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Butalewicz JP, Escobar EE, Wootton CA, Theisen A, Park MA, Seeley EH, Brodbelt JS. Conformational Characterization of Peptides and Proteins by 193 nm Ultraviolet Photodissociation in the Collision Cell of a Trapped Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometer. Anal Chem 2024; 96:16154-16161. [PMID: 39365147 DOI: 10.1021/acs.analchem.4c02686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Ultraviolet photodissociation (UVPD) has been shown to be a versatile ion activation strategy for the characterization of peptides and intact proteins among other classes of biological molecules. Combining the high-performance mass spectrometry (MS/MS) capabilities of UVPD with the high-resolution separation of trapped ion mobility spectrometry (TIMS) presents an opportunity for enhanced structural elucidation of biological molecules. In the present work, we integrate a 193 nm excimer laser in a TIMS-time-of-flight (TIMS-TOF) mass spectrometer for UVPD in the collision cell and use it for the analysis of several mass-mobility-selected species of ubiquitin and myoglobin. The resultant data displayed differences in fragmentation that could be correlated with changes in protein conformation. Additionally, this mobility-resolved UVPD strategy was applied to collision-induced unfolded ions of ubiquitin to follow changes in fragmentation patterns relating to the extent of protein unfolding. This platform and methodology offer new opportunities for exploring how conformational variations are manifested in the fragmentation patterns of gas-phase ions.
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Affiliation(s)
- Jamie P Butalewicz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Alina Theisen
- Bruker Daltonics GmbH & Co. KG, Bremen 28359, Germany
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Erin H Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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2
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Desmurget C, Perilleux A, Souquet J, Borth N, Douet J. Molecular biomarkers identification and applications in CHO bioprocessing. J Biotechnol 2024; 392:11-24. [PMID: 38852681 DOI: 10.1016/j.jbiotec.2024.06.005] [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] [Received: 12/18/2023] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Biomarkers are valuable tools in clinical research where they allow to predict susceptibility to diseases, or response to specific treatments. Likewise, biomarkers can be extremely useful in the biomanufacturing of therapeutic proteins. Indeed, constraints such as short timelines and the need to find hyper-productive cells could benefit from a data-driven approach during cell line and process development. Many companies still rely on large screening capacities to develop productive cell lines, but as they reach a limit of production, there is a need to go from empirical to rationale procedures. Similarly, during bioprocessing runs, substrate consumption and metabolism wastes are commonly monitored. None of them possess the ability to predict the culture behavior in the bioreactor. Big data driven approaches are being adapted to the study of industrial mammalian cell lines, enabled by the publication of Chinese hamster and CHO genome assemblies which allowed the use of next-generation sequencing with these cells, as well as continuous proteome and metabolome annotation. However, if these different -omics technologies contributed to the characterization of CHO cells, there is a significant effort remaining to apply this knowledge to biomanufacturing methods. The correlation of a complex phenotype such as high productivity or rapid growth to the presence or expression level of a specific biomarker could save time and effort in the screening of manufacturing cell lines or culture conditions. In this review we will first discuss the different biological molecules that can be identified and quantified in cells, their detection techniques, and associated challenges. We will then review how these markers are used during the different steps of cell line and bioprocess development, and the inherent limitations of this strategy.
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Affiliation(s)
- Caroline Desmurget
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Arnaud Perilleux
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Jonathan Souquet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Julien Douet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland.
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3
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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Suwanchaikasem P, Rattanapisit K, Strasser R, Phoolcharoen W. Quality control in SARS-CoV-2 RBD-Fc vaccine production using LC-MS to confirm strain selection and detect contaminations from other strains. Sci Rep 2024; 14:9629. [PMID: 38671013 PMCID: PMC11053075 DOI: 10.1038/s41598-024-59860-4] [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] [Received: 01/02/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing outbreak, disrupting human life worldwide. Vaccine development was prioritized to obtain a biological substance for combating the viral pathogen and lessening disease severity. In vaccine production, biological origin and relevant materials must be carefully examined for potential contaminants in conformity with good manufacturing practice. Due to fast mutation, several SARS-CoV-2 variants and sublineages have been identified. Currently, most of COVID-19 vaccines are developed based on the protein sequence of the Wuhan wild type strain. New vaccines specific for emerging SARS-CoV-2 strains are continuously needed to tackle the incessant evolution of the virus. Therefore, in vaccine development and production, a reliable method to identify the nature of subunit vaccines is required to avoid cross-contamination. In this study, liquid chromatography-mass spectrometry using quadrupole-time of flight along with tryptic digestion was developed for distinguishing protein materials derived from different SARS-CoV-2 strains. After analyzing the recombinantly produced receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, nine characteristic peptides were identified with acceptable limits of detection. They can be used together to distinguish 14 SARS-CoV-2 strains, except Kappa and Epsilon. Plant-produced RBD-Fc protein derived from Omicron strains can be easily distinguished from the others with 4-5 unique peptides. Eventually, a peptide key was developed based on the nine peptides, offering a prompt and precise flowchart to facilitate SARS-CoV-2 strain identification in COVID-19 vaccine manufacturing.
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Affiliation(s)
| | | | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, 1180, Vienna, Austria
| | - Waranyoo Phoolcharoen
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, 10330, Thailand.
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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5
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Bianco M, Calvano CD, Ventura G, Losito I, Cataldi TRI. Proteomics for Microalgae Extracts by High-Resolution Mass Spectrometry. Methods Mol Biol 2024; 2820:67-88. [PMID: 38941016 DOI: 10.1007/978-1-0716-3910-8_8] [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: 06/29/2024]
Abstract
Two protocols of protein extraction from Arthrospira platensis (spirulina) microalgae to study their proteome by mass spectrometry (MS) are here presented. The first is based on an aqueous buffer solution of Tris-HCl and the second on cold acetone. The identification of proteins was carried out by a bottom-up approach, which involves enzymatic digestion of extracted proteins followed by either matrix-assisted laser desorption ionization with time-of-flight (MALDI-TOF) MS or liquid chromatography (LC) coupled with electrospray ionization (ESI) and Fourier-transform tandem MS. While MALDI-TOF MS allowed for a fast peptide mass fingerprinting (PMF) check yet identifying less than 20 proteins in the extracted samples, the data-dependent acquisitions (DDA) mode of reversed-phase (RP) LC-ESI tandem FTMS/MS separations allowed us to recognize more than one hundred proteins by searching into dedicated spectral libraries. The application of MALDI-TOF MS analysis was found, however, of great support for preliminary investigations of cyanobacteria samples before proceeding with the RPLC-ESI-MS/MS DDA investigation, which definitively allows for a qualitative proteome analysis also of minor spirulina proteins in processed foodstuffs. Although the protein content in spirulina can be influenced by cultivation and environmental conditions, e.g., light intensity, climate, and water/air quality, here the qualitative chemical profiles of the examined samples were characterized by similar composition in high-quality proteins as phycocyanins and phycoerythrins.
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Affiliation(s)
- Mariachiara Bianco
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Cosima D Calvano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy.
