simultaneously monitoring three distinct molecule classes (metabolites, proteins and RNA) and all elementary reaction types (bimolecular interactions, catalysis, unimolecular changes). Focusing on an eight-reaction co-transcriptional RNA folding network, in a single sample we recorded over 35 time points with over 170 observables each, and accurately determined five core reaction constants in multiplex. This reconstruction revealed unexpected cross-talk between the different reactions. We further observed dynamic phase-separation in a system of five distinct RNA-binding domains in the course of the RNA transcription reaction. Our Systems NMR approach provides a deeper understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of 'omics'.
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Affiliation(s)
- Yaroslav Nikolaev
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
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213
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Absolute Quantitation of Proteins by Acid Hydrolysis Combined with Amino Acid Detection by Mass Spectrometry. Methods Mol Biol 2019. [PMID: 31347106 DOI: 10.1007/978-1-4939-9639-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Amino acid analysis is among the most accurate methods for absolute quantification of proteins and peptides. Here we combine acid hydrolysis with the addition of isotopically labeled standard amino acids and analysis by mass spectrometry for accurate and sensitive protein quantitation. Quantitation of less than 10 fmol of protein standards with errors below 10% has been demonstrated using this method.
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214
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Saleh S, Staes A, Deborggraeve S, Gevaert K. Targeted Proteomics for Studying Pathogenic Bacteria. Proteomics 2019; 19:e1800435. [DOI: 10.1002/pmic.201800435] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/04/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Sara Saleh
- Department of Biomedical SciencesInstitute of Tropical Medicine B‐2000 Antwerp Belgium
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
| | - An Staes
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
| | - Stijn Deborggraeve
- Department of Biomedical SciencesInstitute of Tropical Medicine B‐2000 Antwerp Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology B‐9000 Ghent Belgium
- Department of Biomolecular MedicineGhent University B‐9000 Ghent Belgium
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215
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Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater. Sci Rep 2019; 9:10604. [PMID: 31332202 PMCID: PMC6646388 DOI: 10.1038/s41598-019-46901-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022] Open
Abstract
Dehalococcoides mccartyi (Dhc) bacterial strains expressing active reductive dehalogenase (RDase) enzymes play key roles in the transformation and detoxification of chlorinated pollutants, including chlorinated ethenes. Site monitoring regimes traditionally rely on qPCR to assess the presence of Dhc biomarker genes; however, this technique alone cannot directly inform about dechlorination activity. To supplement gene-centric approaches and provide a more reliable proxy for dechlorination activity, we sought to demonstrate a targeted proteomics approach that can characterize Dhc mediated dechlorination in groundwater contaminated with chlorinated ethenes. Targeted peptide selection was conducted in axenic cultures of Dhc strains 195, FL2, and BAV1. These experiments yielded 37 peptides from housekeeping and structural proteins (i.e., GroEL, EF-TU, rpL7/L2 and the S-layer), as well as proteins involved in the reductive dechlorination activity (i.e., FdhA, TceA, and BvcA). The application of targeted proteomics to a defined bacterial consortium and contaminated groundwater samples resulted in the detection of FdhA peptides, which revealed active dechlorination with Dhc strain-level resolution, and the detection of RDases peptides indicating specific reductive dechlorination steps. The results presented here show that targeted proteomics can be applied to groundwater samples and provide protein level information about Dhc dechlorination activity.
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216
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Murray LA, Combs AN, Rekapalli P, Cristea IM. Methods for characterizing protein acetylation during viral infection. Methods Enzymol 2019; 626:587-620. [PMID: 31606092 DOI: 10.1016/bs.mie.2019.06.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lysine acetylation is a prevalent posttranslational modification that acts as a regulator of protein function, subcellular localization, and interactions. A growing body of work has highlighted the importance of temporal alterations in protein acetylation during infection with a range of human viruses. It has become clear that both cellular and viral proteins are decorated by lysine acetylations, and that these modifications contribute to core host defense and virus replication processes. Further defining the extent and dynamics of protein acetylation events during the progression of an infection can provide an important new perspective on the intricate mechanisms underlying the biology and pathogenesis of virus infections. Here, we provide protocols for identifying, quantifying, and probing the regulation of lysine acetylations during viral infection. We describe the use of acetyl-lysine immunoaffinity purification and quantitative mass spectrometry for assessing the cellular acetylome at different stages of an infection. As an alternative to traditional antibody-mediated western blotting, we discuss the benefits of targeted mass spectrometry approaches for detecting and quantifying site-specific acetylations on proteins of interest. Specifically, we provide a protocol using parallel reaction monitoring (PRM). We further discuss experimental considerations that are specific to studying viral infections. Finally, we provide a brief overview of the types of assays that can be employed to characterize the function of an acetylation event in the context of infection. As a method to interrogate the regulation of acetylation, we describe the Fluor de Lys assay for monitoring the enzymatic activities of deacetylases.
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Affiliation(s)
- Laura A Murray
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States
| | - Ashton N Combs
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States
| | - Pranav Rekapalli
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States.
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217
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Iacobucci C, Suder P, Bodzon‐Kulakowska A, Antolak A, Silberring J, Smoluch M, Mielczarek P, Grasso G, Pawlaczyk A, Szynkowska MI, Tuccitto N, Stefanowicz P, Szewczuk Z, Natale G. Instrumentation. Mass Spectrom (Tokyo) 2019. [DOI: 10.1002/9781119377368.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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218
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Lindoso RS, Kasai-Brunswick TH, Monnerat Cahli G, Collino F, Bastos Carvalho A, Campos de Carvalho AC, Vieyra A. Proteomics in the World of Induced Pluripotent Stem Cells. Cells 2019; 8:cells8070703. [PMID: 31336746 PMCID: PMC6678893 DOI: 10.3390/cells8070703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 02/05/2023] Open
Abstract
Omics approaches have significantly impacted knowledge about molecular signaling pathways driving cell function. Induced pluripotent stem cells (iPSC) have revolutionized the field of biological sciences and proteomics and, in particular, has been instrumental in identifying key elements operating during the maintenance of the pluripotent state and the differentiation process to the diverse cell types that form organisms. This review covers the evolution of conceptual and methodological strategies in proteomics; briefly describes the generation of iPSC from a historical perspective, the state-of-the-art of iPSC-based proteomics; and compares data on the proteome and transcriptome of iPSC to that of embryonic stem cells (ESC). Finally, proteomics of healthy and diseased cells and organoids differentiated from iPSC are analyzed.
