1
|
Nickerson JL, Sheridan LV, Doucette AA. Impact of Surfactants on Cumulative Trypsin Activity in Bottom-Up Proteome Analysis. J Proteome Res 2024; 23:3542-3551. [PMID: 38973097 DOI: 10.1021/acs.jproteome.4c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Trypsin digestion plays a pivotal role in successful bottom-up peptide characterization and quantitation. While denaturants are often incorporated to enhance protein solubility, surfactants are recognized to inhibit enzyme activity. However, several reports have suggested that incorporating surfactants or other solvent additives may enhance digestion and MS detection. Here, we assess the impacts of ionic surfactants on cumulative trypsin activity and subsequently evaluate the total digestion efficiency of a proteome mixture by quantitative MS. Although low surfactant concentrations, such as 0.01% SDS or 0.2% SDC, significantly enhanced the initial trypsin activity (by 14 or 42%, respectively), time course assays revealed accelerated enzyme deactivation, evident by 10- or 40-fold reductions in trypsin activity half-life at these respective surfactant concentrations. Despite enhanced initial tryptic activity, quantitative MS analysis of a common liver proteome extract, digested with various surfactants (0.01 or 0.1% SDS, 0.5% SDC), consistently revealed decreased peptide counts and signal intensity, indicative of a lower digestion efficiency compared to a nonsurfactant control. Furthermore, including detergents for digestion did not improve the detection of membrane proteins, nor hydrophobic peptides. These results stress the importance of assessing cumulative enzyme activity when optimizing the digestion of a proteome mixture, particularly in the presence of denaturants.
Collapse
Affiliation(s)
- Jessica L Nickerson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Allumiqs Corporation, Halifax, Nova Scotia B3H 0A8, Canada
| | - Liam V Sheridan
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| |
Collapse
|
2
|
Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 PMCID: PMC11381016 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
Collapse
Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| |
Collapse
|
3
|
Mansuri MS, Bathla S, Lam TT, Nairn AC, Williams KR. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. J Proteomics 2024; 297:105109. [PMID: 38325732 PMCID: PMC10939724 DOI: 10.1016/j.jprot.2024.105109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
To identify proteins by the bottom-up mass spectrometry workflow, enzymatic digestion is essential to break down proteins into smaller peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity and generation of peptides with desirable positively charged N- and C-terminal amino acid residues that are amenable to reverse phase HPLC separation and MS/MS analyses. However, trypsin can yield variable digestion profiles and its protein cleavage activity is interdependent on trypsin source and quality, digestion time and temperature, pH, denaturant, trypsin and substrate concentrations, composition/complexity of the sample matrix, and other factors. There is therefore a need for a more standardized, general-purpose trypsin digestion protocol. Based on a review of the literature we delineate optimal conditions for carrying out trypsin digestions of complex proteomes from bulk samples to limiting amounts of protein extracts. Furthermore, we highlight recent developments and technological advances used in digestion protocols to quantify complex proteomes from single cells. SIGNIFICANCE: Currently, bottom-up MS-based proteomics is the method of choice for global proteome analysis. Since trypsin is the most utilized protease in bottom-up MS proteomics, delineating optimal conditions for carrying out trypsin digestions of complex proteomes in samples ranging from tissues to single cells should positively impact a broad range of biomedical research.
Collapse
Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA.
| |
Collapse
|
4
|
Waldenmaier HE, Gorre E, Poltash ML, Gunawardena HP, Zhai XA, Li J, Zhai B, Beil EJ, Terzo JC, Lawler R, English AM, Bern M, Mahan AD, Carlson E, Nanda H. "Lab of the Future"─Today: Fully Automated System for High-Throughput Mass Spectrometry Analysis of Biotherapeutics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37186948 DOI: 10.1021/jasms.3c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Here we describe a state-of-the-art, integrated, multi-instrument automated system designed to execute methods involved in mass spectrometry characterization of biotherapeutics. The system includes liquid and microplate handling robotics and utilities, integrated LC-MS, along with data analysis software, to perform sample purification, preparation, and analysis as a seamless integrated unit. The automated process begins with tip-based purification of target proteins from expression cell-line supernatants, which is initiated once the samples are loaded onto the automated system and the metadata are retrieved from our corporate data aggregation system. Subsequently, the purified protein samples are prepared for MS, including deglycosylation and reduction steps for intact and reduced mass analysis, and proteolytic digestions, desalting, and buffer exchange via centrifugation for peptide map analysis. The prepared samples are then loaded into the LC-MS instrumentation for data acquisition. The acquired raw data are initially stored on a local area network storage system that is monitored by watcher scripts that then upload the raw MS data to a network of cloud-based servers. The raw MS data are processed with the appropriately configured analysis workflows such as database search for peptide mapping or charge deconvolution for undigested proteins. The results are verified and formatted for expert curation directly in the cloud. Finally, the curated results are appended to sample metadata in the corporate data aggregation system to accompany the biotherapeutic cell lines in subsequent processes.
Collapse
Affiliation(s)
- Hans E Waldenmaier
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Elsa Gorre
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Michael L Poltash
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Harsha P Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | | | - Jing Li
- Protein Metrics LLC., Cupertino, California 95014, United States
| | - Bo Zhai
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Eric J Beil
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Joseph C Terzo
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Rose Lawler
- Protein Metrics LLC., Cupertino, California 95014, United States
| | | | - Marshall Bern
- Protein Metrics LLC., Cupertino, California 95014, United States
| | - Andrew D Mahan
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Eric Carlson
- Protein Metrics LLC., Cupertino, California 95014, United States
| | - Hirsh Nanda
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
5
|
Nickerson JL, Doucette AA. Maximizing Cumulative Trypsin Activity with Calcium at Elevated Temperature for Enhanced Bottom-Up Proteome Analysis. BIOLOGY 2022; 11:biology11101444. [PMID: 36290348 PMCID: PMC9598648 DOI: 10.3390/biology11101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Simple Summary Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Abstract Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.
Collapse
|
6
|
Optimization and Identification of Single Mutation in Hemoglobin Variants with 2,2,2 Trifluoroethanol Modified Digestion Method and Nano-LC Coupled MALDI MS/MS. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196357. [PMID: 36234894 PMCID: PMC9572498 DOI: 10.3390/molecules27196357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 12/30/2022]
Abstract
Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have their own limitations. Therefore, the present study aims to develop and optimize a specific method of sample processing that could lead to improved sequence coverage and analysis of Hb variants by nano LC-MALDI MS/MS. Methods: In our study, we primarily standardized various sample processing methods such as conventional digestion with trypsin followed by 10% acetonitrile treatment, digestion with multiple proteases like trypsin, Glu-C, Lys-C, and trypsin digestion subsequent to 2,2,2 trifluoroethanol (TFE) treatment. Finally, the peptides were identified by LC-MALDI MS/MS. All of these sample processing steps were primarily tested with recombinant Hb samples. After initial optimization, we found that the TFE method was the most suitable one and the efficiency of this method was applied in Hb variant identification based on high sequence coverage. Results: We developed and optimized a method using an organic solvent TFE and heat denaturation prior to digestion, resulting in 100% sequence coverage in the β-chains and 95% sequence coverage in the α-chains, which further helped in the identification of Hb mutations. A Hb variant protein sequence database was created to specify the search and reduce the search time. Conclusion: All of the mutations were identified using a bottom-up non-target approach. Therefore, a sensitive, robust and reproducible method was developed to identify single substitution mutations in the Hb variants from the sequence of the entire globin chains. Biological Significance: Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. Hb variants generally arise due to point mutation in the globin chains. There is high sequence homology between normal Hb and Hb variant chains. Due to this high homology between the two forms, identification of variants by mass spectrometry is very difficult and requires the full sequence coverage of α- and β-chains. As such, there is a need for a suitable method that provides 100% sequence coverage of globin chains for variant analysis by mass spectrometry. Our study provides a simple, robust, and reproducible method that is suitable for LC-MALDI and provides nearly complete sequence coverage in the globin chains. This method may be used in the near future in routine diagnosis for Hb variant analysis.
Collapse
|
7
|
Ai Y, Xu J, Gunawardena HP, Zare RN, Chen H. Investigation of Tryptic Protein Digestion in Microdroplets and in Bulk Solution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1238-1249. [PMID: 35647885 PMCID: PMC10512443 DOI: 10.1021/jasms.2c00072] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent studies have shown that ultrafast enzymatic digestion of proteins can be achieved in microdroplet within 250 μs. Further investigation of peptides resulting from microdroplet digestion (MD) would be necessary to evaluate it as an alternative to the conventional bulk digestion for bottom-up and biotherapeutic protein characterization. Herein we examined and compared protein tryptic digestion in both MD and bulk solution. In the case of MD of β-lactoglobulin B, the preservation of long peptides was observed due to the short digestion time. In addition, MD is applicable to digest both high- and low-abundance proteins in mixture. In the case of digesting NIST 8671 mAb antibody containing a low level of commonly encountered host cell protein (HCP) PLBL2 (mAb:PLBL2 = 100:1 by weight), MD produced lower levels of digestion-induced chemical modifications of asparagine/glutamine deamidation, compared with overnight digestion. No significant difference between MD and bulk digestion was observed in terms of trypsin digestion specificity based on examination of semi- and unspecific-cleaved peptides. Our study suggests that MD, a fast digestion approach, could be adopted for bottom-up proteomics research and for peptide mapping of mAbs to characterize site-specific deamidation and glycosylation, for the purpose of development of biopharmaceuticals.