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy.
| | - Giovanni Ventura
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Ilario Losito
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Centro Interdipartimentale di Ricerca SMART, Università degli Studi di Bari Aldo Moro, Bari, Italy
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Shama A, Soni T, Jawanda IK, Upadhyay G, Sharma A, Prabha V. The Latest Developments in Using Proteomic Biomarkers from Urine and Serum for Non-Invasive Disease Diagnosis and Prognosis. Biomark Insights 2023; 18:11772719231190218. [PMID: 37528936 PMCID: PMC10387783 DOI: 10.1177/11772719231190218] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
Due to diagnostic improvements, medical diagnostics is demanding non-invasive or minimally invasive methods. Non-invasively obtained body fluids (eg., Urine, serum) can replace cerebral fluid, amniotic fluid, synovial fluid, bronchoalveolar lavage fluid, and others for diagnostic reasons. Many illnesses are induced by perturbations of cellular signaling pathways and associated pathway networks as a result of genetic abnormalities. These disturbances are represented by a shift in the protein composition of the fluids surrounding the tissues and organs that is, tissue interstitial fluid (TIF). These variant proteins may serve as diagnostic "signatures" for a variety of disorders. This review provides a concise summary of urine and serum biomarkers that may be used for the diagnosis and prognosis of a variety of disorders, including cancer, brain diseases, kidney diseases, and other system diseases. The studies reviewed in this article suggest that serum and urine biomarkers of various illnesses may be therapeutically useful for future diagnostics. Correct illness management is crucial for disease prognosis, hence non-invasive serum and urine biomarkers have been extensively studied for diagnosis, subclassification, monitoring disease activity, and predicting treatment results and consequences.
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Affiliation(s)
- Anurag Shama
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Thomson Soni
- Department of Microbiology, Panjab University, Chandigarh, India
| | | | - Garima Upadhyay
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Anshika Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Vijay Prabha
- Department of Microbiology, Panjab University, Chandigarh, India
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7
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Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. J Proteome Res 2023; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
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Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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Gajula SNR, Khairnar AS, Jock P, Kumari N, Pratima K, Munjal V, Kalan P, Sonti R. LC-MS/MS: A sensitive and selective analytical technique to detect COVID-19 protein biomarkers in the early disease stage. Expert Rev Proteomics 2023; 20:5-18. [PMID: 36919634 DOI: 10.1080/14789450.2023.2191845] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
INTRODUCTION The COVID-19 outbreak has put enormous pressure on the scientific community to detect infection rapidly, identify the status of disease severity, and provide an immediate vaccine/drug for the treatment. Relying on immunoassay and a real-time reverse transcription polymerase chain reaction (rRT-PCR) led to many false-negative and false-positive reports. Therefore, detecting biomarkers is an alternative and reliable approach for determining the infection, its severity, and disease progression. Recent advances in liquid chromatography and mass spectrometry (LC-MS/MS) enable the protein biomarkers even at low concentrations, thus facilitating clinicians to monitor the treatment in hospitals. AREAS COVERED This review highlights the role of LC-MS/MS in identifying protein biomarkers and discusses the clinically significant protein biomarkers such as Serum amyloid A, Interleukin-6, C-Reactive Protein, Lactate dehydrogenase, D-dimer, cardiac troponin, ferritin, Alanine transaminase, Aspartate transaminase, gelsolin and galectin-3-binding protein in COVID-19, and their analysis by LC-MS/MS in the early stage. EXPERT OPINION Clinical doctors monitor significant biomarkers to understand, stratify, and treat patients according to disease severity. Knowledge of clinically significant COVID-19 protein biomarkers is critical not only for COVID-19 caused by the coronavirus but also to prepare us for future pandemics of other diseases in detecting by LC-MS/MS at the early stages.
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Affiliation(s)
- Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Ankita Sahebrao Khairnar
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Pallavi Jock
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Nikita Kumari
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Kendre Pratima
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Vijay Munjal
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Pavan Kalan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Balanagar, India
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9
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The antioxidant, wound healing properties and proteomic analysis of water extracts from the tropical cyanobacteria, Nostoc NIES-2111_MUM004. 3 Biotech 2023; 13:71. [PMID: 36742448 PMCID: PMC9895726 DOI: 10.1007/s13205-022-03448-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 12/23/2022] [Indexed: 02/05/2023] Open
Abstract
Cyanobacteria bioactive compounds are chemical treasure troves for product discovery and development. The wound healing effects and antioxidant capacities of water extracts from Nostoc NIES-2111_MUM004 were evaluated via in vitro wound scratch assay and three antioxidant assays respectively. Results showed that the water extracts were protein-rich and exhibited good antioxidant properties in ABTS radical scavenging (11.27 ± 0.205 mg TAE g-1 extract), Ferric reducing antioxidant power (1652.71 ± 110.71 mg TAE g-1 extract) and β-carotene bleaching assay (354.90 ± 31.80 mg TAE g-1 extract). Also, extracts were non-cytotoxic in concentrations up to 250 µg/mL as reflected in cytotoxicity assay. Importantly, water extracts showed considerable proliferation and migration activity at 125 µg/mL with wound closure rate as high as 42.67%. Statistical correlation revealed no significant relationship (p > 0.05) between protein fraction and the wound healing properties, confirming that phycobiliproteins were not solely responsible for wound healing activities. Subsequent Q-TOF-LCMS analysis identified six protein families involved in enhancing the proliferation and migration of epithelial cells. These findings are antecedent in the uncovering of continuous supplies of bioactive compounds from new and sustainable sources. Ultimately, enriching the microalgae menu for applications in pharmaceutical, nutraceutical and cosmeceuticals.
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10
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Sharaf BM, Giddey AD, Al-Hroub HM, Menon V, Okendo J, El-Awady R, Mousa M, Almehdi A, Semreen MH, Soares NC. Mass spectroscopy-based proteomics and metabolomics analysis of triple-positive breast cancer cells treated with tamoxifen and/or trastuzumab. Cancer Chemother Pharmacol 2022; 90:467-488. [PMID: 36264351 DOI: 10.1007/s00280-022-04478-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/22/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE HER2-enriched breast cancer with high levels of hormone receptor expression, known as "triple positive" breast cancer, may represent a new entity with a relatively favourable prognosis against which the combination of chemotherapy, HER-2 inhibition, and endocrine treatment may be considered overtreatment. We explored the effect of the anticancer drugs tamoxifen and trastuzumab, both separately and in combination, on the integrated proteomic and metabolic profile of "triple positive" breast cancer cells (BT-474). METHOD We employed ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry using a Bruker timsTOF to investigate changes in BT-474 cell line treated with either tamoxifen, trastuzumab or a combination. Differentially abundant metabolites were identified using the Bruker Human Metabolome Database metabolite library and proteins using the Uniprot proteome for Homo sapiens using MetaboScape and MaxQuant, respectively, for identification and quantitation. RESULTS A total of 77 proteins and 85 metabolites were found to significantly differ in abundance in BT-474 treated cells with tamoxifen 5 μM/and or trastuzumab 2.5 μM. Findings suggest that by targeting important cellular signalling pathways which regulate cell growth, apoptosis, proliferation, and chemoresistance, these medicines have a considerable anti-growth effect in BT-474 cells. Pathways enriched for dysregulation include RNA splicing, neutrophil degranulation and activation, cellular redox homeostasis, mitochondrial transmembrane transport, ferroptosis and necroptosis, ABC transporters and central carbon metabolism. CONCLUSION Our findings in protein and metabolite level research revealed that anti-cancer drug therapy had a significant impact on the key signalling pathways and molecular processes in triple positive BT-474 cell lines.