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Affiliation(s)
- Rafael Soares Lindoso
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
| | - Tais H Kasai-Brunswick
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
| | - Gustavo Monnerat Cahli
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-598, Brazil
| | - Federica Collino
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy
| | - Adriana Bastos Carvalho
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
| | - Antonio Carlos Campos de Carvalho
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil.
| | - Adalberto Vieyra
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil.
- Graduate Program in Translational Biomedicine, Grande Rio University, Duque de Caxias 25071-202, Brazil.
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219
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TAKAHASHI C, YAZAKI T, SUGIYAMA N, ISHIHAMA Y. Selected Reaction Monitoring of Kinase Activity-Targeted Phosphopeptides. CHROMATOGRAPHY 2019. [DOI: 10.15583/jpchrom.2019.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Tatsuya YAZAKI
- Graduate School of Pharmaceutical Science, Kyoto University
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220
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Nguyen CDL, Malchow S, Reich S, Steltgens S, Shuvaev KV, Loroch S, Lorenz C, Sickmann A, Knobbe-Thomsen CB, Tews B, Medenbach J, Ahrends R. A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells. Sci Rep 2019; 9:8836. [PMID: 31222112 PMCID: PMC6586633 DOI: 10.1038/s41598-019-45237-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/31/2019] [Indexed: 12/27/2022] Open
Abstract
Many cellular events are driven by changes in protein expression, measurable by mass spectrometry or antibody-based assays. However, using conventional technology, the analysis of transcription factor or membrane receptor expression is often limited by an insufficient sensitivity and specificity. To overcome this limitation, we have developed a high-resolution targeted proteomics strategy, which allows quantification down to the lower attomol range in a straightforward way without any prior enrichment or fractionation approaches. The method applies isotope-labeled peptide standards for quantification of the protein of interest. As proof of principle, we applied the improved workflow to proteins of the unfolded protein response (UPR), a signaling pathway of great clinical importance, and could for the first time detect and quantify all major UPR receptors, transducers and effectors that are not readily detectable via antibody-based-, SRM- or conventional PRM assays. As transcription and translation is central to the regulation of UPR, quantification and determination of protein copy numbers in the cell is important for our understanding of the signaling process as well as how pharmacologic modulation of these pathways impacts on the signaling. These questions can be answered using our newly established workflow as exemplified in an experiment using UPR perturbation in a glioblastoma cell lines.
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Affiliation(s)
- Chi D L Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Stefan Reich
- Translational Control Group, Biochemistry I, University of Regensburg, 93053, Regensburg, Germany
| | - Sascha Steltgens
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Konstantin V Shuvaev
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Christin Lorenz
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Medizinische Fakultät, Ruhr-Universität Bochum, Bochum, 44801, Germany.,College of Physical Sciences, University of Aberdeen, Old Aberdeen, AB24 3UE, UK
| | - Christiane B Knobbe-Thomsen
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Björn Tews
- Schaller Research Group, University of Heidelberg and DKFZ, 69120, Heidelberg, Germany.,Molecular Mechanisms of Tumor Invasion, DKFZ, 69120, Heidelberg, Germany
| | - Jan Medenbach
- Translational Control Group, Biochemistry I, University of Regensburg, 93053, Regensburg, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.
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221
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Edfors F, Forsström B, Vunk H, Kotol D, Fredolini C, Maddalo G, Svensson AS, Boström T, Tegel H, Nilsson P, Schwenk JM, Uhlen M. Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. J Proteome Res 2019; 18:2706-2718. [PMID: 31094526 DOI: 10.1021/acs.jproteome.8b00924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.
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Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Björn Forsström
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Helian Vunk
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - David Kotol
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Gianluca Maddalo
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Anne-Sophie Svensson
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Tove Boström
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Atlas Antibodies AB , SE - 114 21 Stockholm , Sweden
| | - Hanna Tegel
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Peter Nilsson
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Department of Neuroscience - Karolinska Institute , SE - 171 65 Solna , Sweden.,Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , DK - 2970 Hørsholm , Denmark
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222
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Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nat Commun 2019; 10:2524. [PMID: 31175306 PMCID: PMC6555818 DOI: 10.1038/s41467-019-10513-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/16/2019] [Indexed: 01/18/2023] Open
Abstract
Deterioration of biomolecules in clinical tissues is an inevitable pre-analytical process, which affects molecular measurements and thus potentially confounds conclusions from cohort analyses. Here, we investigate the degradation of mRNA and protein in 68 pairs of adjacent prostate tissue samples using RNA-Seq and SWATH mass spectrometry, respectively. To objectively quantify the extent of protein degradation, we develop a numerical score, the Proteome Integrity Number (PIN), that faithfully measures the degree of protein degradation. Our results indicate that protein degradation only affects 5.9% of the samples tested and shows negligible correlation with mRNA degradation in the adjacent samples. These findings are confirmed by independent analyses on additional clinical sample cohorts and across different mass spectrometric methods. Overall, the data show that the majority of samples tested are not compromised by protein degradation, and establish the PIN score as a generic and accurate indicator of sample quality for proteomic analyses. Protein degradation in clinical samples is largely unexplored. Here, the authors analyze the transcriptome and proteome of clinical tissue samples and develop an algorithm to assess protein degradation, showing that protein degradation is negligible in most tissue samples and does not correlate with transcript degradation.