Collapse
Affiliation(s)
- Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Jeffrey Xu
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Harsha P. Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, USA
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| |
Collapse
|
8
|
Smirnova TA, Viskin A, Hoskova M, Habartova L, Setnicka V, Cejnar P, Kuckova S. Comparison of proteomic approaches used for the detection of potential biomarkers of Alzheimer's disease in blood plasma. J Sep Sci 2021; 44:4132-4140. [PMID: 34545700 DOI: 10.1002/jssc.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/03/2021] [Accepted: 09/12/2021] [Indexed: 11/10/2022]
Abstract
At present, Alzheimer's disease is detected mainly using psychological tests, which can only confirm the disease in its more advanced phases. Therefore, bioanalytical possibilities for detecting this disease earlier are being investigated. To date, the results of analyses, which focus mainly on the study of lipids and proteins either in cerebrospinal fluid or much less often in blood plasma, do not provide satisfactory results. In addition, cerebrospinal fluid sampling is uncomfortable for the patients and involves many health risks. In this work, we deal with proteomic analysis using Matrix-Assisted Laser Desorption/Ionisation-Time of Flight and Liquid Chromatography coupled to tandem Mass Spectrometry of blood plasma with a focus on various ways of preanalytical sample treatments. This should lead to results improvement and facilitate the subsequent evaluation using principal component analysis and partial least squares discriminant analysis. The obtained results indicate the direction of further research, namely the study of interactions between proteins and lipids contained in blood plasma. These substances may be regarded as potential biomarkers allowing for the diagnosis of Alzheimer´s disease even in its early stages.
Collapse
Affiliation(s)
- Tatiana Anatolievna Smirnova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Anton Viskin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Martina Hoskova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Lucie Habartova
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Vladimir Setnicka
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Pavel Cejnar
- Department of Computing and Control Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Stepanka Kuckova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| |
Collapse
|
9
|
Hynek R, Michalus I, Cejnar P, Šantrůček J, Seidlová S, Kučková Š, Sázelová P, Kašička V. In-bone protein digestion followed by LC-MS/MS peptide analysis as a new way towards the routine proteomic characterization of human maxillary and mandibular bone tissue in oral surgery. Electrophoresis 2021; 42:2552-2562. [PMID: 34453862 DOI: 10.1002/elps.202100211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/12/2021] [Accepted: 08/26/2021] [Indexed: 11/11/2022]
Abstract
Proteomic characterization of alveolar bones in oral surgery represents an analytical challenge due to their insoluble character. The implementation of a straightforward technique could lead to the routine use of proteomics in this field. This work thus developed a simple technique for the characterization of bone tissue for human maxillary and mandibular bones. It is based on the direct in-bone tryptic digestion of proteins in both healthy and pathological human maxillary and mandibular bone samples. The released peptides were then identified by the LC-MS/MS. Using this approach, a total of 1120 proteins were identified in the maxillary bone and 1151 proteins in the mandibular bone. The subsequent partial least squares-discrimination analysis (PLS-DA) of protein data made it possible to reach 100% discrimination between the samples of healthy alveolar bones and those of the bone tissue surrounding the inflammatory focus. These results indicate that the in-bone protein digestion followed by the LC-MS/MS and subsequent statistical analysis can provide a deeper insight into the field of oral surgery at the molecular level. Furthermore, it could also have a diagnostic potential in the differentiation between the proteomic patterns of healthy and pathological alveolar bone tissue. Data are available via ProteomeXchange with the identifier PXD026775.
Collapse
Affiliation(s)
- Radovan Hynek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Iva Michalus
- First Faculty of Medicine, Charles University, Kateřinská 32, Prague 2, 121 08, Czech Republic
| | - Pavel Cejnar
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Jiří Šantrůček
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Sabina Seidlová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Štěpánka Kučková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Petra Sázelová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo 542/2, Prague 6, 166 10, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo 542/2, Prague 6, 166 10, Czech Republic
| |
Collapse
|
10
|
Tharp KM, Higuchi-Sanabria R, Timblin GA, Ford B, Garzon-Coral C, Schneider C, Muncie JM, Stashko C, Daniele JR, Moore AS, Frankino PA, Homentcovschi S, Manoli SS, Shao H, Richards AL, Chen KH, Hoeve JT, Ku GM, Hellerstein M, Nomura DK, Saijo K, Gestwicki J, Dunn AR, Krogan NJ, Swaney DL, Dillin A, Weaver VM. Adhesion-mediated mechanosignaling forces mitohormesis. Cell Metab 2021; 33:1322-1341.e13. [PMID: 34019840 PMCID: PMC8266765 DOI: 10.1016/j.cmet.2021.04.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/09/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022]
Abstract
Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of aging. However, the physical characteristics of the extracellular matrix are also altered in cancerous and aging tissues. Here, we demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial function via solute carrier family 9 member A1-dependent ion exchange and heat shock factor 1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.
Collapse
Affiliation(s)
- Kevin M Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryo Higuchi-Sanabria
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Greg A Timblin
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carlos Garzon-Coral
- Chemical Engineering Department, Stanford University, Stanford, CA 94305, USA
| | - Catherine Schneider
- Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathon M Muncie
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Connor Stashko
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph R Daniele
- MD Anderson Cancer Center, South Campus Research, Houston, CA 77054, USA
| | - Andrew S Moore
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Phillip A Frankino
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Stefan Homentcovschi
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Sagar S Manoli
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kuei-Ho Chen
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Johanna Ten Hoeve
- UCLA Metabolomics Center, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gregory M Ku
- Diabetes Center, Division of Endocrinology and Metabolism, Department of Medicine, UCSF, San Francisco, CA 94143, USA
| | - Marc Hellerstein
- Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Karou Saijo
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jason Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexander R Dunn
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrew Dillin
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences and Department of Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
11
|
Oyler JM, Tran BQ, Kilgour DPA. Rapid Denaturing Organic Digestion Method for Targeted Protein Identification and Characterization. Anal Chem 2021; 93:5046-5053. [PMID: 33728904 DOI: 10.1021/acs.analchem.0c04143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bottom-up mass spectrometry-based protein analysis methods employing protease digestion are routinely used to identify and characterize proteins with high specificity and sensitivity. Method performance is generally measured by sequence coverage capability and the total number of characteristic peptides identified, when compared to predicted databases. Limitations to commonly used solvent-based digestion methods currently employed include long digestion times (18-24 h or more), leading to protease autolysis, which also precludes automation, decreases sensitivity, and increases both intra- and inter-day performance variability. This report describes the development and validation of a simple, 5 min tryptic denaturing organic digestion (DOD) method for use with tandem mass spectrometry in bottom-up protein identification and characterization. It has been evaluated across select protein toxins and diagnostic clinical protein targets, substantially improving digestion performance when compared to other solution-based and enzyme-immobilized methods. The method was compared to two currently used bottom-up methods, the 24 h filter-aided sample prep (FASP) and Flash Digest (1 and 4 h) methods. Single proteins used to compare the methods included the ricin light chain, ricin heavy chain, ricin holotoxin, serotype A Clostridium botulinum toxin, Staphylococcus enterotoxin B, ribonuclease A, and thyroglobulin. In tests, across the proteins investigated, the 5 min DOD digestion method resulted in sequence coverages ranging from 55 to 100%, with relatively high reproducibility and precision; results were better than or equal to FASP method results and were greatly enhanced when compared to Flash method results. Importantly, DOD method intra- and inter-day precision was much improved as compared to results for both FASP and Flash digestions. These data indicated that the DOD method, when compared to the FASP and Flash Digest methods, dramatically reduced digestion time, while maintaining or improving the ability to detect and characterize targeted proteins, and reduced analytical variability for tryptic digestion, resulting in markedly faster and more precise analyses.