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Affiliation(s)
- Basma M Sharaf
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates.,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Alexander D Giddey
- Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Hamza M Al-Hroub
- Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Varsha Menon
- Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road Observatory, Cape Town, 7925, South Africa
| | - Raafat El-Awady
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates.,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates
| | - Muath Mousa
- Research Institute of Science and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Ahmed Almehdi
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Mohammad H Semreen
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates. .,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates.
| | - Nelson C Soares
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box. 27272, Sharjah, United Arab Emirates. .,Research Institute for Medical and Health Sciences (RIHMS), University of Sharjah, Sharjah, United Arab Emirates.
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11
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Li L, Sun R, Zenga J, Himburg H, Wang L, Duan S, Liu J, Bui D, Xie Z, Du T, Xie L, Yin T, Wong S, Gao S, Hu M. Comparison of Absolute Expression and Turnover Number of COX-1 and COX-2 in Human and Rodent Cells and Tissues. J Inflamm Res 2022; 15:4435-4447. [PMID: 35958187 PMCID: PMC9359786 DOI: 10.2147/jir.s365842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Objective We aim to quantify the absolute protein expression of cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) in various cells and tissues to determine the relative contribution of COX-1 and COX-2 to PGE2 production. Methods An LC-MS method was developed and validated, then used for quantifying the absolute amounts of COX-1 and COX-2 in recombinant human COX-1 and COX-2, lysates from different cells, tissue microsomes of rodents and humans, Pirc rat colonic polyps, and biopsy specimens from squamous cell carcinoma (SCC) patients. The COX-1 and COX-2 turnover numbers were subsequently calculated based on apparent formation rates of PGE2. Results A robust LC-MS method for quantification of COX-1 and COX-2 was developed and validated and then used to calculate their apparent turnover numbers. The results showed that COX-1 expression levels were much higher than that of COX-2 in all the tested tissues including the colonic epithelium of F344 (28-fold) and Pirc rats (20-fold), colonic polyps of Pirc rats (8-fold), and biopsy specimens of SCC patients (11–17-fold). In addition, both COX-1 and COX-2 were higher in polyps when compared to adjacent mucosa of Pirc rats. The turnover number of recombinant human COX-2 was 14-fold higher than that of recombinant human COX-1. LPS stimulation increased COX-2 protein expression in three cell lines (Raw 264.7, SCC9 and EOMA) as expected but unexpectedly increased COX-1 protein expression (13.8-fold) in EOMA cells. Conclusion In human oral cancer tissues and cells as well as Pirc rat colon, COX-1 plays an unexpectedly but more important role than COX-2 in abnormal PGE2 production since COX-1 expression is much higher than COX-2. In addition, COX-1 expression levels are inducible in cells, and higher in polyps than surrounding mucosa in Pirc rat colon. These results indicate that targeted suppression of local COX-1 should be considered to reduce colon-specific PGE2-mediated inflammation.
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Affiliation(s)
- Li Li
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Rongjin Sun
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Joseph Zenga
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Heather Himburg
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lu Wang
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Shengnan Duan
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Jingwen Liu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Dinh Bui
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Zuoxu Xie
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Ting Du
- Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Lijun Xie
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Taijun Yin
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Stu Wong
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Song Gao
- Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
- Song Gao, Department of Pharmaceutical Science, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA, Email
| | - Ming Hu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
- Correspondence: Ming Hu, Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA, Email
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12
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Xu T, Chen J, Yang K, Qiao W, Zhao J, Chen L. Quantitative Determination of Whey Protein to Casein Ratio in Infant Formula Milk Powder. Front Chem 2022; 10:872251. [PMID: 35620655 PMCID: PMC9127462 DOI: 10.3389/fchem.2022.872251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022] Open
Abstract
This study was aimed to establish a method for quantitatively determining the ratio of whey protein in the total protein of infant formula by respectively selecting two characteristic peptides from whey protein and casein and calculating the ratio between the characteristic peptides. A nanoliter high-performance liquid chromatography tandem high-resolution mass spectrometry (Q Exactive) was used to simultaneously detect the characteristic peptides of two main whey proteins and two main caseins. The characteristic peptides were calculated, predicted, and screened using the ExPASy website, and peptide information was confirmed by database retrieval after the analysis by using a high-resolution mass spectrometer. The matrix effect was compensated by comparing the characteristic peptides in whey protein with those in casein protein, in which isotope internal standards were not required. The influence of the changes of the protein content in whey protein and casein on the detection method was eliminated by the calculation formula designed by ourselves. In this detection method, the sample was stable in the total protein concentration range of between 0.1 and 0.4 mg/ml. In the simulated industrial processing environment, with desalted whey powder, the recovery rate was 98.63–113.33% under different spiked levels with good reproducibility (RSD<8%). The RSDs of intraday and interday precisions were 2.03–9.35% and 0.61–11.02%, respectively. The different processing procedures of samples had no significant impact on the detection of whey protein (RSD% for milk samples treated by different processing techniques was 2.97%). The quantitation method of whey protein was applied to evaluate the whey protein content in different brands of commercially available milk powder. In summary, the proposed method was applicable for quantitative analysis of whey proteins in the infant formula.
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Affiliation(s)
- Tao Xu
- School of Bioengineering, Dalian Polytechnic University, Dalian, China
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Jingyao Chen
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Kai Yang
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Weicang Qiao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Sanyuan Foods Co. Ltd., Beijing, China
| | - Junying Zhao
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- South Asia Branch of National Engineering Center of Dairy for Maternal and Child Health, Guilin University of Technology, Guilin, China
| | - Lijun Chen
- National Engineering Research Center of Dairy Health for Maternal and Child, Beijing Sanyuan Foods Co. Ltd, Beijing, China
- Beijing Engineering Research Center of Dairy, Beijing Sanyuan Foods Co. Ltd., Beijing, China
- South Asia Branch of National Engineering Center of Dairy for Maternal and Child Health, Guilin University of Technology, Guilin, China
- *Correspondence: Lijun Chen,
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Jia H, Wen Y, Aw W, Saito K, Kato H. Ameliorating Effects of Coriander on Gastrocnemius Muscles Undergoing Precachexia in a Rat Model of Rheumatoid Arthritis: A Proteomics Analysis. Nutrients 2021; 13:4041. [PMID: 34836295 PMCID: PMC8621435 DOI: 10.3390/nu13114041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 01/06/2023] Open
Abstract
Coriander is a commonly used vegetable, spice, and folk medicine, possessing both nutritional and medicinal properties. Up to two-thirds of patients with rheumatoid arthritis (RA) exhibit loss of body mass, predominately skeletal muscle mass, a process called rheumatoid cachexia, and this has major effects of the quality of life of patients. Owing to a lack of effective treatments, the initial stage of cachexia has been proposed as an important period for prevention and decreasing pathogenesis. In the current study, we found that cachexia-like molecular disorders and muscle weight loss were in progress in gastrocnemius muscle after only 5 days of RA induction in rats, although rheumatoid cachexia symptoms have been reported occurring approximately 45 days after RA induction. Oral administration of coriander slightly restored muscle loss. Moreover, iTRAQ-based quantitative proteomics revealed that coriander treatment could partially restore the molecular derangements induced by RA, including impaired carbon metabolism, deteriorated mitochondrial function (tricarboxylic acid cycle and oxidative phosphorylation), and myofiber-type alterations. Therefore, coriander could be a promising functional food and/or complementary therapy for patients with RA against cachexia.