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223
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Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
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224
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Complementary use of mass spectrometry and cryo-electron microscopy to assess the maturity of live attenuated dengue vaccine viruses. Vaccine 2019; 37:3580-3587. [DOI: 10.1016/j.vaccine.2019.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/25/2019] [Accepted: 05/05/2019] [Indexed: 01/19/2023]
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225
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Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods 2019; 16:509-518. [DOI: 10.1038/s41592-019-0426-7] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/18/2019] [Indexed: 11/08/2022]
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226
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Feasibility of Utilizing Stable-Isotope Dimethyl Labeling in Liquid Chromatography⁻Tandem Mass Spectrometry-Based Determination for Food Allergens-Case of Kiwifruit. Molecules 2019; 24:molecules24101920. [PMID: 31109069 PMCID: PMC6571768 DOI: 10.3390/molecules24101920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 12/28/2022] Open
Abstract
Stable-isotope dimethyl labeling is a highly reactive and cost-effective derivatization procedure that could be utilized in proteomics analysis. In this study, a liquid chromatography- tandem mass spectrometry in multiple reaction monitoring mode (LC-MS-MRM) platform for the quantification of kiwi allergens was first developed using this strategy. Three signature peptides for target allergens Act d 1, Act d 5, and Act d 11 were determined and were derivatized with normal and deuterated formaldehyde as external calibrants and internal standards, respectively. The results showed that sample preparation with the phenol method provided comprehensive protein populations. Recoveries at four different levels ranging from 72.5-109.3% were achieved for the H-labeled signature peptides of Act d 1 (SPA1-H) and Act d 5 (SPA5-H) with precision ranging from 1.86-9.92%. The limit of quantification (LOQ) was set at 8 pg mL-1 for SPA1-H and at 8 ng mL-1 for SPA5-H. The developed procedure was utilized to analyze seven kinds of hand-made kiwi foods containing 0.0175-0.0515 mg g-1 of Act d 1 and 0.0252-0.0556 mg g-1 of Act d 5. This study extended the applicability of stable-isotope dimethyl labeling to the economical and precise determination of food allergens and peptides.
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227
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Koike H, Kanda M, Hayashi H, Matsushima Y, Ohba Y, Nakagawa Y, Nagano C, Sekimura K, Hirai A, Shindo T, Otsuka K, Kamiie J, Sasamoto T, Hashimoto T. Quantification of staphylococcal enterotoxin type A in cow milk by using a stable isotope-labelled peptide via liquid chromatography-tandem mass spectrometry. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1098-1108. [PMID: 31094669 DOI: 10.1080/19440049.2019.1615641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, the staphylococcal enterotoxin type A (SEA) contaminant was quantified in cow milk by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with the use of a stable isotope-labelled peptide of SEA as an internal standard. SEA was cleaned up in a two-step process that included pH control and trichloroacetic acid (TCA) precipitation. The pH control phase eliminated other proteins. TCA precipitation cleaned up SEA without special equipment. An appropriate enzyme-to-protein ratio maximised tryptic digestion. A desalting process guaranteed the stable retention of SEA-digested peptides. The coverage of amino-acid sequences (>10%) clearly identified the toxin's presence. SEA was accurately quantified using LC-MS/MS based on a multiple-reaction monitoring mode. The developed method was validated based on spiked recovery tests at 50 and 100 µg kg-1 conducted with two samples collected on a daily basis for five days based on Japanese validation guidelines. The new method exhibited good accuracy which ranged from 80% to 82%. The relative standard deviations of repeatability were 13-14% and the relative standard deviations of within-laboratory reproducibility were 13-18%. These standard deviations satisfied the criteria of the Japanese validation guidelines. The quantification limit was estimated to be 10 µg kg-1.
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Affiliation(s)
- Hiroshi Koike
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Maki Kanda
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Hiroshi Hayashi
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yoko Matsushima
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yumi Ohba
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yukiko Nakagawa
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Chieko Nagano
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Kotaro Sekimura
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Akihiko Hirai
- b Department of Microbiology , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Tetsuya Shindo
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Kenji Otsuka
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Junichi Kamiie
- c Laboratory of Veterinary Pathology, School of Veterinary Medicine , Azabu University , Sagamihara , Japan
| | - Takeo Sasamoto
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Tsuneo Hashimoto
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
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228
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Pappireddi N, Martin L, Wühr M. A Review on Quantitative Multiplexed Proteomics. Chembiochem 2019; 20:1210-1224. [PMID: 30609196 PMCID: PMC6520187 DOI: 10.1002/cbic.201800650] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/27/2018] [Indexed: 12/11/2022]
Abstract
Over the last few decades, mass spectrometry-based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which, in a single experiment, enabled the global quantification of proteins across multiple samples. Herein, these methods are referred to as multiplexed proteomics. The principles, advantages, and drawbacks of various multiplexed proteomics techniques are discussed and compared with alternative approaches. We also discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high-quality quantification of very low abundance proteins across multiple conditions. Lastly, we suggest that fusing multiplexed proteomics with data-independent acquisition approaches might enable the comparison of hundreds of different samples without missing values, while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.
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Affiliation(s)
- Nishant Pappireddi
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- The Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- The Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- The Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
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229
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Naegeli A, Bratanis E, Karlsson C, Shannon O, Kalluru R, Linder A, Malmström J, Collin M. Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis. J Exp Med 2019; 216:1615-1629. [PMID: 31092533 PMCID: PMC6605743 DOI: 10.1084/jem.20190293] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 12/19/2022] Open
Abstract
EndoS from Streptococcus pyogenes hydrolyzes the functionally important glycan on the Fc portion of IgG during infections in humans. In mice with IgG mediated immunity against the M1 protein on the bacteria, EndoS is a virulence factor. Streptococcus pyogenes (Group A streptococcus; GAS) is a human pathogen causing diseases from uncomplicated tonsillitis to life-threatening invasive infections. GAS secretes EndoS, an endoglycosidase that specifically cleaves the conserved N-glycan on IgG antibodies. In vitro, removal of this glycan impairs IgG effector functions, but its relevance to GAS infection in vivo is unclear. Using targeted mass spectrometry, we characterized the effects of EndoS on host IgG glycosylation during the course of infections in humans. Substantial IgG glycan hydrolysis occurred at the site of infection and systemically in the severe cases. We demonstrated decreased resistance to phagocytic killing of GAS lacking EndoS in vitro and decreased virulence in a mouse model of invasive infection. This is the first described example of specific bacterial IgG glycan hydrolysis during infection and thereby verifies the hypothesis that EndoS modifies antibodies in vivo. This mechanisms of immune evasion could have implications for treatment of severe GAS infections and for future efforts at vaccine development.