Collapse
Affiliation(s)
- Jonathan M Oyler
- US Army Medical Research Institute of Chemical Defense, 8350 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400, United States.,Technical Inspections Division (SAIG-TI), The US Army Inspector General Agency, 2530 Crystal Drive, Suite 12039, Arlington, Virginia 22202-3912, United States.,Nottingham Trent University, Clifton Campus, College Drive, Nottingham NG11 8NS, U.K
| | - Bao Q Tran
- US Army 20th Support Command CBRNE Analytical and Remediation Activity, Building E 1947, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010-5424, United States
| | - David P A Kilgour
- Nottingham Trent University, Clifton Campus, College Drive, Nottingham NG11 8NS, U.K
| |
Collapse
|
12
|
Zhao P, Gunawardena HP, Zhong X, Zare RN, Chen H. Microdroplet Ultrafast Reactions Speed Antibody Characterization. Anal Chem 2021; 93:3997-4005. [PMID: 33590747 DOI: 10.1021/acs.analchem.0c04974] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recently, microdroplet reactions have aroused much interest because the microdroplet provides a unique medium where organic reactions could be accelerated by a factor of 103 or more. However, microdroplet reactions of proteins have been rarely studied. We report the occurrence of multiple-step reactions of a large protein, specifically, the digestion, reduction, and deglycosylation of an intact antibody, which can take place in microseconds with high reaction yields in aqueous microdroplets at room temperature. As a result, fast structural characterization of a monoclonal antibody, essential for assessing its quality as a therapeutic drug, can be enabled. We found that the IgG1 antibody can be digested completely by the IdeS protease in aqueous microdroplets in 250 microseconds, a 7.5 million-fold improvement in speed in comparison to traditional digestion in bulk solution (>30 min). Strikingly, inclusion of the reductant tris(2-carboxyethyl)phosphine in the spray solution caused simultaneous antibody digestion and disulfide bond reduction. Digested and reduced antibody fragments were either collected or analyzed online by mass spectrometry. Further addition of PNGase F glycosylase into the spray solution led to antibody deglycosylation, thereby producing reduced and deglycosylated fragments of analytical importance. In addition, glycated fragments of IgG1 derived from glucose modification were identified rapidly with this ultrafast digestion/reduction technique. We suggest that microdroplets can serve as powerful microreactors for both exploring large-molecule reactions and speeding their structural analyses.
Collapse
Affiliation(s)
- Pengyi Zhao
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Harsha P Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Xiaoqin Zhong
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| |
Collapse
|
13
|
Burdman I, Burckhardt BB. Human prorenin determination by hybrid immunocapture liquid chromatography/mass spectrometry: A mixed-solvent-triggered digestion utilizing D-optimal design. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8932. [PMID: 32845569 DOI: 10.1002/rcm.8932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/03/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Human prorenin, representing the precursor of mature renin, has been discussed as a potential biomarker, e.g. in diagnosing primary hyperaldosteronism or diabetes-induced nephropathy. Currently, only immunoassays are available for prorenin quantification. As the similarity of prorenin to active renin impedes its accurate determination by immunoassay, mass spectrometry appears as an accurate alternative for differentiation of that protein. METHODS Immunoaffinity purification plus a mixed-solvent-triggered digestion was combined with liquid chromatography/mass spectrometry (LC/MS) to enable a fast, sensitive, and less laboratory-intensive approach to the quantification of prorenin. Statistical experimental planning, which is known as Design of Experiments (DOE), was used to identify the optimal conditions for the generation of the signature peptides within a manageable number of experiments. The efficiency of the mixed-solvent-triggered digestion by trypsin was investigated using four different organic solvents: acetonitrile, acetone, tetrahydrofuran and methanol. RESULTS By utilizing a D-optimal design, we found that the optimal mixed-solvent type for the generation of both signature peptides was acetonitrile at a concentration of 84% and an incubation temperature of 16°C. Using the mixed-solvent-triggered digestion, the procedure time allowed a fast analysis of active renin and prorenin with a short digestion time of 98 min. This optimized mixed-solvent-triggered digestion procedure was applied to detect renin and prorenin successfully in human plasma by the newly developed hybrid approach. CONCLUSIONS The identification of unique surrogates for human prorenin enabled the mass spectrometric differentiation between the two similar proteins. The novel hybrid approach successfully proved its ability to purify, detect and distinguish between prorenin and active renin in human plasma.
Collapse
Affiliation(s)
- Ilja Burdman
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University, Universitaetsstr. 1, Dusseldorf, Germany
| | - Bjoern B Burckhardt
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University, Universitaetsstr. 1, Dusseldorf, Germany
| |
Collapse
|
14
|
Liu CC, Liang LH, Yang Y, Yu HL, Yan L, Li XS, Chen B, Liu SL, Xi HL. Direct Acetonitrile-Assisted Trypsin Digestion Method Combined with LC-MS/MS-Targeted Peptide Analysis for Unambiguous Identification of Intact Ricin. J Proteome Res 2020; 20:369-380. [PMID: 33108200 DOI: 10.1021/acs.jproteome.0c00458] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ricin is a type II ribosome-inactivating protein toxin consisting of A and B chains linked by one interchain disulfide bond. Because of its high toxicity depending on both chains together, confirming the presence of both A and B chains of intact ricin is required during the investigation of the illegal production and application. Here, we report a novel and sensitive acetonitrile (ACN)-assisted trypsin digestion method for unambiguous identification of intact ricin by simultaneous detection of its marker peptides from A and B chains. Marker peptides were generated with a simple procedure by direct cleaving the native ricin at 45 °C for 4 h using Promega modified sequencing grade trypsin under the assistance of 10% ACN, and then directly analyzed by ultrahigh performance liquid chromatography tandem mass spectrometry. The type of trypsin was found to be one critical factor for cleavage of intact ricin based on a significant difference in the yields of specific peptides generated while using various types of trypsin. A low content of ACN in enzymatic buffer significantly reduced the digestion time from overnight to 4 h. There was commonly a better MS response of marker peptides when using the developed ACN-assisted trypsin digestion method than methanol-assisted trypsin digestion within the same 4 h. Totally, seven specific peptides with high sensitivity and specificity including three in the A-chain (TA7, TA11, and TA10) and four in the B-chain (TB6, TB14-ss-TB16, TB20, and TB18) were obtained as good marker peptides for unambiguous identification of intact ricin. The lowest concentration of native ricin for unambiguous identification was 20 ng/mL, in which three marker peptides from both the A-chain and B-chain could be measured with a minimum of three ion transitions. Combined with affinity enrichment, the developed approach was successfully applied for the measurement of intact ricin from the complicated matrix samples of the second, third, and fourth biotoxin exercises organized by the Organisation for the Prohibition of Chemical Weapons (OPCW). This study has provided a recommended detection method combined with one novel ACN-assisted trypsin digestion with MS for forensic unambiguous confirmation of trace ricin intact with high confidence.
Collapse
Affiliation(s)
- Chang-Cai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Long-Hui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Yang Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Hui-Lan Yu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Long Yan
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Xiao-Sen Li
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Bo Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Shi-Lei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Hai-Ling Xi
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| |
Collapse
|
15
|
Ultrafast enzymatic digestion of proteins by microdroplet mass spectrometry. Nat Commun 2020; 11:1049. [PMID: 32103000 PMCID: PMC7044307 DOI: 10.1038/s41467-020-14877-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/21/2020] [Indexed: 11/15/2022] Open
Abstract
Enzymatic digestion for protein sequencing usually requires much time, and does not always result in high sequence coverage. Here we report the use of aqueous microdroplets to accelerate enzymatic reactions and, in particular, to improve protein sequencing. When a room temperature aqueous solution containing 10 µM myoglobin and 5 µg mL−1 trypsin is electrosonically sprayed (−3 kV) from a homemade setup to produce tiny (∼9 µm) microdroplets, we obtain 100% sequence coverage in less than 1 ms of digestion time, in sharp contrast to 60% coverage achieved by incubating the same solution at 37 °C for 14 h followed by analysis with a commercial electrospray ionization source that produces larger (∼60 µm) droplets. We also confirm the sequence of the therapeutic antibody trastuzumab (∼148 kDa), with a sequence coverage of 100% for light chains and 85% for heavy chains, demonstrating the practical utility of microdroplets in drug development. Mass spectrometry (MS)-based protein sequencing usually relies on in-solution proteolytic digestion, which is time-consuming and inefficient for certain proteins. Here, the authors achieve full protein sequence coverage in less than 1 ms by subjecting protein-protease mixtures to electrosonic spray ionization-MS.
Collapse
|
16
|
Feldberg L, Schuster O, Elhanany E, Laskar O, Yitzhaki S, Gura S. Rapid and sensitive identification of ricin in environmental samples based on lactamyl agarose beads using LC-MS/MS (MRM). JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4482. [PMID: 31782217 DOI: 10.1002/jms.4482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Ricin, a plant-derived toxin extracted from the seeds of Ricinus communis (castor bean plant), is one of the most toxic proteins known. Ricin's high toxicity, widespread availability, and ease of its extraction make it a potential agent for bioterrorist attacks. Most ricin detection methods are based on immunoassays. These methods may suffer from low efficiency in matrices containing interfering substances, or from false positive results due to antibody cross reactivity, with highly homologous proteins. In this study, we have developed a simple, rapid, sensitive, and selective mass spectrometry assay, for the identification of ricin in complex environmental samples. This assay involves three main stages: (a) Ricin affinity capture by commercial lactamyl-agarose (LA) beads. (b) Tryptic digestion. (c) LC-MS/MS (MRM) analysis of tryptic fragments. The assay was validated using 60 diverse environmental samples such as soil, asphalt, and vegetation, taken from various geographic regions. The assay's selectivity was established in the presence of high concentrations of competing lectin interferences. Based on our findings, we have defined strict criteria for unambiguous identification of ricin. Our novel method, which combines affinity capture beads followed by MRM-based analysis, enabled the identification of 1 ppb ricin spiked into complex environmental matrices. This methodology has the potential to be extended for the identification of ricin in body fluids from individuals exposed (deliberately or accidentally) to the toxin, contaminated food or for the detection of the entire family of RIP-II toxins, by applying multiplex format.