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Affiliation(s)
- Huijuan Jia
- Health Nutrition, Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.W.); (W.A.); (K.S.)
| | - Ya Wen
- Health Nutrition, Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.W.); (W.A.); (K.S.)
- Department of Physiology and Pharmacology, Karolinska Institutet, Bioclinicum, J8:30, SE-171 77 Stockholm, Sweden
| | - Wanping Aw
- Health Nutrition, Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.W.); (W.A.); (K.S.)
- Institute for Advanced Biosciences, Keio University, 246-2, Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Kenji Saito
- Health Nutrition, Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.W.); (W.A.); (K.S.)
| | - Hisanori Kato
- Health Nutrition, Department of Applied Biological Chemistry, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.W.); (W.A.); (K.S.)
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Yuan ZC, Hu B. Mass Spectrometry-Based Human Breath Analysis: Towards COVID-19 Diagnosis and Research. JOURNAL OF ANALYSIS AND TESTING 2021; 5:287-297. [PMID: 34422436 PMCID: PMC8364943 DOI: 10.1007/s41664-021-00194-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
COVID-19 is a highly contagious respiratory disease that can be infected through human exhaled breath. Human breath analysis is an attractive strategy for rapid diagnosis of COVID-19 in a non-invasive way by monitoring breath biomarkers. Mass spectrometry (MS)-based approaches offer a promising analytical platform for human breath analysis due to their high speed, specificity, sensitivity, reproducibility, and broad coverage, as well as its versatile coupling methods with different chromatographic separation, and thus can lead to a better understanding of the clinical and biochemical processes of COVID-19. Herein, we try to review the developments and applications of MS-based approaches for multidimensional analysis of COVID-19 breath samples, including metabolites, proteins, microorganisms, and elements. New features of breath sampling and analysis are highlighted. Prospects and challenges on MS-based breath analysis related to COVID-19 diagnosis and study are discussed.
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Affiliation(s)
- Zi-Cheng Yuan
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632 China
| | - Bin Hu
- Guangdong Provincial Engineering Research Center for On-line Source Apportionment System of Air Pollution, Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632 China
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15
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Puspita S, Sunarintyas S, Anwar C, Mulyawati E, HNE Soesatyo M. Amino acid identification of Bombyx mori fibroin cocoon as biomaterial using liquid chromatography/mass spectrometry. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202802001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A fibroin is a natural polymer that serves as a biomaterial because of the mechanical properties, biocompatible, biodegradable and amino acid composition. The mechanical properties of fibroin are influenced by crystalline structures of amino acid and are related to the amino acid composition. it can accelerate the wound healing because it promotes the proliferation of exposure tissue and inhibits inflammation. The study aimed to identify amino acid of Bombyx mori (B. mori) fibroin cocoon as biomaterial that was cultivated in Central Java Indonesia. Liquid Chromatography/Mass Spectrometry (LC/MS-Water, USA) was employed. This study found that fibroin of B. mori contains seventeen amino acids and the most abundant amino acid is L-Valin 4.81 % (mg kg–1).
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16
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Nys G, Cobraiville G, Fillet M. Multidimensional performance assessment of micro pillar array column chromatography combined to ion mobility-mass spectrometry for proteome research. Anal Chim Acta 2019; 1086:1-13. [DOI: 10.1016/j.aca.2019.08.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 01/23/2023]
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17
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Contreras-Aguilar MD, Escribano D, Martínez-Subiela S, Martín-Cuervo M, Lamy E, Tecles F, Cerón JJ. Changes in saliva analytes in equine acute abdominal disease: a sialochemistry approach. BMC Vet Res 2019; 15:187. [PMID: 31170977 PMCID: PMC6554884 DOI: 10.1186/s12917-019-1933-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The biochemical components of saliva can change in certain pathologies in horses, for example in acute abdominal disease. The aim of this study was (1) to evaluate if a panel of biochemical analytes usually used in serum can be measured in saliva of horses and (2) to study the possible changes of these biochemical analytes in saliva of horses affected by acute abdominal disease. A panel of 23 analytes was analytically validated in saliva of horses and possible changes in these analytes in a pilot study with six healthy horses and six horses with acute abdominal disease were evaluated. The analytes with significant changes were then evaluated in a larger population of 20 healthy and 37 diseased horses. RESULTS Seven analytes showed significant increases in the pilot study which were confirmed in the larger population. The analytes which showed significant changes, and their median fold increase and significance shown in the larger population were salivary γ-glutamyl transferase (gGT, 2.3 fold, P = 0.001), creatine kinase (CK, 6.2 fold, P < 0.001), urea (2.3 fold, P = 0.001), total bilirubin (2.6 fold, P < 0.001), total proteins (3.2 fold, P < 0.001), phosphorus (P, 4.5 fold, P < 0.001) and alpha-amylase (sAA, 8.5 fold, P < 0.001). Total proteins, P and sAA showed sensitivities higher than 70% at their optimal cut-off points and a specificity of 100% in differentiating between healthy horses and those with acute abdominal disease. CONCLUSIONS A panel of 23 biochemical analytes can be measured in saliva of horses, where gGT, CK, urea, total bilirubin, total protein, P and sAA levels are raised in horses with acute abdominal disease.
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Affiliation(s)
- María Dolores Contreras-Aguilar
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - Damián Escribano
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
- Department of Food and Animal Science, School of Veterinary Medicine, University of Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Silvia Martínez-Subiela
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - María Martín-Cuervo
- Animal Medicine, Faculty of Veterinary Medicine of Cáceres, University of Extremadura, Av. de la Universidad S-N, 10005 Cáceres, Spain
| | - Elsa Lamy
- Institute of Mediterranean Agricultural and Environmental Sciences, University of Évora, Núcleo da Mitra, Apartado 94, 7006-554 Évora, Portugal
| | - Fernando Tecles
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
| | - Jose Joaquín Cerón
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain
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Perez JJ, Chen CY. Implementation of normalized retention time (iRT) for bottom-up proteomic analysis of the aminoglycoside phosphotransferase enzyme facilitating method distribution. Anal Bioanal Chem 2018; 411:4701-4708. [DOI: 10.1007/s00216-018-1377-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 09/13/2018] [Indexed: 01/05/2023]
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Mahendran SM, Oikonomopoulou K, Diamandis EP, Chandran V. Synovial fluid proteomics in the pursuit of arthritis mediators: An evolving field of novel biomarker discovery. Crit Rev Clin Lab Sci 2017; 54:495-505. [DOI: 10.1080/10408363.2017.1408561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Shalini M. Mahendran
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Katerina Oikonomopoulou
- Centre for Prognosis Studies in Rheumatic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Vinod Chandran
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Centre for Prognosis Studies in Rheumatic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
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Bommana R, Mozziconacci O, John Wang Y, Schöneich C. An Efficient and Rapid Method to Monitor the Oxidative Degradation of Protein Pharmaceuticals: Probing Tyrosine Oxidation with Fluorogenic Derivatization. Pharm Res 2017; 34:1428-1443. [DOI: 10.1007/s11095-017-2159-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/03/2017] [Indexed: 01/07/2023]
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Csősz É, Deák E, Kalló G, Csutak A, Tőzsér J. Diabetic retinopathy: Proteomic approaches to help the differential diagnosis and to understand the underlying molecular mechanisms. J Proteomics 2016; 150:351-358. [PMID: 27373871 DOI: 10.1016/j.jprot.2016.06.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/28/2016] [Indexed: 12/12/2022]
Abstract
Diabetic retinopathy is the most common diabetic eye disease and a leading cause of blindness among patients with diabetes. The appearance and the severity of the symptoms correlate with the duration of diabetes and poor blood glucose level management. Diabetic retinopathy is also categorized as a chronic low-level inflammatory disease; the high blood glucose level promotes the accumulation of the advanced glycation end products and leads to the stimulation of monocytes and macrophages. Examination of protein level alterations in tears using state-of the art proteomics techniques have identified several proteins as possible biomarkers for the different stages of the diabetic retinopathy. Some of the differentially expressed tear proteins have a role in the barrier function of tears linking the diabetic retinopathy with another eye complication of diabetes, namely the diabetic keratopathy resulting in impaired wound healing. Understanding the molecular events leading to the eye complications caused by hyperglycemia may help the identification of novel biomarkers as well as therapeutic targets in order to improve quality of life of diabetic patients. BIOLOGICAL SIGNIFICANCE Diabetic retinopathy (DR), the leading cause of blindness among diabetic patients can develop without any serious symptoms therefore the early detection is crucial. Because of the increasing prevalence there is a high need for improved screening methods able to diagnose DR as soon as possible. The non-invasive collection and the relatively high protein concentration make the tear fluid a good source for biomarker discovery helping the early diagnosis. In this work we have reviewed the administration of advanced proteomics techniques used in tear biomarker studies and the identified biomarkers with potential to improve the already existing screening methods for DR detection.