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Affiliation(s)
- Andreas Naegeli
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Eleni Bratanis
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Christofer Karlsson
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Oonagh Shannon
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Raja Kalluru
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Adam Linder
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Johan Malmström
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Mattias Collin
- Faculty of Medicine, Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
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230
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Cui YH, Liu Q, Xu ZY, Li JH, Hu ZX, Li MJ, Zheng WL, Li ZJ, Pan HW. Quantitative proteomic analysis of human corneal epithelial cells infected with HSV-1. Exp Eye Res 2019; 185:107664. [PMID: 31085182 DOI: 10.1016/j.exer.2019.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/22/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
HSV-1 infection in corneal epithelium initiates the process of herpes simplex keratitis. We investigated the dynamic change of the host proteins in corneal epithelial cells infected with HSV-1 to understand the virus-host interaction. iTRAQ coupled with LC-MS/MS was applied to quantitatively analyze the protein profiles in HSV-1 infected corneal epithelial cells at 6 and 24 h post-infection (hpi), and the results were validated by multiple reaction monitoring (MRM). We also performed bioinformatic analysis to investigate the potentially important signal pathways and protein interaction networks in the host response to HSV-1 infection. We identified 292 proteins were up-regulated and 168 proteins were down-regulated at 6 hpi, while 132 proteins were up-regulated and 89 proteins were down-regulated at 24 hpi, which were validated by MRM analysis. We found the most enriched GO terms were translational initiation, cytosol, poly(A) RNA binding, mRNA splicing via spliceosome and extracellular exosome for the dysregulated proteins. KEGG pathway analysis revealed significant changes in metabolism pathway characterized by decreased tricarboxylic acid cycle activity and increased glycolysis. Proteins interaction network analysis indicated several proteins including P4HB, ACLY, HSP90AA1 and EIF4A3, might be critical proteins in the host-virus response. Our study for the first time analyzed the protein profile of HSV-1 infected primary corneal epithelial cells by quantitative proteomics. These findings help to better understand the host-virus interaction and the pathogenesis of herpes simplex keratitis.
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Affiliation(s)
- Yu-Hong Cui
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China; Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qun Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhi-Yi Xu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China; Department of Ophthalmology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jia-Hui Li
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China
| | - Zi-Xuan Hu
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China
| | - Mei-Jun Li
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China; Department of Ophthalmology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wen-Lin Zheng
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China
| | - Zhi-Jie Li
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
| | - Hong-Wei Pan
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China; Department of Ophthalmology, The First Affiliated Hospital, Jinan University, Guangzhou, China; Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China.
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231
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Zhou M, Duong DM, Johnson ECB, Dai J, Lah JJ, Levey AI, Seyfried NT. Mass Spectrometry-Based Quantification of Tau in Human Cerebrospinal Fluid Using a Complementary Tryptic Peptide Standard. J Proteome Res 2019; 18:2422-2432. [PMID: 30983353 DOI: 10.1021/acs.jproteome.8b00920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here, we report a method for the generation of complementary tryptic (CompTryp) isotope-labeled peptide standards for the relative and absolute quantification of proteins by mass spectrometry (MS). These standards can be digested in parallel with either trypsin (Tryp-C) or trypsin-N (Tryp-N), to generate peptides that significantly overlap in primary sequence having C- and N-terminal arginine and lysine residues, respectively. As a proof of concept, an isotope-labeled CompTryp standard was synthesized for Tau, a well-established biomarker in Alzheimer's disease (AD), which included both N- and C-terminal heavy isotope-labeled (15N and 13C) arginine residues and flanking amino acid sequences to monitor proteolytic digestion. Despite having the exact same mass, the N- and C-terminal heavy Tau peptides are distinguishable by retention time and MS/MS fragmentation profiles. The isotope-labeled Tau CompTryp standard was added to human cerebrospinal fluid (CSF) followed by parallel digestion with Tryp-N and Tryp-C. The native and isotope-labeled peptide pairs were quantified by parallel reaction monitoring (PRM) in a single assay. Notably, both tryptic peptides were effective at quantifying Tau in human CSF, and both showed a significant difference in CSF Tau levels between AD and controls. Treating these CompTryp Tau peptide measurements as independent replicates also improved the coefficient of variation and correlation with Tau immunoassays. More broadly, we propose that CompTryp standards can be generated for any protein of interest, providing an efficient method to improve the robustness and reproducibility for MS analysis of clinical and research samples.
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Affiliation(s)
| | | | | | - Jingting Dai
- Department of Neurology, Second Xiangya Hospital , Central South University , Changsha , Hunan 410078 , China
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232
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Taga Y, Iwasaki Y, Shigemura Y, Mizuno K. Improved in Vivo Tracking of Orally Administered Collagen Hydrolysate Using Stable Isotope Labeling and LC-MS Techniques. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4671-4678. [PMID: 30929424 DOI: 10.1021/acs.jafc.9b00571] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Collagen-derived hydroxyproline (Hyp)-containing oligopeptides, known to have various physiological functions, are detected in blood at markedly higher concentrations after oral ingestion of collagen hydrolysate. Monitoring the absorption and metabolism of the bioactive peptides is essential to investigate the beneficial effects of collagen hydrolysate. We previously developed an internal standard mixture by sequential protease digestion of stable isotope-labeled collagen, which enabled highly accurate quantitation of collagen-derived oligopeptides by liquid chromatography-mass spectrometry (LC-MS). However, the use of proteases caused a profound imbalance in the generated peptides. Here, we employed partial acid hydrolysis to achieve more efficient and balanced peptide generation. Various stable isotope-labeled oligopeptides were detected after 0.5 h acid hydrolysis, and marked enhancement of peptide generation compared with the previous enzymatic method was observed, especially for Hyp-Gly (27.8 ± 0.6 ng/μg vs 0.231 ± 0.02 ng/μg). The acid hydrolysate was then heated to generate labeled cyclic dipeptides. Using the novel internal standard mixture in LC-MS, we were able to simultaneously quantitate 23 collagen-derived oligopeptides in human plasma and urine after oral administration of collagen hydrolysate.