Collapse
Affiliation(s)
- Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Schuster
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eytan Elhanany
- Department of Biochemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Orly Laskar
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shmuel Yitzhaki
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sigalit Gura
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| |
Collapse
|
17
|
Affiliation(s)
- Yasushi ISHIHAMA
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University
| |
Collapse
|
18
|
Loraine J, Alhumaidan O, Bottrill AR, Mistry SC, Andrew P, Mukamolova GV, Turapov O. Efficient Protein Digestion at Elevated Temperature in the Presence of Sodium Dodecyl Sulfate and Calcium Ions for Membrane Proteomics. Anal Chem 2019; 91:9516-9521. [PMID: 31259536 DOI: 10.1021/acs.analchem.9b00484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The growing significance of membrane proteins inspires continuous development and improvement of methods for robust membrane proteomics. Here, we developed a very simple and efficient method for membrane protein digestion using an ionic detergent, sodium dodecyl sulfate (SDS), at high temperature, conditions where trypsin is normally inactivated. Our results suggest that trypsin can be stabilized by a combination of calcium ions and sodium chloride, which enables protein digestion at elevated temperature in the presence of strong ionic detergents such as SDS. Finding the conditions for stabilization of trypsin offers novel opportunities for the application of detergents for the investigation of membrane proteins.
Collapse
Affiliation(s)
- Jessica Loraine
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom
| | - Ohoud Alhumaidan
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Clinical Laboratory Sciences , King Saud University , Riyadh 11433 , Saudi Arabia
| | - Andrew R Bottrill
- Protein Nucleic Acid Chemistry Laboratory , University of Leicester , Leicester LE1 7RH , United Kingdom
| | - Sharad C Mistry
- Protein Nucleic Acid Chemistry Laboratory , University of Leicester , Leicester LE1 7RH , United Kingdom
| | - Peter Andrew
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom
| | - Galina V Mukamolova
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom
| | - Obolbek Turapov
- Department of Infection, Immunity and Inflammation , University of Leicester , Leicester LE1 9HN , United Kingdom.,Department of Respiratory Sciences , University of Leicester , Leicester LE1 9HN , United Kingdom
| |
Collapse
|
19
|
Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
Collapse
Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
20
|
Acetonitrile-assisted enzymatic digestion can facilitate the bottom-up identification of proteins of cancer origin. Anal Biochem 2019; 570:1-4. [DOI: 10.1016/j.ab.2019.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 02/07/2023]
|
21
|
Complementarity of Matrix- and Nanostructure-Assisted Laser Desorption/Ionization Approaches. NANOMATERIALS 2019; 9:nano9020260. [PMID: 30769830 PMCID: PMC6410089 DOI: 10.3390/nano9020260] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 01/06/2023]
Abstract
In recent years, matrix-assisted laser desorption/ionization (MALDI) has become the main tool for the study of biological macromolecules, such as protein nano-machines, especially in the determination of their molecular masses, structure, and post-translational modifications. A key role in the classical process of desorption and ionization of the sample is played by a matrix, usually a low-molecular weight weak organic acid. Unfortunately, the interpretation of mass spectra in the mass range of below m/z 500 is difficult, and hence the analysis of low molecular weight compounds in a matrix-assisted system is an analytical challenge. Replacing the classical matrix with nanomaterials, e.g., silver nanoparticles, allows improvement of the selectivity and sensitivity of spectrometric measurement of biologically important small molecules. Nowadays, the nanostructure-assisted laser desorption/ionization (NALDI) approach complements the classic MALDI in the field of modern bioanalytics. In particular, the aim of this work is to review the recent advances in MALDI and NALDI approaches.
Collapse
|
22
|
Ladner Y, Mas S, Coussot G, Montels J, Perrin C. In-line tryptic digestion of therapeutic molecules by capillary electrophoresis with temperature control. Talanta 2019; 193:146-151. [DOI: 10.1016/j.talanta.2018.09.090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/26/2022]
|
23
|
Han X, Xie Y, Wu Q, Wu S. A novel protein digestion method with the assistance of alternating current denaturation for high efficient protein digestion and mass spectrometry analysis. Talanta 2018; 184:382-387. [PMID: 29674058 DOI: 10.1016/j.talanta.2018.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 12/24/2022]
Abstract
Protein denaturation has always displayed a huge necessity for mass spectrometry (MS)-based protein identification methods in proteomics. In this research, a novel protein digestion method with the assistance of alternating current (AC) denaturation has been proposed and evaluated. In this method, merely, 200 mM ammonium bicarbonate buffer solution (pH, 8.2) was used to dissolve proteins and act as the electrolyte, and protein denaturation could be achieved in several seconds. For apo-transferrin, ovalbumin and bovine serum albumin that are resistant to digestion in their native states, confident amino acid sequence coverage by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis were obtained after 200 v AC denaturation. The applicability of this method was further investigated via analyzing a rat liver proteome sample using nano reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry (nanoRPLC-ESI-MS/MS). As a result, 458 proteins were identified which is comparable to the in-solution digestion via 8 M urea denaturation (375 proteins). All these results demonstrated that AC denaturation could offer an efficient assistance for a clean and high-throughput digestion in the individual level and proteome level.
Collapse
Affiliation(s)
- Xiaoxun Han
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Cihu Road No. 11, Huangshi 435002, China
| | - Yiming Xie
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Cihu Road No. 11, Huangshi 435002, China
| | - Qin Wu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Cihu Road No. 11, Huangshi 435002, China
| | - Shuaibin Wu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Cihu Road No. 11, Huangshi 435002, China.
| |
Collapse
|
24
|
Vildhede A, Kimoto E, Rodrigues AD, Varma MVS. Quantification of Hepatic Organic Anion Transport Proteins OAT2 and OAT7 in Human Liver Tissue and Primary Hepatocytes. Mol Pharm 2018; 15:3227-3235. [PMID: 29906129 DOI: 10.1021/acs.molpharmaceut.8b00320] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Organic anion transporter (OAT) 2 and OAT7 were recently shown to be involved in the hepatic uptake of drugs; however, there is limited understanding of the population variability in the expression of these transporters in liver. There is also a need to derive relative expression-based scaling factors (REFs) that can be used to bridge in vitro functional data to the in vivo drug disposition. To this end, we quantified OAT2 and OAT7 surrogate peptide abundance in a large number of human liver tissue samples ( n = 52), as well as several single-donor cryopreserved human hepatocyte lots ( n = 30) by a novel, validated liquid chromatography tandem mass spectrometry (LC-MS/MS) method. The average surrogate peptide expression of OAT2 and OAT7 in the liver samples was 1.52 ± 0.57 and 4.63 ± 1.58 fmol/μg membrane protein, respectively. While we noted statistically significant differences ( p < 0.05) in hepatocyte and liver tissue abundances for both OAT2 and OAT7, the differences were relatively small (1.8- and 1.5-fold difference in median values, respectively). Large interindividual variability was noted in the hepatic expression of OAT2 (16-fold in liver tissue and 23-fold in hepatocytes). OAT7, on the other hand, showed less interindividual variability (4-fold) in the livers, but high variability for the hepatocyte lots (27-fold). A significant positive correlation in OAT2 and OAT7 expression was observed, but expression levels were neither associated with age nor sex. In conclusion, our data suggest marked interindividual variability in the hepatic expression of OAT2/7, which may contribute to the pharmacokinetic variability of their substrates. Because both transporters were less abundant in hepatocytes than livers, a REF-based approach is recommended when scaling in vitro hepatocyte transport data to predict hepatic drug clearance and liver exposure of OAT2/7 substrates.