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Affiliation(s)
- Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Eszter Deák
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary; Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Hungary
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary.
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22
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Sethi S, Chourasia D, Parhar IS. Approaches for targeted proteomics and its potential applications in neuroscience. J Biosci 2016; 40:607-27. [PMID: 26333406 DOI: 10.1007/s12038-015-9537-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other 'omics' approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.
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Affiliation(s)
- Sumit Sethi
- Brain Research Institute, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor Darul Ehsan, Malaysia,
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The omic approach to parasitic trematode research—a review of techniques and developments within the past 5 years. Parasitol Res 2016; 115:2523-43. [DOI: 10.1007/s00436-016-5079-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/26/2022]
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Gladilovich V, Greifenhagen U, Sukhodolov N, Selyutin A, Singer D, Thieme D, Majovsky P, Shirkin A, Hoehenwarter W, Bonitenko E, Podolskaya E, Frolov A. Immobilized metal affinity chromatography on collapsed Langmuir-Blodgett iron(III) stearate films and iron(III) oxide nanoparticles for bottom-up phosphoproteomics. J Chromatogr A 2016; 1443:181-90. [PMID: 27016113 DOI: 10.1016/j.chroma.2016.03.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 01/27/2023]
Abstract
Phosphorylation is the enzymatic reaction of site-specific phosphate transfer from energy-rich donors to the side chains of serine, threonine, tyrosine, and histidine residues in proteins. In living cells, reversible phosphorylation underlies a universal mechanism of intracellular signal transduction. In this context, analysis of the phosphoproteome is a prerequisite to better understand the cellular regulatory networks. Conventionally, due to the low contents of signaling proteins, selective enrichment of proteolytic phosphopeptides by immobilized metal affinity chromatography (IMAC) is performed prior to their LC-MS or -MS/MS analysis. Unfortunately, this technique still suffers from low selectivity and compromised analyte recoveries. To overcome these limitations, we propose IMAC systems comprising stationary phases based on collapsed Langmuir-Blodgett films of iron(III) stearate (FF) or iron(III) oxide nanoparticles (FO) and mobile phases relying on ammonia, piperidine and heptadecafluorooctanesulfonic acid (PFOS). Experiments with model phosphopeptides and phosphoprotein tryptic digests showed superior binding capacity, selectivity and recovery for both systems in comparison to the existing commercial analogs. As evidenced by LC-MS/MS analysis of the HeLa phosphoproteome, these features of the phases resulted in increased phosphoproteome coverage in comparison to the analogous commercially available phases, indicating that our IMAC protocol is a promising chromatographic tool for in-depth phosphoproteomic research.
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Affiliation(s)
- Vladimir Gladilovich
- Institute of Toxicology, Russian Federal Agency for Biology and Medicine, Russia
| | - Uta Greifenhagen
- Universität Leipzig, Faculty of Chemistry and Mineralogy, Germany
| | | | | | - David Singer
- Universität Leipzig, Faculty of Chemistry and Mineralogy, Germany
| | - Domenika Thieme
- Leibniz Institute of Plant Biochemistry, Proteome Analytics Research Group, Germany
| | - Petra Majovsky
- Leibniz Institute of Plant Biochemistry, Proteome Analytics Research Group, Germany
| | - Alexey Shirkin
- Institute of Analytical Instrumentation, Russian Academy of Science, Russia
| | | | - Evgeny Bonitenko
- Institute of Toxicology, Russian Federal Agency for Biology and Medicine, Russia
| | - Ekaterina Podolskaya
- Institute of Toxicology, Russian Federal Agency for Biology and Medicine, Russia; Institute of Analytical Instrumentation, Russian Academy of Science, Russia
| | - Andrej Frolov
- Universität Leipzig, Faculty of Chemistry and Mineralogy, Germany; Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Germany.
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25
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Zhou L, Wang K, Li Q, Nice EC, Zhang H, Huang C. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives. Expert Rev Proteomics 2016; 13:367-81. [PMID: 26923776 DOI: 10.1586/14789450.2016.1159959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.
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Affiliation(s)
- Li Zhou
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Kui Wang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Qifu Li
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Edouard C Nice
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
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26
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Oral squamous cell carcinoma: Key clinical questions, biomarker discovery, and the role of proteomics. Arch Oral Biol 2016; 63:53-65. [DOI: 10.1016/j.archoralbio.2015.11.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 09/08/2015] [Accepted: 11/20/2015] [Indexed: 12/19/2022]
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27
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Baumgartner C. The Era of Big Data: From Data-Driven Research to Data-Driven Clinical Care. TRANSLATIONAL BIOINFORMATICS 2016. [DOI: 10.1007/978-94-017-7543-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Reumer A, Maes E, Mertens I, Cho WCS, Landuyt B, Valkenborg D, Schoofs L, Baggerman G. Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare? Expert Rev Proteomics 2014; 11:449-463. [PMID: 24702250 DOI: 10.1586/14789450.2014.905743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.
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Affiliation(s)
- Ank Reumer
- KU Leuven, Animal Physiology and Neurobiology Section, Naamsestraat 59, BE-3000 Leuven, Belgium
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29
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Lill JR, Wertz IE. Toward understanding ubiquitin-modifying enzymes: from pharmacological targeting to proteomics. Trends Pharmacol Sci 2014; 35:187-207. [PMID: 24717260 DOI: 10.1016/j.tips.2014.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/20/2022]
Abstract
Ubiquitination is a highly conserved post-translational modification that regulates protein trafficking, function, and turnover. Ubiquitin ligases (E3s) conjugate ubiquitin polypeptides on substrates, whereas deubiquitnases (DUBs) reverse ubiquitination. Engineering of chemical antagonists and inhibitors of ubiquitin ligases and DUBs has considerably aided the study of enzymes that participate in ubiquitin modification of substrates. In addition, proteomic tools have been developed to characterize the enzymes, substrates, and modifications regulated by DUBs and E3s. Here we review inhibitors and antagonists that have been developed against DUBs and E3s, focusing on enzymes that participate in ubiquitin editing or in the reciprocal ubiquitin regulation of substrates. We outline the cellular biology that is regulated by these DUBs and E3s and highlight how the inhibitory compounds have improved our understanding of these pathways. Finally, we discuss the challenges and future directions for pharmacologically targeting ubiquitin-modifying enzymes, as well as the development of proteomic methods to evaluate ubiquitin modification of substrates.