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Affiliation(s)
- Yuki Taga
- Nippi Research Institute of Biomatrix , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan
| | - Yu Iwasaki
- Department of Nutrition, Faculty of Domestic Science , Tokyo Kasei University , 1-18-1 Kaga , Itabashi-ku, Tokyo 173-8602 , Japan
| | - Yasutaka Shigemura
- Department of Nutrition, Faculty of Domestic Science , Tokyo Kasei University , 1-18-1 Kaga , Itabashi-ku, Tokyo 173-8602 , Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix , 520-11 Kuwabara , Toride , Ibaraki 302-0017 , Japan
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233
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Lee J, Kim H, Sohn A, Yeo I, Kim Y. Cost-Effective Automated Preparation of Serum Samples for Reproducible Quantitative Clinical Proteomics. J Proteome Res 2019; 18:2337-2345. [PMID: 30985128 DOI: 10.1021/acs.jproteome.9b00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reproducible sample preparation remains a significant challenge in large-scale clinical research using selected reaction monitoring-mass spectrometry (SRM-MS), which enables a highly sensitive multiplexed assay. Although automated liquid-handling platforms have tremendous potential for addressing this issue, the high cost of their consumables is a drawback that renders routine operation expensive. Here we evaluated the performance of a liquid-handling platform in preparing serum samples compared with a standard experiment while reducing the outlay for consumables, such as tips, wasted reagents, and reagent stock plates. A total of 26 multiplex assays were quantified by SRM-MS using four sets of 24 pooled human serum aliquots; the four sets used a fixed number (1, 4, 8, or 24) of tips to dispense digestion reagents. This study demonstrated that the use of 4 or 8 tips is comparable to 24 tips (standard experiment), as evidenced by their coefficients of variation: 13.5% (for 4 and 8 tips) versus 12.0% (24 tips). Thus we can save 37% of the total experimental cost compared with the standard experiment, maintaining nearly equivalent reproducibility. The routine operation of cost-effective liquid-handling platforms can enable researchers to process large-scale samples with high throughput, adding credibility to their findings by minimizing human error.
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Affiliation(s)
| | - Hyunsoo Kim
- Institute of Medical and Biological Engineering, MRC , Seoul National University , Seoul , Korea
| | | | - Injoon Yeo
- Interdisciplinary Program of Bioengineering , Seoul National University College of Engineering , Seoul , Korea
| | - Youngsoo Kim
- Institute of Medical and Biological Engineering, MRC , Seoul National University , Seoul , Korea.,Interdisciplinary Program of Bioengineering , Seoul National University College of Engineering , Seoul , Korea
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234
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Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol 2019; 16:256-268. [PMID: 30487530 PMCID: PMC6448780 DOI: 10.1038/s41571-018-0135-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer genomics research aims to advance personalized oncology by finding and targeting specific genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients on the basis of the findings of tumour genome sequencing. This personalized approach has prolonged the survival of subsets of patients with cancer. However, many patients do not respond to the predicted therapies based on the genomic profiles of their tumours. Furthermore, studies pairing genomic and proteomic analyses of samples from the same tumours have shown that the proteome contains novel information that cannot be discerned through genomic analysis alone. This observation has led to the concept of proteogenomics, in which both types of data are leveraged for a more complete view of tumour biology that might enable patients to be more successfully matched to effective treatments than they would using genomics alone. In this Perspective, we discuss the added value of proteogenomics over the current genome-driven approach to the clinical characterization of cancers and summarize current efforts to incorporate targeted proteomic measurements based on selected/multiple reaction monitoring (SRM/MRM) mass spectrometry into the clinical laboratory to facilitate clinical proteogenomics.
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Affiliation(s)
- Bing Zhang
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Cell, Development and Cancer Biology, Oregon Health & Sciences University, Portland, OR, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
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235
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Menneteau T, Fabre B, Garrigues L, Stella A, Zivkovic D, Roux-Dalvai F, Mouton-Barbosa E, Beau M, Renoud ML, Amalric F, Sensébé L, Gonzalez-de-Peredo A, Ader I, Burlet-Schiltz O, Bousquet MP. Mass Spectrometry-based Absolute Quantification of 20S Proteasome Status for Controlled Ex-vivo Expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells. Mol Cell Proteomics 2019; 18:744-759. [PMID: 30700495 PMCID: PMC6442357 DOI: 10.1074/mcp.ra118.000958] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/21/2019] [Indexed: 01/18/2023] Open
Abstract
The proteasome controls a multitude of cellular processes through protein degradation and has been identified as a therapeutic target in oncology. However, our understanding of its function and the development of specific modulators are hampered by the lack of a straightforward method to determine the overall proteasome status in biological samples. Here, we present a method to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes based on a robust, absolute SILAC-based multiplexed LC-Selected Reaction Monitoring (SRM) quantitative mass spectrometry assay with high precision, accuracy, and sensitivity. The method was initially optimized and validated by comparison with a reference ELISA assay and by analyzing the dynamics of catalytic subunits in HeLa cells following IFNγ-treatment and in range of human tissues. It was then successfully applied to reveal IFNγ- and O2-dependent variations of proteasome status during primary culture of Adipose-derived-mesenchymal Stromal/Stem Cells (ADSCs). The results show the critical importance of controlling the culture conditions during cell expansion for future therapeutic use in humans. We hypothesize that a shift from the standard proteasome to the immunoproteasome could serve as a predictor of immunosuppressive and differentiation capacities of ADSCs and, consequently, that quality control should include proteasomal quantification in addition to examining other essential cell parameters. The method presented also provides a new powerful tool to conduct more individualized protocols in cancer or inflammatory diseases where selective inhibition of the immunoproteasome has been shown to reduce side effects.