Collapse
Affiliation(s)
- Anna Vildhede
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| | - Emi Kimoto
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| | - A David Rodrigues
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| | - Manthena V S Varma
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| |
Collapse
|
25
|
Chu S, Baker MR, Leong G, Letcher RJ, Li QX. Covalent binding of the organophosphate insecticide profenofos to tyrosine on α- and β-tubulin proteins. CHEMOSPHERE 2018; 199:154-159. [PMID: 29433029 PMCID: PMC5847477 DOI: 10.1016/j.chemosphere.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
Organophosphorus (OP) compounds can bind covalently to many types of proteins and form protein adducts. These protein adducts can indicate the exposure to and neurotoxicity of OPs. In the present work, we studied adduction of tubulin with the OP insecticide profenofos in vitro and optimized the method for detection of adducted peptides. Porcine tubulin was incubated with profenofos and was then digested with trypsin, followed by mass spectrometric identification of the profenofos-modified tubulin and binding sites. With solvent-assisted digestion (80% acetonitrile in digestion solution), the protein was digested for peptide identification, especially for some peptides with low mass. The MALDI-TOF-MS and LC-ESI-TOF-MS analysis results showed that profenofos bound covalently to Tyr83 in porcine α-tubulin (TGTY*83R) and to Tyr281 in porcine β-tubulin (GSQQY*281R) with a mass increase of 166.02 Da from the original peptide fragments of porcine tubulin proteins. Tyrosine adduct sites were also confirmed by MALDI-TOF/TOF-MS analysis. This result may partially explain the neurotoxicity of profenofos at low doses and prolonged periods of exposure.
Collapse
Affiliation(s)
- Shaogang Chu
- Ecotoxicology and Wildlife Health Division, Wildlife and Landscape Science Directorate, National Wildlife Research Centre, Environment and Climate Change Canada, 1125 Colonel By Dr., Carleton University, Ottawa, ON, K1A 0H3, Canada
| | - Margaret R Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East West Road, Honolulu, HI, 96822, USA
| | - Gladys Leong
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East West Road, Honolulu, HI, 96822, USA
| | - Robert J Letcher
- Ecotoxicology and Wildlife Health Division, Wildlife and Landscape Science Directorate, National Wildlife Research Centre, Environment and Climate Change Canada, 1125 Colonel By Dr., Carleton University, Ottawa, ON, K1A 0H3, Canada
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East West Road, Honolulu, HI, 96822, USA.
| |
Collapse
|
26
|
Li J, Li B, Song J, Liu H, Bi W, Dong G, Zhou T. Characteristic and mechanism of immobilization effect of Staphylococcus aureus on human spermatozoa. Microb Pathog 2018; 119:28-34. [PMID: 29601868 DOI: 10.1016/j.micpath.2018.03.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 10/17/2022]
Abstract
OBJECTIVE This study was designed to investigate the impacts of Staphylococcus aureus isolated from sperm of male infertility patients, and explore the mechanism of the spermatozoa immobilization attributed to S. aureus. METHODS S. aureus MJ015 and MJ163, the representative strains of immobilization positive and negative group respectively, were obtained from semen of infertile men. Computer-aided sperm analysis (CASA) were performed to measure sperm motility. Transmission electron microscopy (TEM) was utilized to assess morphological alterations of spermatozoa. Two-dimensional gel electrophoresis (2-DE) and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) were undertaken to analyse the difference between the secretory proteins of MJ015 and MJ163. RESULTS A highly significant decline in motility of spermatozoa after incubating with cultured supernatant of MJ015 by sperm motility measurements, which was not observed when co-cultured with the supernatant of MJ163. TEM illustrated that the culture supernatant of MJ015 contributed to apparently ultrastructural impairment and inhibitory impacts on sperm motility. Various proteins expressed by two samples were identified. Data processing and database search preliminarily establish a link between four differential proteins and spermatozoal immobilization ability. CONCLUSIONS Our data manifested that the clinical isolates of S. aureus have a key role on the motility and morphology of sperm. A better correlation between four identified differentially expressed proteins and the marked decline of the motility of spermatozoa was established.
Collapse
Affiliation(s)
- Jiahui Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Bin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, 310003, China
| | - Jiangning Song
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia; Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia
| | - Haiyang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Wenzi Bi
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Guofeng Dong
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| |
Collapse
|
27
|
Bataille J, Viodé A, Pereiro I, Lafleur JP, Varenne F, Descroix S, Becher F, Kutter JP, Roesch C, Poüs C, Taverna M, Pallandre A, Smadja C, Le Potier I. On-a-chip tryptic digestion of transthyretin: a step toward an integrated microfluidic system for the follow-up of familial transthyretin amyloidosis. Analyst 2018; 143:1077-1086. [DOI: 10.1039/c7an01737e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
TTR digestion on TE-chip: production of a fragment of interest allowing the therapeutic follow-up of the familial transthyretin amyloidosis.
Collapse
|
28
|
Taoka M, Fujii M, Tsuchiya M, Uekita T, Ichimura T. A Sensitive Microbead-Based Organic Media-Assisted Method for Proteomics Sample Preparation from Dilute and Denaturing Solutions. ACS APPLIED MATERIALS & INTERFACES 2017; 9:42661-42667. [PMID: 29161009 DOI: 10.1021/acsami.7b16095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We developed a robust and sensitive sample preparation method for proteomics termed microbead-based and organic-media-assisted proteolysis strategy (BOPs). BOPs combines two advantages of current techniques, (1) unbiased binding of reversed-phase polymeric microbeads to any type of protein and (2) enhanced trypsin digestion efficiency in CH3CN-aqueous solvent systems, into a single-tube workflow. Compared with conventional techniques, this method effectively concentrates proteins and improves proteolytic digestion, and can be used with submicromolar protein samples in dilute or denaturing solutions, such as 70% formic acid, 8 M urea, or 7 M guanidine hydrochloride without any sample pretreatment. Proteome analysis of single Caenorhabditis elegans organisms demonstrates that BOPs has the sensitivity, reproducibility, and unbiasedness required to characterize worm proteins at a single organism level. We also show that, by simply incorporating an acetone washing step for detergent removal, BOPs is applicable to low concentration samples contaminated with a variety of detergents, including sodium dodecyl sulfate, with negligible protein loss. Moreover, the utility of this modification has also been demonstrated through proteomic characterization of 2000 human (HEK293T) cells lysed using 1% Triton X-100. The simplicity and availability of the present BOPs make it especially attractive for next-stage proteomics of rare and sample-limited systems.
Collapse
Affiliation(s)
- Masato Taoka
- Department of Chemistry, Tokyo Metropolitan University , Tokyo 192-0397, Japan
| | - Michihiko Fujii
- Graduate School of Nanobioscience, Yokohama City University , Yokohama 236-0027, Japan
| | - Masahiro Tsuchiya
- Department of Applied Chemistry, National Defense Academy , Yokosuka 239-8686, Japan
| | - Takamasa Uekita
- Department of Applied Chemistry, National Defense Academy , Yokosuka 239-8686, Japan
| | - Tohru Ichimura
- Department of Applied Chemistry, National Defense Academy , Yokosuka 239-8686, Japan
| |
Collapse
|
29
|
Dapic I, Uwugiaren N, Jansen PJ, Corthals GL. Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Anal Chem 2017; 89:10769-10775. [PMID: 28910098 PMCID: PMC5647562 DOI: 10.1021/acs.analchem.7b01937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Human
tissues are an important link between organ-specific spatial
molecular information, patient pathology, and patient treatment options.
However, patient tissues are uniquely obtained by time and location,
and limited in their availability and size. Currently, little knowledge
exists about appropriate and simplified protocols for routine MS-based
analysis of the various types and sizes of tissues. Following standard
procedures used in pathology, we selected small fresh frozen uterine
tissue samples to investigate how the tissue preparation protocol
affected the subsequent proteomics analysis. First, we observed that
protein extraction with 0.1% SDS followed by extraction with a 30%
ACN/urea resulted in a decrease in the number of identified proteins,
when compared to extraction with 30% ACN/urea only. The decrease in
the number of proteins was approximately 55% and 20%, for 10 and 16
μm thick tissue, respectively. Interestingly, the relative abundance
of the proteins shared between the two methods was higher when SDS/ACN/urea
was used, compared to the 30% ACN/urea extraction, indicating the
role of SDS to be beneficial for protein solubility. Second, the influence
of tissue thickness was investigated by comparing the results obtained
for 10, 16, and 20 μm thick (1 mm2) tissue using
urea/30% ACN. We observed an increase in the number of identified
proteins and corresponding quantity with an increase in the tissue
thickness. Finally, by analyzing very small amounts of tissues (∼0.2
mm2) of 10, 16, and 20 μm thickness, we observed
that the increase in tissue thickness resulted in a higher number
of protein identifications and corresponding quantitative values.