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Affiliation(s)
- Jennie R Lill
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, M/S 413A, South San Francisco, CA 94080, USA.
| | - Ingrid E Wertz
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, M/S 40, South San Francisco, CA 94080, USA.
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30
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Kwon HJ, Kurono S, Kaneko Y, Ohmiya Y, Yasuda K. Analysis of proteins showing differential changes during ATP oscillations in chondrogenesis. Cell Biochem Funct 2014; 32:429-37. [PMID: 24578328 DOI: 10.1002/cbf.3033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/02/2014] [Accepted: 01/30/2014] [Indexed: 01/02/2023]
Abstract
Prechondrogenic condensation is a critical step for skeletal pattern formation. Our previous study showed that ATP oscillations play an essential role in prechondrogenic condensation because they induce oscillatory secretion. However, the molecular mechanisms that underlie ATP oscillations remain poorly understood. We examined how differential changes in proteins are implicated in ATP oscillations during chondrogenesis by using liquid chromatography/mass spectrometry. Our analysis showed that a number of proteins involved in ATP synthesis/consumption, catabolic/anabolic processes, actin dynamics, cell migration and adhesion were detected at either the peak or the trough of ATP oscillations, which implies that these proteins have oscillatory expression patterns that are coupled to ATP oscillations. On the basis of the results, we suggest that (1) the oscillatory expression of proteins involved in ATP synthesis/consumption and catabolic/anabolic processes can contribute to the generation or maintenance of ATP oscillations and that (2) the oscillatory expression of proteins involved in actin dynamics, cell migration and adhesion plays key roles in prechondrogenic condensation by inducing collective adhesion and migration in cooperation with ATP oscillations.
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Affiliation(s)
- Hyuck Joon Kwon
- Department of Physical Therapy, College of Health Science, Eulji University, Gyeonggi, South Korea
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31
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Leung KSY, Fong BMW. LC–MS/MS in the routine clinical laboratory: has its time come? Anal Bioanal Chem 2013; 406:2289-301. [DOI: 10.1007/s00216-013-7542-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/18/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
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32
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High-resolution MS for structural characterization of protein therapeutics: advances and future directions. Bioanalysis 2013; 5:1299-313. [DOI: 10.4155/bio.13.80] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
High-resolution MS (HRMS) is a central analytical technique for the study of biomolecules and is widely used in the biopharmaceutical industry. This paper reviews recent advances in commonly used HRMS instrumentation and experimental strategies for HRMS-based structural characterization of protein therapeutics. An overview of protein higher order structural characterization using HRMS-based technologies is presented, including the use of hydrogen/deuterium exchange and hydroxyl radical footprinting methods for probing protein conformational dynamics and interactions in solution. Future directions in application of HRMS for characterizing protein therapeutics are also described.
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33
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Renes J, Mariman E. Application of proteomics technology in adipocyte biology. MOLECULAR BIOSYSTEMS 2013; 9:1076-91. [PMID: 23629546 DOI: 10.1039/c3mb25596d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Obesity and its associated complications have reached epidemic proportions in Western-type societies. Concomitantly, the obesity incidence in developing countries is increasing. One hallmark of obesity is the differentiation of pre-adipocytes into mature triglyceride-loaded adipocytes present in subcutaneous and visceral adipose tissue depots. This may ultimately lead to dysfunctional adipose tissue together with detrimental changes in the profiles of (pre-)adipocyte-secreted proteins, known as adipokines. Obesity-induced alterations in adipokine profiles contribute to the development of obesity-associated disorders. Consequently, the interest in the molecular events responsible for adipose tissue modifications during weight gain and weight loss as well as in the aetiology of obesity-associated disorders is growing. Molecular mechanisms involved in pre-adipocyte differentiation and alterations in adipokine profiles have been examined at the gene and protein level by high-throughput technologies. Independent proteomics studies have contributed significantly to further insight into adipocyte biology, particularly with respect to adipokine profiling. In this review novel findings obtained with adipo-proteomics studies are highlighted and the relevance of proteomics technologies to further understand molecular aspects of adipocyte biology is discussed.
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Affiliation(s)
- Johan Renes
- Department of Human Biology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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34
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Nováková L, Vaast A, Stassen C, Broeckhoven K, De Pra M, Swart R, Desmet G, Eeltink S. High-resolution peptide separations using nano-LC at ultra-high pressure. J Sep Sci 2013; 36:1192-9. [DOI: 10.1002/jssc.201201087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/16/2013] [Accepted: 01/16/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Lucie Nováková
- Vrije Universiteit Brussel, Department of Chemical Engineering; Brussels Belgium
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University in Prague; Hradec Králové Czech Republic
| | - Axel Vaast
- Vrije Universiteit Brussel, Department of Chemical Engineering; Brussels Belgium
| | - Catherine Stassen
- Vrije Universiteit Brussel, Department of Chemical Engineering; Brussels Belgium
| | - Ken Broeckhoven
- Vrije Universiteit Brussel, Department of Chemical Engineering; Brussels Belgium
| | - Mauro De Pra
- Thermo Fisher Scientific; Amsterdam The Netherlands
| | - Remco Swart
- Thermo Fisher Scientific; Amsterdam The Netherlands
| | - Gert Desmet
- Vrije Universiteit Brussel, Department of Chemical Engineering; Brussels Belgium
| | - Sebastiaan Eeltink
- Vrije Universiteit Brussel, Department of Chemical Engineering; Brussels Belgium
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35
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Lee HJ, Jeong SK, Na K, Lee MJ, Lee SH, Lim JS, Cha HJ, Cho JY, Kwon JY, Kim H, Song SY, Yoo JS, Park YM, Kim H, Hancock WS, Paik YK. Comprehensive Genome-Wide Proteomic Analysis of Human Placental Tissue for the Chromosome-Centric Human Proteome Project. J Proteome Res 2013; 12:2458-66. [DOI: 10.1021/pr301040g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hyoung-Joo Lee
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Seul-Ki Jeong
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Keun Na
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Min Jung Lee
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Sun Hee Lee
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Jong-Sun Lim
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Hyun-Jeong Cha
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
| | | | - Hoguen Kim
- Yonsei University College of Medicine, Seoul, Korea
| | | | - Jong Shin Yoo
- Division of Mass Spectrometry
Research, Korea Basic Science Institute, Ochang, Chungbuk, Korea
| | - Young Mok Park
- Division of Mass Spectrometry
Research, Korea Basic Science Institute, Ochang, Chungbuk, Korea
| | - Hail Kim
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - William S. Hancock
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
- Barnnet Institute and Department of
Chemistry, Northeastern University, Boston,
Massachusetts, United States
| | - Young-Ki Paik
- Yonsei Proteome Research Center
and Department of Integrated Omics for Biomedical Science, World Class
University Program, Yonsei University,
Seoul, Korea
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36
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Li F, Glinskii OV, Glinsky VV. Glycobioinformatics: Current strategies and tools for data mining in MS-based glycoproteomics. Proteomics 2012; 13:341-54. [DOI: 10.1002/pmic.201200149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/06/2012] [Accepted: 11/06/2012] [Indexed: 12/18/2022]
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37
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Jafari M, Primo V, Smejkal GB, Moskovets EV, Kuo WP, Ivanov AR. Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling. Electrophoresis 2012; 33:2516-26. [PMID: 22899259 PMCID: PMC4234072 DOI: 10.1002/elps.201200031] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.