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Affiliation(s)
- Thomas Menneteau
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;; §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Bertrand Fabre
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Luc Garrigues
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Alexandre Stella
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Dusan Zivkovic
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Florence Roux-Dalvai
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Mathilde Beau
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Marie-Laure Renoud
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - François Amalric
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Luc Sensébé
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Anne Gonzalez-de-Peredo
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Isabelle Ader
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;.
| | - Marie-Pierre Bousquet
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;.
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236
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Müller F, Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J. Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry. Mol Cell Proteomics 2019; 18:786-795. [PMID: 30651306 PMCID: PMC6442367 DOI: 10.1074/mcp.tir118.001276] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Indexed: 11/24/2022] Open
Abstract
Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.
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Affiliation(s)
- Fränze Müller
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Lars Kolbowski
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany;; §Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
| | | | | | - Juri Rappsilber
- From the ‡Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany;; §Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom;.
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237
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Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
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238
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Wagner R, Dittrich J, Thiery J, Ceglarek U, Burkhardt R. Simultaneous LC/MS/MS quantification of eight apolipoproteins in normal and hypercholesterolemic mouse plasma. J Lipid Res 2019; 60:900-908. [PMID: 30723096 PMCID: PMC6446716 DOI: 10.1194/jlr.d084301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Apolipoproteins are major structural and functional constituents of lipoprotein particles. As modulators of lipid metabolism, adipose tissue biology, and energy homeostasis, apolipoproteins may serve as biomarkers or potential therapeutic targets for cardiometabolic diseases. Mice are the preferred model to study metabolic disease and CVD, but a comprehensive method to quantify circulating apolipoproteins in mice is lacking. We developed and validated a targeted proteomics assay to quantify eight apolipoproteins in mice via proteotypic signature peptides and corresponding stable isotope-labeled analogs. The LC/MS/MS method requires only a 3 µl sample volume to simultaneously determine mouse apoA-I, apoA-II, apoA-IV, apoB-100, total apoB, apoC-I, apoE, and apoJ concentrations. ApoB-48 concentrations can be calculated by subtracting apoB-100 from total apoB. After we established the analytic performance (sensitivity, linearity, and imprecision) and compared results for selected apolipoproteins against immunoassays, we applied the method to profile apolipoprotein levels in plasma and isolated HDL from normocholesterolemic C57BL/6 mice and from hypercholesterolemic Ldl-receptor- and Apoe-deficient mice. In conclusion, we present a robust, quantitative LC/MS/MS method for the multiplexed analysis of eight apolipoproteins in mice. This assay can be applied to investigate the effects of genetic manipulation or dietary interventions on apolipoprotein levels in plasma and isolated lipoprotein fractions.
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Affiliation(s)
- Richard Wagner
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Germany.
| | - Ralph Burkhardt
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany.
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239
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Li Q, Kailemia MJ, Merleev AA, Xu G, Serie D, Danan LM, Haj FG, Maverakis E, Lebrilla CB. Site-Specific Glycosylation Quantitation of 50 Serum Glycoproteins Enhanced by Predictive Glycopeptidomics for Improved Disease Biomarker Discovery. Anal Chem 2019; 91:5433-5445. [DOI: 10.1021/acs.analchem.9b00776] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Muchena J. Kailemia
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Alexander A. Merleev
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California 95817, United States
| | - Gege Xu
- Venn Biosciences Corporation, 800 Chesapeake Dr., Redwood City, California 94063, United States
| | - Daniel Serie
- Venn Biosciences Corporation, 800 Chesapeake Dr., Redwood City, California 94063, United States
| | - Lieza M. Danan
- Venn Biosciences Corporation, 800 Chesapeake Dr., Redwood City, California 94063, United States
| | - Fawaz G. Haj
- Department of Nutrition, University of California, One Shields Avenue, Davis, California 95616, United States
- Department of Internal Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of California Davis, Sacramento, California 95817, United States
| | - Emanual Maverakis
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California 95817, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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240
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Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol 2019; 3:679-690. [PMID: 30858588 DOI: 10.1038/s41559-019-0822-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection.
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241
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Simultaneous extraction and analysis of multiple cystine-dense peptides by μSPE and microflow-MS/MS from plasma. Bioanalysis 2019; 11:485-493. [DOI: 10.4155/bio-2018-0276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aim: Develop a universal extraction and liquid chromatography-mass spectrometer method to simultaneously analyze cystine-dense peptide (CDP) miniproteins from rat and human plasma. The results of the analysis will be used to assist selection of therapeutic drug candidates from the vast CDP library. Methods & results: A micro-elution solid-phase extraction method was developed for the sample preparation of the CDP peptides in rat and human plasma followed by analysis by microflow liquid chromatography MS/MS. The methods developed for drug discovery were found to be accurate (±≤15.2% from nominal concentrations) and precise (≤13.4% CV), with a dynamic range of 1.00–500 ng/ml and extraction recoveries of 47.2–99.0%. Conclusion: This bioanalytical method can be utilized to screen CDP proteins and other miniproteins for drug discovery, candidate selection and further drug development.