Collapse
Affiliation(s)
- Irena Dapic
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Naomi Uwugiaren
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Petra J Jansen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L Corthals
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
30
|
Guo Z, Cheng J, Sun H, Sun W. A qualitative and quantitative evaluation of the peptide characteristics of microwave- and ultrasound-assisted digestion in discovery and targeted proteomic analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1353-1362. [PMID: 28557149 DOI: 10.1002/rcm.7913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Fast digestion methods can dramatically accelerate enzyme digestion and increase the throughput of proteomic analysis. However, the peptide characteristics of fast digestion methods and their performance in discovery and targeted proteomic analysis must be systematically evaluated. METHODS Three digestion methods, including overnight digestion, microwave-assisted protein enzymatic digestion (MAPED), and high-intensity focused ultrasonic-assisted enzymatic digestion (HIFUSAED), in trypsin or in trypsin/Lys-C were comprehensively compared in both discovery and targeted proteomics analysis using the HeLa cell proteome. In discovery proteomic analysis, the highest numbers of peptides and proteins were identified when the sample was digested via the MAPED method with trypsin/Lys-C. RESULTS The fast digestion methods showed a higher mis-cleavage rate and a lower semi-tryptic rate than the overnight digestion method. In both label-free quantitative analysis and targeted proteomic analysis, both fully cleaved peptides (FCPs) and mis-cleaved peptides (MCPs) from the fast digestion methods and the overnight digestion method showed good reproducibility if they showed good abundance. CONCLUSIONS When both the FCPs and MCPs were included in the analysis, the MAPED with trypsin/Lys-C method showed the best results for both discovery proteomic analysis and relative quantitative targeted proteomic analysis. These results will be beneficial for the application of fast digestion methods to proteomics.
Collapse
Affiliation(s)
- Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Cheng
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
31
|
Zhang Y, Sun H, Zhang J, Brasier AR, Zhao Y. Quantitative Assessment of the Effects of Trypsin Digestion Methods on Affinity Purification-Mass Spectrometry-based Protein-Protein Interaction Analysis. J Proteome Res 2017; 16:3068-3082. [PMID: 28726418 DOI: 10.1021/acs.jproteome.7b00432] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Affinity purification-mass spectrometry (AP-MS) has become the method of choice for discovering protein-protein interactions (PPIs) under native conditions. The success of AP-MS depends on the efficiency of trypsin digestion and the recovery of the tryptic peptides for MS analysis. Several different protocols have been used for trypsin digestion of protein complexes in AP-MS studies, but no systematic studies have been conducted on the impact of trypsin digestion conditions on the identification of PPIs. Here, we used NFκB/RelA and Bromodomain-containing protein 4 (BRD4) as baits and test five distinct trypsin digestion methods (two using "on-beads," three using "elution-digestion" protocols). Although the performance of the trypsin digestion protocols change slightly depending on the different baits, antibodies and cell lines used, we found that elution-digestion methods consistently outperformed on-beads digestion methods. The high-abundance interactors can be identified universally by all five methods, but the identification of low-abundance RelA interactors is significantly affected by the choice of trypsin digestion method. We also found that different digestion protocols influence the selected reaction monitoring (SRM)-MS quantification of PPIs, suggesting that optimization of trypsin digestion conditions may be required for robust targeted analysis of PPIs.
Collapse
Affiliation(s)
- Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Hong Sun
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Jing Zhang
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB) , Galveston, Texas 77555, United States.,Institute for Translational Sciences, UTMB , Galveston, Texas 77555, United States.,Sealy Center for Molecular Medicine, UTMB , Galveston, Texas 77555, United States
| |
Collapse
|
32
|
Wang Y, Wu X, Wang Q, Zheng M, Pang L. Annexin A2 functions downstream of c‑Jun N‑terminal kinase to promote skin fibroblast cell migration. Mol Med Rep 2017; 15:4207-4216. [PMID: 28487977 DOI: 10.3892/mmr.2017.6535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 02/01/2017] [Indexed: 11/06/2022] Open
Abstract
Delayed healing of skin wounds is one of the outcomes of diabetes mellitus (DM), a condition that affects a significant number of patients worldwide. However, the underlying mechanisms remain unknown. In order to examine proteome alterations in DM, a rat model of type 1 diabetes was developed using streptozotocin injections. The proteomic responses of normal and DM rat skin were analyzed by two‑dimensional electrophoresis, and differentially expressed proteins were identified using a liquid chromatography/mass spectrometry system. DM induced 36 and repressed 41 differentially expressed proteins, respectively. Altered proteins were involved in a number of biological processes, including RNA and protein metabolism, the tricarboxylic acid cycle, glycolysis, cytoskeleton regulation, hydrogen detoxification and calcium‑mediated signal transduction. In addition, overexpression of annexin A2, one of the signaling proteins altered by DM, accelerated the rate of human skin fibroblast cell migration. Application of SP600125, an inhibitor of a key regulator of cell migration c‑Jun N‑terminal kinase (JNK), inhibited the migration of normal cells. By contrast, SP600125 treatment did not inhibit the migration of annexin A2‑overexpressed cells, indicating that annexin A2 may function downstream of JNK. In conclusion, the results of the present study reveal the potential proteomic responses to DM in skin tissues, and demonstrate a positive functional role of annexin A2 in fibroblast cell migration.
Collapse
Affiliation(s)
- Youpei Wang
- Clinical Examination Center, The Affiliated Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Xinmei Wu
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Qing Wang
- Function Experiment Teaching Center of Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Meiqin Zheng
- Clinical Examination Center, The Affiliated Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Lingxia Pang
- Function Experiment Teaching Center of Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| |
Collapse
|
33
|
Devi S, Wu BH, Chu PY, Liu YP, Wu HL, Ho YP. Studying the effect of microwave heating on the digestion process and identification of proteins. Electrophoresis 2016; 38:429-440. [PMID: 27770443 DOI: 10.1002/elps.201600392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 11/07/2022]
Abstract
The impact of microwave irradiation on the in-solution digestion processes and the detection limit of proteins are systematically studied. Kinetic processes of many peptides produced through the trypsin digestion of various proteins under microwave heating at 50°C were investigated with MALDI-MS. This study also examines the detection limits and digestion completeness of individual proteins under microwave heating at 50°C and at different time intervals (1, 5 and 30 min) using LC-MS. We conclude that if the peptides without missed cleavage dictate the detection limit, conventional digestion will lead to a better detection limit. The detection limit may not differ between the microwave and conventional heating if the peptides with missed cleavage sites and strong intensity are formed at the very early stage (i.e., less than 1 min) and are not further digested throughout the entire digestion process. The digestion of Escherichia coli lysate was compared under conventional and short time (microwave) conditions. The number of proteins identified under conventional heating exceeded that obtained from microwave heating over heating periods less than 5 min. The overall results show that the microwave-assisted digestion is not complete. Although the sequence coverage might be better, the detection limit might be worse than that under conventional heating.
Collapse
Affiliation(s)
- Shobha Devi
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Bo-Hung Wu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Pei-Yu Chu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Yue-Pei Liu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Hsin-Lin Wu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| |
Collapse
|
34
|
Karner A, Gesslbauer B, Spreitzer A, Almer J, Smidt M, Schüler W, Fartmann B, Zimmermann W, Meinke A, Kungl AJ. Profiling the Membrane and Glycosaminoglycan-Binding Proteomes of Moraxella catarrhalis. J Proteome Res 2016; 15:3055-97. [DOI: 10.1021/acs.jproteome.6b00187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anita Karner
- Institute
of Pharmaceutical Sciences, University of Graz, Universitaetsplatz
1, A-8010 Graz, Austria
| | - Bernd Gesslbauer
- Institute
of Pharmaceutical Sciences, University of Graz, Universitaetsplatz
1, A-8010 Graz, Austria
| | - Anton Spreitzer
- Institute
of Pharmaceutical Sciences, University of Graz, Universitaetsplatz
1, A-8010 Graz, Austria
| | - Johannes Almer
- Institute
of Pharmaceutical Sciences, University of Graz, Universitaetsplatz
1, A-8010 Graz, Austria
| | | | | | | | | | | | - Andreas J. Kungl
- Institute
of Pharmaceutical Sciences, University of Graz, Universitaetsplatz
1, A-8010 Graz, Austria
| |
Collapse
|
35
|
Moore SM, Hess SM, Jorgenson JW. Extraction, Enrichment, Solubilization, and Digestion Techniques for Membrane Proteomics. J Proteome Res 2016; 15:1243-52. [PMID: 26979493 PMCID: PMC5488330 DOI: 10.1021/acs.jproteome.5b01122] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of membrane proteins in biological systems is indisputable; however, their amphipathic nature makes them difficult to analyze. In this study, the most popular techniques for extraction, enrichment, solubilization, and digestion are compared, resulting in an overall improved workflow for the insoluble portion of Saccharomyces cerevisiae cell lysate. Yeast cells were successfully lysed using a French press pressure cell at 20 000 psi, and resulting proteins were fractionated prior to digestion to reduce sample complexity. The proteins were best solubilized with the addition of ionic detergent sodium deoxycholate (1%) and through the application of high-frequency sonication prior to a tryptic digestion at 37 °C. Overall, the improved membrane proteomic workflow resulted in a 26% increase in membrane protein identifications for baker's yeast. In addition, more membrane protein identifications were unique to the improved protocol. When comparing membrane proteins that were identified in the improved protocol and the standard operating procedure (176 proteins), 93% of these proteins were present in greater abundance (higher intensity) when using the improved method.
