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Gilbert C, Bathany K, Claverol S, Scanvion Q, Hedouin V, Bertrand B, Tokarski C. Successive Protein Extraction Using Hydroxylamine to Increase the Depth of Proteome Coverage in Fresh, Forensic, and Archaeological Bones. Anal Chem 2024; 96:3247-3252. [PMID: 38349005 DOI: 10.1021/acs.analchem.3c02803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Proteomics is continually being applied to a wider range of applications, now including the analysis of archaeological samples and anatomical specimens, particularly collagen-containing tissues such as bones and teeth. Here, we present the application of a chemical digestion-based proteomics sample preparation protocol to the analysis of fresh, anatomical, and archaeological samples. We describe and discuss two protocols: one that uses hydroxylamine as an additional step of the proteomic workflow, applied to the insoluble fraction, and another that applies hydroxylamine directly on demineralized bones and teeth. We demonstrate the additional information that can be extracted using both protocols, including an increase in the sequence coverage and number of peptides detected in modern and archaeological samples and an increase in the number of proteins identified in archaeological samples. By targeting research related to collagens or extracellular matrix proteins, the use of this protocol will open new insights, considering both fresh and ancient mineralized samples.
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Affiliation(s)
- Catherine Gilbert
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Proteome Platform, Université de Bordeaux, F-33000 Bordeaux, France
| | - Katell Bathany
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Proteome Platform, Université de Bordeaux, F-33000 Bordeaux, France
| | | | - Quentin Scanvion
- Université de Lille, CHU Lille, Institut de Médecine Légale, EA 7367 UTML - Unité de Taphonomie Médico-Légale, 59000 Lille, France
| | - Valery Hedouin
- Université de Lille, CHU Lille, Institut de Médecine Légale, EA 7367 UTML - Unité de Taphonomie Médico-Légale, 59000 Lille, France
| | - Benoit Bertrand
- Université de Lille, CHU Lille, Institut de Médecine Légale, EA 7367 UTML - Unité de Taphonomie Médico-Légale, 59000 Lille, France
| | - Caroline Tokarski
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Proteome Platform, Université de Bordeaux, F-33000 Bordeaux, France
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC. Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering. Mol Cell Proteomics 2015; 14:961-73. [PMID: 25660013 PMCID: PMC4390273 DOI: 10.1074/mcp.m114.045260] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/06/2015] [Indexed: 01/20/2023] Open
Abstract
The use of extracellular matrix (ECM) scaffolds, derived from decellularized tissues for engineered organ generation, holds enormous potential in the field of regenerative medicine. To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs.
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Affiliation(s)
- Ryan C Hill
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045
| | | | - Monika Dzieciatkowska
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045
| | - Laura E Niklason
- §Department of Biomedical Engineering and Anesthesiology, ¶Yale University, New Haven, CT 06519
| | - Kirk C Hansen
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045,
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Dunston CR, Herbert R, Griffiths HR. Improving T cell-induced response to subunit vaccines: opportunities for a proteomic systems approach. ACTA ACUST UNITED AC 2015; 67:290-9. [PMID: 25708693 DOI: 10.1111/jphp.12383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 11/23/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Prophylactic vaccines are an effective strategy to prevent development of many infectious diseases. With new and re-emerging infections posing increasing risks to food stocks and the health of the population in general, there is a need to improve the rationale of vaccine development. One key challenge lies in development of an effective T cell-induced response to subunit vaccines at specific sites and in different populations. OBJECTIVES In this review, we consider how a proteomic systems-based approach can be used to identify putative novel vaccine targets, may be adopted to characterise subunit vaccines and adjuvants fully. KEY FINDINGS Despite the extensive potential for proteomics to aid our understanding of subunit vaccine nature, little work has been reported on identifying MHC 1-binding peptides for subunit vaccines generating T cell responses in the literature to date. SUMMARY In combination with predictive and structural biology approaches to mapping antigen presentation, proteomics offers a powerful and as yet un-tapped addition to the armoury of vaccine discovery to predict T-cell subset responses and improve vaccine design strategies.
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Affiliation(s)
- Christopher R Dunston
- Life & Health Sciences, Aston University, Birmingham, West Midlands, UK; Mologic, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YP
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Plum S, Steinbach S, Abel L, Marcus K, Helling S, May C. Proteomics in neurodegenerative diseases: Methods for obtaining a closer look at the neuronal proteome. Proteomics Clin Appl 2014; 9:848-71. [DOI: 10.1002/prca.201400030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/25/2014] [Accepted: 09/03/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Sarah Plum
- Medizinisches Proteom-Center; Funktionelle Proteomik; Ruhr-Universität Bochum; Bochum Germany
| | - Simone Steinbach
- Medizinisches Proteom-Center; Medical Proteomics/Bioanalytics; Ruhr-Universität Bochum; Bochum Germany
| | - Laura Abel
- Medizinisches Proteom-Center; Medical Proteomics/Bioanalytics; Ruhr-Universität Bochum; Bochum Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center; Funktionelle Proteomik; Ruhr-Universität Bochum; Bochum Germany
| | - Stefan Helling
- Medizinisches Proteom-Center; Funktionelle Proteomik; Ruhr-Universität Bochum; Bochum Germany
| | - Caroline May
- Medizinisches Proteom-Center; Medical Proteomics/Bioanalytics; Ruhr-Universität Bochum; Bochum Germany
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Kim BH, Moon PG, Lee JE, Lee S, Kim SK, Lee JK, Kim SH, Baek MC. Identification of Potential Serum Biomarkers in Mercury-Treated Mice Using a Glycoproteomic Approach. Int J Toxicol 2013; 32:368-75. [DOI: 10.1177/1091581813504969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mercury is a well-recognized health hazard and a deleterious environmental contaminant. Exposure to mercury can cause neurotoxic manifestations, nephrotoxicity, and immune function alterations; however, the mechanisms and related proteins responsible for these effects are still unclear. Our goal is to understand the relationship between the toxicity of mercury and the proteins affected by this toxic heavy metal and to define biomarkers for mercury intoxication. Two different forms of mercury, organic methylmercury or inorganic mercury sulfide, were orally administered to the mice for 4 weeks. To reduce complexity of the serum proteome, we enriched glycoproteins from mice serum with lectin concanavalin A resin, and the tryptic peptides of the purified glycoproteins were subjected to nanoultra performance liquid chromatography-Quadrupole time-of-flight for identification and label-free quantification. In this study, we characterized approximately 209 proteins from mice serum, and, among them, 21 proteins were differentially expressed in organic methylmercury-treated mice serum compared with the control group. Two proteins, serum amyloid P component (SAP) and inter α-trypsin inhibitor heavy chain 4 (ITI-H4), were upregulated in organic methylmercury-treated mice and confirmed with different doses of both types of mercury by Western blot analysis. Results of immunohistochemistry also confirmed the validity of SAP and ITI-H4 as biomarker candidates for organic methylmercury exposure. Findings of this study may assist in understanding the relationship between toxicity of mercury and upregulated proteins in mouse serum. Furthermore, the proteins identified here might be used as biomarker candidates in mercury intoxication.
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Affiliation(s)
- Bong-Hwa Kim
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Pyong-Gon Moon
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-Eun Lee
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Soyoung Lee
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sook-Kyung Kim
- Division of Metrology for Quality of Life, Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Jong Kwon Lee
- Toxicological Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Chungbuk, Republic of Korea
| | - Sang-Hyun Kim
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Moon-Chang Baek
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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