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242
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Tierbach A, Groh KJ, Schönenberger R, Schirmer K, Suter MJF. Glutathione S-Transferase Protein Expression in Different Life Stages of Zebrafish (Danio rerio). Toxicol Sci 2019; 162:702-712. [PMID: 29361160 PMCID: PMC5888913 DOI: 10.1093/toxsci/kfx293] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Zebrafish is a widely used animal model in biomedical sciences and toxicology. Although evidence for the presence of phases I and II xenobiotic defense mechanisms in zebrafish exists on the transcriptional and enzyme activity level, little is known about the protein expression of xenobiotic metabolizing enzymes. Given the important role of glutathione S-transferases (GSTs) in phase II biotransformation, we analyzed cytosolic GST proteins in zebrafish early life stages and different organs of adult male and female fish, using a targeted proteomics approach. The established multiple reaction monitoring-based assays enable the measurement of the relative abundance of specific GST isoenzymes and GST classes in zebrafish through a combination of proteotypic peptides and peptides shared within the same class. GSTs of the classes alpha, mu, pi and rho are expressed in zebrafish embryo as early as 4 h postfertilization (hpf). The majority of GST enzymes are present at 72 hpf followed by a continuous increase in expression thereafter. In adult zebrafish, GST expression is organ dependent, with most of the GST classes showing the highest expression in the liver. The expression of a wide range of cytosolic GST isoenzymes and classes in zebrafish early life stages and adulthood supports the use of zebrafish as a model organism in chemical-related investigations.
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Affiliation(s)
- Alena Tierbach
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600 Dübendorf, Switzerland.,School of Architecture, Civil and Environmental Engineering, EPF Lausanne, 1015 Lausanne, Switzerland
| | - Ksenia J Groh
- Food Packaging Forum Foundation, 8045 Zürich, Switzerland
| | - René Schönenberger
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600 Dübendorf, Switzerland
| | - Kristin Schirmer
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600 Dübendorf, Switzerland.,School of Architecture, Civil and Environmental Engineering, EPF Lausanne, 1015 Lausanne, Switzerland.,Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Marc J-F Suter
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600 Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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243
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Cobley JN, Sakellariou GK, Husi H, McDonagh B. Proteomic strategies to unravel age-related redox signalling defects in skeletal muscle. Free Radic Biol Med 2019; 132:24-32. [PMID: 30219702 DOI: 10.1016/j.freeradbiomed.2018.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/22/2018] [Accepted: 09/12/2018] [Indexed: 01/06/2023]
Abstract
Increased oxidative damage and disrupted redox signalling are consistently associated with age-related loss of skeletal muscle mass and function. Redox signalling can directly regulate biogenesis and degradation pathways and indirectly via activation of key transcription factors. Contracting skeletal muscle fibres endogenously generate free radicals (e.g. superoxide) and non-radical derivatives (e.g. hydrogen peroxide). Exercise induced redox signalling can promote beneficial adaptive responses that are disrupted by age-related redox changes. Identifying and quantifying the redox signalling pathways responsible for successful adaptation to exercise makes skeletal muscle an attractive physiological model for redox proteomic approaches. Site specific identification of the redox modification and quantification of site occupancy in the context of protein abundance remains a crucial concept for redox proteomics approaches. Notwithstanding, the technical limitations associated with skeletal muscle for proteomic analysis, we discuss current approaches for the identification and quantification of transient and stable redox modifications that have been employed to date in ageing research. We also discuss recent developments in proteomic approaches in skeletal muscle and potential implications and opportunities for investigating disrupted redox signalling in skeletal muscle ageing.
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Affiliation(s)
- James N Cobley
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | | | - Holger Husi
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | - Brian McDonagh
- Discipline of Physiology, School of Medicine, NUI Galway, Ireland.
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244
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Arora A, Somasundaram K. Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us? Bioessays 2019; 41:e1800042. [PMID: 30734933 DOI: 10.1002/bies.201800042] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 11/28/2018] [Indexed: 12/22/2022]
Abstract
While mass spectrometry (MS)-based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is the proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided. A special emphasis is placed on upcoming areas such as peptidomics, proteoform research, and mass spectrometry imaging, where the utilization of targeted proteomics is expected to bring forth new avenues. The limitations associated with the acceptance of this technique for mainstream usage are also highlighted. Also see the video abstract here https://youtu.be/mieB47B8gZw.
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Affiliation(s)
- Anjali Arora
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
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245
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Mason KE, Paul PH, Chu F, Anex DS, Hart BR. Development of a Protein‐based Human Identification Capability from a Single Hair. J Forensic Sci 2019; 64:1152-1159. [DOI: 10.1111/1556-4029.13995] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Katelyn E. Mason
- Forensic Science Center Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Phillip H. Paul
- Forensic Science Center Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Fanny Chu
- Forensic Science Center Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
- Department of Chemistry Michigan State University 578 S Shaw Ln East Lansing MI 48824
| | - Deon S. Anex
- Forensic Science Center Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
| | - Bradley R. Hart
- Forensic Science Center Lawrence Livermore National Laboratory 7000 East Avenue Livermore CA 94550
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246
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Wu W, Dai RT, Bendixen E. Comparing SRM and SWATH Methods for Quantitation of Bovine Muscle Proteomes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1608-1618. [PMID: 30624930 DOI: 10.1021/acs.jafc.8b05459] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mass spectrometry (MS) has become essential for efficient and accurate quantification of proteins and proteomes and, thus, a key technology throughout all biosciences. However, validated MS methods are still scarce for meat quality research applications. The objective of this work was to develop and compare two targeted proteomic methods, namely, selected reaction monitoring (SRM) and sequential window acquisition of all theoretical spectra (SWATH), for the quantification of 11 bovine muscle proteins that may be indicators of meat color. Both methods require evaluation of spectra from proteotypic and quantotypic peptides, and we here report our evaluation of which peptides and MS parameters are best suited for robust quantification of these 11 proteins. We observed that the SRM approach provides better reproducibility, linearity, and sensitivity than SWATH and is therefore ideal for targeted quantification of low-abundance proteins, while the SWATH approach provides a more time-efficient method for targeted protein quantification of high-abundance proteins and, additionally, supports the search for novel biomarkers.