Collapse
Affiliation(s)
- Stephanie M. Moore
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie M. Hess
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James W. Jorgenson
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
36
|
Meyer NA, Root K, Zenobi R, Vidal-de-Miguel G. Gas-Phase Dopant-Induced Conformational Changes Monitored with Transversal Modulation Ion Mobility Spectrometry. Anal Chem 2016; 88:2033-40. [PMID: 26845079 DOI: 10.1021/acs.analchem.5b02750] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The potential of a Transversal Modulation Ion Mobility Spectrometry (TMIMS) instrument for protein analysis applications has been evaluated. The Collision Cross Section (CCS) of cytochrome c measured with the TMIMS is in agreement with values reported in the literature. Additionally, it enables tandem IMS-IMS prefiltration in dry gas and in vapor doped gas. The chemical specificity of the different dopants enables interesting studies on the structure of proteins as CCS changed strongly depending on the specific dopant. Hexane produced an unexpectedly high CCS shift, which can be utilized to evaluate the exposure of hydrophobic parts of the protein. Alcohols produced higher shifts with a dual behavior: an increase in CCS due to vapor uptake at specific absorption sites, followed by a linear shift typical for unspecific and unstable vapor uptake. The molten globule +8 shows a very specific transition. Initially, its CCS follows the trend of the compact folded states, and then it rapidly increases to the levels of the unfolded states. This strong variation suggests that the +8 charge state undergoes a dopant-induced conformational change. Interestingly, more sterically demanding alcohols seem to unfold the protein more effectively also in the gas phase. This study shows the capabilities of the TMIMS device for protein analysis and how tandem IMS-IMS with dopants could provide better understanding of the conformational changes of proteins.
Collapse
Affiliation(s)
- Nicole Andrea Meyer
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland
| | - Guillermo Vidal-de-Miguel
- Department of Chemistry and Applied Biosciences, ETH Zurich , CH-8093, Zurich, Switzerland.,Fossil Ion Technology (FIT) , Cipreses 18, 28036, Madrid, Spain
| |
Collapse
|
37
|
de Michele R, McFarlane HE, Parsons HT, Meents MJ, Lao J, González Fernández-Niño SM, Petzold CJ, Frommer WB, Samuels AL, Heazlewood JL. Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings. J Proteome Res 2016; 15:900-13. [PMID: 26781341 DOI: 10.1021/acs.jproteome.5b00876] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane using biochemical fractionation techniques. In this study, two-phase partitioning was combined with free-flow electrophoresis to produce a population of highly purified plasma membrane vesicles that were subsequently characterized by tandem mass spectroscopy. This combined high-quality plasma membrane isolation technique produced a reproducible proteomic library of over 1000 proteins with an extended dynamic range including plasma membrane-associated proteins. The approach enabled the detection of a number of putative plasma membrane proteins not previously identified by other studies, including peripheral membrane proteins. Utilizing multiple data sources, we developed a PM-confidence score to provide a value indicating association to the plasma membrane. This study highlights over 700 proteins that, while seemingly abundant at the plasma membrane, are mostly unstudied. To validate this data set, we selected 14 candidates and transiently localized 13 to the plasma membrane using a fluorescent tag. Given the importance of the plasma membrane, this data set provides a valuable tool to further investigate important proteins. The mass spectrometry data are available via ProteomeXchange, identifier PXD001795.
Collapse
Affiliation(s)
- Roberto de Michele
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States.,Institute of Biosciences and Bioresources (CNR-IBBR), National Research Council of Italy , Palermo 90129, Italy
| | - Heather E McFarlane
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada.,Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany
| | - Harriet T Parsons
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Plant and Environmental Sciences, University of Copenhagen , Copenhagen C-1871, Denmark
| | - Miranda J Meents
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Susana M González Fernández-Niño
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science , Stanford, California 94305, United States
| | - A Lacey Samuels
- Department of Botany, University of British Columbia , Vancouver, BC V6T 1Z4, Canada
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne , Melbourne, Victoria 3010, Australia
| |
Collapse
|
38
|
Unraveling Mesenchymal Stem Cells' Dynamic Secretome Through Nontargeted Proteomics Profiling. Methods Mol Biol 2016; 1416:521-49. [PMID: 27236694 DOI: 10.1007/978-1-4939-3584-0_32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The modulatory and regenerative potential shown by the use of MSC secretomes has emphasized the importance of their proteomics profiling. Proteomic analysis, initially focused on the targeted analysis of some candidate proteins or the identification of the secreted proteins, has been changing to an untargeted profiling also based on the quantitative evaluation of the secreted proteins.The study of the secretome can be accomplished through several different proteomics-based approaches; however this analysis must overcome one key challenge of secretome analysis: the low amount of secreted proteins and usually their high dilution.In this chapter, a general workflow for the untargeted proteomic profile of MSC's secretome is presented, in combination with a comprehensive description of the major techniques/procedures that can be used. Special focus is given to the main procedures to obtain the secreted proteins, from secretome concentration by ultrafiltration to protein precipitation. Lastly, different proteomics-based approaches are presented, emphasizing alternative digestion techniques and available mass spectrometry-based quantitative methods.
Collapse
|
39
|
Kori Y, Patel R, Neill A, Liu H. A conventional procedure to reduce Asn deamidation artifacts during trypsin peptide mapping. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1009-1010:107-13. [DOI: 10.1016/j.jchromb.2015.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/12/2022]
|
40
|
Dulay MT, Eberlin LS, Zare RN. Protein Analysis by Ambient Ionization Mass Spectrometry Using Trypsin-Immobilized Organosiloxane Polymer Surfaces. Anal Chem 2015; 87:12324-30. [PMID: 26567450 DOI: 10.1021/acs.analchem.5b03669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the growing field of proteomic research, rapid and simple protein analysis is a crucial component of protein identification. We report the use of immobilized trypsin on hybrid organic-inorganic organosiloxane (T-OSX) polymers for the on-surface, in situ digestion of four model proteins: melittin, cytochrome c, myoglobin, and bovine serum albumin. Tryptic digestion products were sampled, detected, and identified using desorption electrospray ionization mass spectrometry (DESI-MS) and nanoDESI-MS. These novel, reusable T-OSX arrays on glass slides allow for protein digestion in methanol:water solvents (1:1, v/v) and analysis directly from the same polymer surface without the need for sample preparation, high temperature, and pH conditions typically required for in-solution trypsin digestions. Digestion reactions were conducted with 2 μL protein sample droplets (0.35 mM) at incubation temperatures of 4, 25, 37, and 65 °C and digestion reaction times between 2 and 24 h. Sequence coverages were dependent on the hydrophobicity of the OSX polymer support and varied by temperature and digestion time. Under the best conditions, the sequence coverages, determined by DESI-MS, were 100% for melittin, 100% for cytochrome c, 90% for myoglobin, and 65% for bovine serum albumin.
Collapse
Affiliation(s)
- Maria T Dulay
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Livia S Eberlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| |
Collapse
|
41
|
Hedrick VE, LaLand MN, Nakayasu ES, Paul LN. Digestion, Purification, and Enrichment of Protein Samples for Mass Spectrometry. ACTA ACUST UNITED AC 2015; 7:201-222. [PMID: 26331527 DOI: 10.1002/9780470559277.ch140272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Victoria E. Hedrick
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Mercedes N. LaLand
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Ernesto S. Nakayasu
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Lake N. Paul
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| |
Collapse
|
42
|
Humphrey SJ, Azimifar SB, Mann M. High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics. Nat Biotechnol 2015; 33:990-5. [DOI: 10.1038/nbt.3327] [Citation(s) in RCA: 340] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/27/2015] [Indexed: 01/15/2023]
|
43
|
Šlechtová T, Gilar M, Kalíková K, Tesařová E. Insight into Trypsin Miscleavage: Comparison of Kinetic Constants of Problematic Peptide Sequences. Anal Chem 2015; 87:7636-43. [PMID: 26158323 DOI: 10.1021/acs.analchem.5b00866] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trypsin, a high fidelity protease, is the most widely used enzyme for protein digestion in proteomic research. Optimal digestion conditions are well-known and so are the expected cleavage products. However, missed cleavage sites are frequently observed when acidic amino acids, aspartic and glutamic acids, are present near the cleavage site. Also, the sequence motifs with successive lysine and/or arginine residues represent a source of missed cleaved sites. In spite of an adverse role of missed cleaved peptides on proteomic research, the digestion kinetics of these problematic sequences is not well-known. In this work, synthetic peptides with various sequence motifs were used as trypsin substrates. Cleavage products were analyzed with reversed-phase high performance liquid chromatography, and the kinetic constants for selected missed cleavage sites were calculated. Relative digestion speed for lysine and arginine sites is compared, including the digestion motifs flanked with aspartic and glutamic acid. Our findings show that DK and DTR motifs are cleaved by trypsin with 3 orders of magnitude lower speed than the arginine site. These motifs are likely to produce missed cleavage peptides in protein tryptic digests even at prolonged digestion times.