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Affiliation(s)
- Mohieddin Jafari
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
- School of Paramedical Science, Shahid Beheshti University of Medical Science, Tehran, Iran
- School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Vincent Primo
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
| | - Gary B. Smejkal
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
| | | | - Winston P. Kuo
- Harvard Catalyst, The Harvard Clinical and Translational Science Center, Laboratory for Innovative Translational Technologies, Boston, MA, USA
- Harvard School of Dental Medicine, Department of Developmental Biology, Boston, MA, USA
| | - Alexander R. Ivanov
- HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
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38
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Gunther NW, Paul M, Nuñez A, Liu Y. pH fractionation and identification of proteins: comparing column chromatofocusing versus liquid isoelectric focusing techniques. J Sep Sci 2012; 35:1399-405. [PMID: 22740249 DOI: 10.1002/jssc.201100865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In proteomic investigations, a number of different separation techniques can be applied to fractionate whole cell proteomes into more manageable fractions for subsequent analysis. In this work, utilizing HPLC and mass spectrometry for protein identification, two different fractionation methods were compared and contrasted to determine the potential of each method for the simple and reproducible fractionation of a bacterial proteome. Column-based chromatofocusing and liquid-based isoelectric focusing both utilized pH gradients to produce similar results in terms of the numbers of proteins successfully identified (402 and 378 proteins) and the consistency of proteins identified from one experiment to the next (<10% change). However, there was limited overlap in the protein sets with <50% of the proteins identified as common between the sets of proteins identified by the different systems. In addition to the numbers of proteins identified and consistency of those identified, the reduced monetary costs of experimentation and increased assay flexibility produced by using isoelectric focusing was considered in order to adopt a system best suited for comparative proteomic projects.
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Affiliation(s)
- Nereus W Gunther
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA 19038, USA.
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39
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Doneanu CE, Xenopoulos A, Fadgen K, Murphy J, Skilton SJ, Prentice H, Stapels M, Chen W. Analysis of host-cell proteins in biotherapeutic proteins by comprehensive online two-dimensional liquid chromatography/mass spectrometry. MAbs 2012; 4:24-44. [PMID: 22327428 DOI: 10.4161/mabs.4.1.18748] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Assays for identification and quantification of host-cell proteins (HCPs) in biotherapeutic proteins over 5 orders of magnitude in concentration are presented. The HCP assays consist of two types: HCP identification using comprehensive online two-dimensional liquid chromatography coupled with high resolution mass spectrometry (2D-LC/MS), followed by high-throughput HCP quantification by liquid chromatography, multiple reaction monitoring (LC-MRM). The former is described as a "discovery" assay, the latter as a "monitoring" assay. Purified biotherapeutic proteins (e.g., monoclonal antibodies) were digested with trypsin after reduction and alkylation, and the digests were fractionated using reversed-phase (RP) chromatography at high pH (pH 10) by a step gradient in the first dimension, followed by a high-resolution separation at low pH (pH 2.5) in the second dimension. As peptides eluted from the second dimension, a quadrupole time-of-flight mass spectrometer was used to detect the peptides and their fragments simultaneously by alternating the collision cell energy between a low and an elevated energy (MSE methodology). The MSE data was used to identify and quantify the proteins in the mixture using a proven label-free quantification technique ("Hi3" method). The same data set was mined to subsequently develop target peptides and transitions for monitoring the concentration of selected HCPs on a triple quadrupole mass spectrometer in a high-throughput manner (20 min LC-MRM analysis). This analytical methodology was applied to the identification and quantification of low-abundance HCPs in six samples of PTG1, a recombinant chimeric anti-phosphotyrosine monoclonal antibody (mAb). Thirty three HCPs were identified in total from the PTG1 samples among which 21 HCP isoforms were selected for MRM monitoring. The absolute quantification of three selected HCPs was undertaken on two different LC-MRM platforms after spiking isotopically labeled peptides in the samples. Finally, the MRM quantitation results were compared with TOF-based quantification based on the Hi3 peptides, and the TOF and MRM data sets correlated reasonably well. The results show that the assays provide detailed valuable information to understand the relative contributions of purification schemes to the nature and concentrations of HCP impurities in biopharmaceutical samples, and the assays can be used as generic methods for HCP analysis in the biopharmaceutical industry.
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Abstract
Mass spectrometry-based quantitative analysis and biomarker discovery using metabolomics approach represent one of the major platforms in clinical fields including for the prognosis or diagnosis, assessment of severity and response to therapy in a number of clinical disease states as well as therapeutic drug monitoring (TDM). This review first summarizes our mass spectrometry-based research strategy and some results on relationship between cysteinyl leukotriene (cysLT), thromboxane (TX), 12-hydroxyeicosatetraenoic acid (12-HETE) and other metabolites of arachidonic acid and diseases such as atopic dermatitis, rheumatoid arthritis and diabetes mellitus. For the purpose of evaluating the role of these metabolites of arachidonic acid in disease status, we have developed sensitive determination methods with simple solid-phase extraction and applied in clinical settings. In addition to these endogenous compounds, using mass spectrometry, we have developed actually applicable quantitative methods for TDM. Representative example was a method of TDM for sirolimus, one of the immunosuppressant agents for a recipient of organ transplant, which requires rigorous monitoring of blood level. As we recognized great potential in mass spectrometry during these researches, we have become interested in metabolomics as the non-targeted analysis of metabolites. Now, established strategy for the metabolomics investigation applies to samples from cells, animals and humans to separate groups based on altered patterns of metabolites in biological fluids and to identify metabolites as potential biomarkers discriminating groups. We would be honored if our research using mass spectrometry would contribute to provide useful information in the field of medical pharmacy.
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Affiliation(s)
- Naoto Suzuki
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
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Hoekman B, Breitling R, Suits F, Bischoff R, Horvatovich P. msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies. Mol Cell Proteomics 2012; 11:M111.015974. [PMID: 22318370 DOI: 10.1074/mcp.m111.015974] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Data processing forms an integral part of biomarker discovery and contributes significantly to the ultimate result. To compare and evaluate various publicly available open source label-free data processing workflows, we developed msCompare, a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a novel scoring method to evaluate their overall performance. We used msCompare to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and our in-house developed modules on peptide-spiked urine and trypsin-digested cerebrospinal fluid (CSF) samples. We found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. Our scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is open source software (https://trac.nbic.nl/mscompare), and we provide a web-based data processing service for our framework by integration into the Galaxy server of the Netherlands Bioinformatics Center (http://galaxy.nbic.nl/galaxy) to allow scientists to determine which combination of modules provides the most accurate processing for their particular LC-MS data sets.