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Affiliation(s)
- Wei Wu
- College of Food Science and Nutritional Engineering , China Agricultural University , No. 17 Qinghua East Road , Haidian District, Beijing 100083 , P. R. China
- Department of Molecular Biology and Genetics, Faculty of Science and Technology , Aarhus University , Gustav Wieds Vej 10 , 8000 Aarhus , Denmark
| | - Rui-Tong Dai
- College of Food Science and Nutritional Engineering , China Agricultural University , No. 17 Qinghua East Road , Haidian District, Beijing 100083 , P. R. China
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology , Aarhus University , Gustav Wieds Vej 10 , 8000 Aarhus , Denmark
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247
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Identification and quantification of DNA repair protein poly(ADP ribose) polymerase 1 (PARP1) in human tissues and cultured cells by liquid chromatography/isotope-dilution tandem mass spectrometry. DNA Repair (Amst) 2019; 75:48-59. [PMID: 30743082 DOI: 10.1016/j.dnarep.2019.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 12/14/2022]
Abstract
Poly(ADP ribose) polymerase 1 (PARP1) is a multifunctional DNA repair protein of the base excision repair pathway and plays a major role in the repair of DNA strand breaks and in replication and transcriptional regulation among other functions. Mounting evidence points to the predictive and prognostic value of PARP1 expression in human cancers. Thus, PARP1 has become an important target in cancer therapy, leading to the development of inhibitors as anticancer drugs. In the past, PARP1 expression levels in tissue samples have generally been estimated by indirect and semi-quantitative immunohistochemical methods. Accurate measurement of PARP1 in normal tissues and malignant tumors of patients will be essential for evaluating PARP1 as a predictive and prognostic biomarker in cancer and other diseases, and for the development and use of its inhibitors in cancer therapy. In this work, we present an approach involving liquid chromatography-isotope-dilution tandem mass spectrometry to positively identify and accurately quantify PARP1 in human tissues and cultured cells. We identified and quantified PARP1 in human normal ovarian tissues and malignant ovarian tumors, and in three pairs of human cell lines, each pair consisting of a normal cell line and its cancerous counterpart. Significantly greater expression of PARP1 was observed in malignant ovarian tissues than in normal ovarian tissues. In the case of one pair of cell lines, the cancerous cell line also exhibited greater expression of PARP1 than in normal cell line. We also show the simultaneous measurement of PARP1 and apurinic/apyrimidinic endonuclease 1 (APE1) in a given protein extract. The approach presented in this work is expected to contribute to the accurate quantitative assessment of PARP1 levels in basic research and clinical studies.
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248
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Xia YG, Guo XD, Song Y, Liang J, Gong FQ, Wang TL, Yang BY, Kuang HX. A generic strategy based on gas phase decomposition of protonated and ammoninted precursors producing predictable MRM-MS ion pairs and collision energies for direct analysis of plant triterpene glycosides. J Pharm Biomed Anal 2019; 165:292-303. [DOI: 10.1016/j.jpba.2018.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
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249
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Devi S, Lin YC, Ho YP. Quantitative analysis of genetically modified soya using multiple reaction monitoring mass spectrometry with endogenous peptides as internal standards. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:50-57. [PMID: 30253653 DOI: 10.1177/1469066718802548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A simple label-free method was developed for the quantification of the herbicide-resistant gene-related protein 5-enolpyruvylshikimate-3-phosphate synthase using multiple reaction monitoring liquid chromatography-mass spectrometry. Sample pretreatment procedures including ion exchange chromatography and CaCl2 precipitation were used to purify the 5-enolpyruvylshikimate-3-phosphate synthase protein. Quantification of various percentages of genetically modified soya (0.5-100%) was performed by selecting suitable endogenous soybean peptides as internal standards. Results indicated that Gly P (QGDVFVVPR) and Lec P (LQLNK) are useful internal standards for the quantification of low and high percentages of genetically modified soya, respectively. Linear regression analysis of both calibration curves yielded good linearity with R2 of 0.99. This approach is a convenient and accurate quantification method for genetically modified soya at a level as low as 0.5% (less than the current EU threshold for labeling genetically modified soya).
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Affiliation(s)
- Shobha Devi
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
- In memory of Professor Robert C. Dunbar who had endless enthusiasm for science
| | - Yi-Cheng Lin
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
- In memory of Professor Robert C. Dunbar who had endless enthusiasm for science
| | - Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
- In memory of Professor Robert C. Dunbar who had endless enthusiasm for science
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250
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Zhu J, Garrigues L, Van den Toorn H, Stahl B, Heck AJR. Discovery and Quantification of Nonhuman Proteins in Human Milk. J Proteome Res 2019; 18:225-238. [PMID: 30489082 PMCID: PMC6326037 DOI: 10.1021/acs.jproteome.8b00550] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 01/11/2023]
Abstract
The question whether and which nonhuman peptides or proteins are present in human milk was raised many decades ago. However, due to cross-reactivity or nonspecific antibody recognition, the accuracy of detection by immunochemical methods has been a concern. Additionally, the relative low-abundance of nonhuman peptides/proteins in the complex milk sample makes them a challenging target to detect. Here, by deep proteome profiling, we detected several nonhuman peptides, which could be grouped as nonhuman proteins. We next estimated their concentration in human milk by combining data-dependent shotgun proteomics and parallel reaction monitoring. First, we fractionated human milk at the protein level and were able to detect 1577 human proteins. Additionally, we identified 109 nonhuman peptides, of which 71 were grouped into 36 nonhuman proteins. In the next step, we targeted 37 nonhuman peptides and nine of them could be repeatedly quantified in human milk samples. Peptides/proteins originating from bovine milk products were the dominant nonhuman proteins observed, notably bovine caseins (α-S1-, α-S2-, β-, κ-caseins) and β-lactoglobulin. The method we present here can be expanded to investigate more about nonhuman peptides and proteins in human milk and give a better understanding of how human milk plays a role in allergy prevention.
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Affiliation(s)
- Jing Zhu
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Luc Garrigues
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Henk Van den Toorn
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Bernd Stahl
- Danone
Nutricia Research, 3584
CT Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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