Collapse
Affiliation(s)
- Tereza Šlechtová
- †Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague, Czech Republic
| | - Martin Gilar
- ‡Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, United States
| | - Květa Kalíková
- †Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague, Czech Republic
| | - Eva Tesařová
- †Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague, Czech Republic
| |
Collapse
|
44
|
Wang X, Hwang SY, Cong WT, Jin LT, Choi JK. A rapid and simple 8-quinolinol-based fluorescent stain of phosphoproteins in polyacrylamide gel after electrophoresis. Electrophoresis 2015; 36:2522-9. [PMID: 26177935 DOI: 10.1002/elps.201500249] [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: 02/23/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 01/15/2023]
Abstract
In order to obtain an easy and rapid protocol to visualize phosphoproteins in SDS-PAGE, a fluorescent detection method named 8-Quinolinol (8-Q) stain is described. 8-Q can form ternary complexes in the gel matrix contributed by the affinity of aluminum ion (Al(3+) ) to the phosphate groups on the proteins and the metal chelating property of 8-Quinolinol, exhibiting strong fluorescence in ultraviolet light. It can visualize as little as 4∼8 ng of α-casein and β-casein, 16∼32 ng of ovalbumin and κ-casein which is more sensitive than Stains-All but less sensitive than Pro-Q Diamond. The protocol of 8-Q requires only 70 min in 0.75 mm mini-size or 1.0 mm large-size gels with five changes of solutions without destaining step; Pro-Q takes at least 250 min with 11 changes of solutions. In addition, the new method was confirmed by the study of dephosphorylation and LC-MS/MS, respectively. The approach to visualize phosphoprotein utilizing 8-Q could be an alternative to simplify the analytical operations for phosphoproteomics research.
Collapse
Affiliation(s)
- Xu Wang
- School of Pharmaceutical Sciences, Key Laboratory of Biotechnology Pharmaceutical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Sun-Young Hwang
- College of Pharmacy & Research Institute of Drug Development, Chonnam National University, Gwangju, South Korea
| | - Wei-Tao Cong
- School of Pharmaceutical Sciences, Key Laboratory of Biotechnology Pharmaceutical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Li-Tai Jin
- School of Pharmaceutical Sciences, Key Laboratory of Biotechnology Pharmaceutical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Jung-Kap Choi
- College of Pharmacy & Research Institute of Drug Development, Chonnam National University, Gwangju, South Korea
| |
Collapse
|
45
|
Enrichment of single neurons and defined brain regions from human brain tissue samples for subsequent proteome analysis. J Neural Transm (Vienna) 2015; 122:993-1005. [PMID: 26123835 DOI: 10.1007/s00702-015-1414-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/11/2015] [Indexed: 12/11/2022]
Abstract
Brain function in normal aging and neurological diseases has long been a subject of interest. With current technology, it is possible to go beyond descriptive analyses to characterize brain cell populations at the molecular level. However, the brain comprises over 100 billion highly specialized cells, and it is a challenge to discriminate different cell groups for analyses. Isolating intact neurons is not feasible with traditional methods, such as tissue homogenization techniques. The advent of laser microdissection techniques promises to overcome previous limitations in the isolation of specific cells. Here, we provide a detailed protocol for isolating and analyzing neurons from postmortem human brain tissue samples. We describe a workflow for successfully freezing, sectioning and staining tissue for laser microdissection. This protocol was validated by mass spectrometric analysis. Isolated neurons can also be employed for western blotting or PCR. This protocol will enable further examinations of brain cell-specific molecular pathways and aid in elucidating distinct brain functions.
Collapse
|
46
|
Longo LVG, Nakayasu ES, Pires JHS, Gazos-Lopes F, Vallejo MC, Sobreira TJP, Almeida IC, Puccia R. Characterization of Lipids and Proteins Associated to the Cell Wall of the Acapsular Mutant Cryptococcus neoformans Cap 67. J Eukaryot Microbiol 2015; 62:591-604. [PMID: 25733123 DOI: 10.1111/jeu.12213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/22/2014] [Accepted: 01/13/2015] [Indexed: 01/02/2023]
Abstract
Cryptococcus neoformans is an opportunistic human pathogen that causes life-threatening meningitis. In this fungus, the cell wall is exceptionally not the outermost structure due to the presence of a surrounding polysaccharide capsule, which has been highly studied. Considering that there is little information about C. neoformans cell wall composition, we aimed at describing proteins and lipids extractable from this organelle, using as model the acapsular mutant C. neoformans cap 67. Purified cell wall preparations were extracted with either chloroform/methanol or hot sodium dodecyl sulfate. Total lipids fractionated in silica gel 60 were analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS), while trypsin digested proteins were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). We detected 25 phospholipid species among phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, and phosphatidic acid. Two glycolipid species were identified as monohexosyl ceramides. We identified 192 noncovalently linked proteins belonging to different metabolic processes. Most proteins were classified as secretory, mainly via nonclassical mechanisms, suggesting a role for extracellular vesicles (EV) in transwall transportation. In concert with that, orthologs from 86% of these proteins have previously been reported both in fungal cell wall and/or in EV. The possible role of the presently described structures in fungal-host relationship is discussed.
Collapse
Affiliation(s)
- Larissa V G Longo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| | - Ernesto S Nakayasu
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso (UTEP), El Paso, 79968-0519, Texas, USA
| | - Jhon H S Pires
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| | - Felipe Gazos-Lopes
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso (UTEP), El Paso, 79968-0519, Texas, USA
| | - Milene C Vallejo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| | - Tiago J P Sobreira
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, 13083-970, São Paulo, Brazil
| | - Igor C Almeida
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso (UTEP), El Paso, 79968-0519, Texas, USA
| | - Rosana Puccia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-UNIFESP, São Paulo, 04023-062, São Paulo, Brazil
| |
Collapse
|
47
|
Shen JX, Liu G, Zhao Y. Strategies for improving sensitivity and selectivity for the quantitation of biotherapeutics in biological matrix using LC-MS/MS. Expert Rev Proteomics 2015; 12:125-31. [DOI: 10.1586/14789450.2015.1024225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
48
|
Vorob’ev MM, Strauss K, Vogel V, Mäntele W. Demasking of Peptide Bonds During Tryptic Hydrolysis of β-casein in the Presence of Ethanol. FOOD BIOPHYS 2015. [DOI: 10.1007/s11483-015-9391-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
49
|
Bigeard J, Pflieger D, Colcombet J, Gérard L, Mireau H, Hirt H. Protein complexes characterization in Arabidopsis thaliana by tandem affinity purification coupled to mass spectrometry analysis. Methods Mol Biol 2015; 1171:237-50. [PMID: 24908132 DOI: 10.1007/978-1-4939-0922-3_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Proteins are major elements participating in all the key functions of the cells. They rarely fulfill their physiological roles in an autonomous way but rather act as part of more complex cellular machines. Indeed they can bind different types of molecules (proteins, nucleic acids, metabolites, etc.), via stable or transient interactions, depending on their nature and functions. The identification of the molecular partners of a given protein is hence essential to better understand its roles, regulation, and mechanisms of action.This chapter describes the use of a tandem affinity purification approach followed by mass spectrometry analysis to try to identify and characterize the proteins involved in protein complexes in Arabidopsis thaliana and decipher some mechanisms of regulation of the modules. Important elements to consider in such an approach are first extensively exposed in the introduction. This technique, in combination with complementary approaches like yeast two-hybrid and bimolecular fluorescence complementation, can be an interesting source of data to identify and characterize in vivo protein complexes.
Collapse
Affiliation(s)
- Jean Bigeard
- URGV Plant Genomics, UMR INRA-1165/CNRS-ERL8196/Université d'Evry Val d'Essonne, 2, rue Gaston Crémieux, CP5708, 91057, Evry Cedex, France
| | | | | | | | | | | |
Collapse
|
50
|
Krahmer J, Hindle MM, Martin SF, Le Bihan T, Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods Enzymol 2014; 551:405-31. [PMID: 25662467 PMCID: PMC4427183 DOI: 10.1016/bs.mie.2014.10.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Systems biological approaches to study the Arabidopsis thaliana circadian clock have mainly focused on transcriptomics while little is known about the proteome, and even less about posttranslational modifications. Evidence has emerged that posttranslational protein modifications, in particular phosphorylation, play an important role for the clock and its output. Phosphoproteomics is the method of choice for a large-scale approach to gain more knowledge about rhythmic protein phosphorylation. Recent plant phosphoproteomics publications have identified several thousand phosphopeptides. However, the methods used in these studies are very labor-intensive and therefore not suitable to apply to a well-replicated circadian time series. To address this issue, we present and compare different strategies for sample preparation for phosphoproteomics that are compatible with large numbers of samples. Methods are compared regarding number of identifications, variability of quantitation, and functional categorization. We focus on the type of detergent used for protein extraction as well as methods for its removal. We also test a simple two-fraction separation of the protein extract.
Collapse
Affiliation(s)
- Johanna Krahmer
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthew M Hindle
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah F Martin
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thierry Le Bihan
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
| |
Collapse
|