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Affiliation(s)
- Berend Hoekman
- Department of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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Savino R, Terracciano R. Mesopore-assisted profiling strategies in clinical proteomics for drug/target discovery. Drug Discov Today 2012; 17:143-52. [DOI: 10.1016/j.drudis.2011.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/23/2011] [Accepted: 10/07/2011] [Indexed: 12/29/2022]
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43
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Application of proteomics in the mechanistic study of traditional Chinese medicine. Biochem Soc Trans 2012; 39:1348-52. [PMID: 21936813 DOI: 10.1042/bst0391348] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Systems biology is considered to be the possible technology that could bring breakthroughs in the study of TCM (traditional Chinese medicine). Proteomics, as one of the major components of systems biology, has been used in the mechanistic study of TCM, providing some interesting results. In the present paper, we review the current application of proteomics in the mechanistic study of TCM. Proteomics technologies and strategies that might be used in the future to improve study of TCM are also discussed.
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Kido J, Bando M, Hiroshima Y, Iwasaka H, Yamada K, Ohgami N, Nambu T, Kataoka M, Yamamoto T, Shinohara Y, Sagawa I, Nagata T. Analysis of proteins in human gingival crevicular fluid by mass spectrometry. J Periodontal Res 2012; 47:488-99. [DOI: 10.1111/j.1600-0765.2011.01458.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Stolarczyk EI, Reiling CJ, Paumi CM. Regulation of ABC transporter function via phosphorylation by protein kinases. Curr Pharm Biotechnol 2011; 12:621-35. [PMID: 21118091 DOI: 10.2174/138920111795164075] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 04/07/2010] [Indexed: 11/22/2022]
Abstract
ATP-binding cassette (ABC) transporters are multispanning membrane proteins that utilize ATP to move a broad range of substrates across cellular membranes. ABC transporters are involved in a number of human disorders and diseases. Overexpression of a subset of the transporters has been closely linked to multidrug resistance in both bacteria and viruses and in cancer. A poorly understood and important aspect of ABC transporter biology is the role of phosphorylation as a mechanism to regulate transporter function. In this review, we summarize the current literature addressing the role of phosphorylation in regulating ABC transporter function. A comprehensive list of all the phosphorylation sites that have been identified for the human ABC transporters is presented, and we discuss the role of individual kinases in regulating transporter function. We address the potential pitfalls and difficulties associated with identifying phosphorylation sites and the corresponding kinase(s), and we discuss novel techniques that may circumvent these problems. We conclude by providing a brief perspective on studying ABC transporter phosphorylation.
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Schubert B, Oberacher H. Impact of solvent conditions on separation and detection of basic drugs by micro liquid chromatography–mass spectrometry under overloading conditions. J Chromatogr A 2011; 1218:3413-22. [DOI: 10.1016/j.chroma.2011.03.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 03/11/2011] [Accepted: 03/18/2011] [Indexed: 10/18/2022]
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47
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Application of mass spectrometry-based chromatographic technologies in the diagnosis of Alzheimer’s disease. Se Pu 2011; 29:293-7. [DOI: 10.3724/sp.j.1123.2011.00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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48
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Sá-Correia I, Teixeira MC. 2D electrophoresis-based expression proteomics: a microbiologist's perspective. Expert Rev Proteomics 2011; 7:943-53. [PMID: 21142894 DOI: 10.1586/epr.10.76] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative proteomics based on 2D electrophoresis (2-DE) coupled with peptide mass fingerprinting is still one of the most widely used quantitative proteomics approaches in microbiology research. Our view on the exploitation of this global expression analysis technique and its contribution and potential to push forward the field of molecular microbial physiology towards a molecular systems microbiology perspective is discussed in this article. The advances registered in 2-DE-based quantitative proteomic analysis leading to increased protein resolution, sensitivity and accuracy, and the promising use of 2-DE to gain insights into post-translational modifications at a proteome-wide level (considering all the proteins/protein forms expressed by the genome) are focused on. Given the progress made in this field, it is foreseen that the 2-DE-based approach to quantitative proteomics will continue to be a fundamental tool for microbiologists working at a genome-wide scale. Guidelines are also provided for the exploitation of expression proteomics data, based on useful computational tools, and for the integration of these data with other genome-wide expression information. The advantages and limitations of a complete 2-DE-based expression proteomics analysis, envisaging the quantification of the global changes occurring in the proteome of a given cell depending on environmental or genetic manipulations, are discussed from the microbiologist's perspective. Particular focus is given to the emerging field of toxicoproteomics, a new systems toxicity approach that offers a powerful tool to directly monitor the earliest stages of the toxicological response by identifying critical proteins and pathways that are affected by, and respond to, a chemical stress. The experimental design and the bioinformatics analysis of data used in our laboratory to gain mechanistic insights through expression proteomics into the responses of the eukaryotic model Saccharomyces cerevisiae or of Pseudomonas strains to environmental toxicants are presented as case studies.
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Affiliation(s)
- Isabel Sá-Correia
- Institute for Biotechnology and Bioengineering, Biological Sciences Research Group, Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Technical University of Lisbon, Av. Rovisco Pais, Lisbon, Portugal.
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49
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Weigoldt M, Meens J, Doll K, Fritsch I, Möbius P, Goethe R, Gerlach GF. Differential proteome analysis of Mycobacterium avium subsp. paratuberculosis grown in vitro and isolated from cases of clinical Johne's disease. Microbiology (Reading) 2011; 157:557-565. [DOI: 10.1099/mic.0.044859-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bovine Johne's disease (paratuberculosis), caused by Mycobacterium avium subspecies paratuberculosis, poses a significant economic problem to the beef and dairy industry worldwide. Despite its relevance, however, pathogenesis of Johne's disease is still only partially resolved. Since mycobacterial membrane proteins expressed during infection are likely to play an important role in pathogenesis, membrane-enriched fractions, namely mucosa-derived membranes (MDM) and culture-derived membranes (CDM), of M. avium subsp. paratuberculosis from three cows with clinical paratuberculosis were investigated. An initial analysis by 2D difference gel electrophoresis (2D DIGE) and MALDI-TOF-MS analysis revealed four differentially expressed proteins with only one predicted membrane protein. Due to this limited outcome, membrane preparations were subjected to a tube–gel trypsin digestion and investigated by using nanoflow-liquid-chromatography-coupled tandem MS. Based on this approach a total of 212 proteins were detected in MDM including 32 proteins of bovine origin; 275 proteins were detected in CDM; 59 % of MDM and CDM proteins were predicted to be membrane-associated. A total of 130 of the proteins were detected in both MDM and CDM and 48 predicted membrane proteins were detected in MDM from at least two cows. Four of these proteins were not detected in CDM, implying differential expression in the host. All membrane-associated proteins, especially the four identified as being differentially expressed, might be relevant targets for further analyses into the pathogenesis of bovine paratuberculosis.
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Affiliation(s)
- Mathias Weigoldt
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Klaus Doll
- Clinic for Ruminants and Swine (Internal Medicine and Surgery), Justus-Liebig-University, Giessen, Germany
| | - Isabel Fritsch
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
| | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
| | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Gerald. F. Gerlach
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
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50
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Creese AJ, Grant MM, Chapple ILC, Cooper HJ. On-line liquid chromatography neutral loss-triggered electron transfer dissociationmass spectrometry for the targeted analysis of citrullinated peptides. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2011; 3:259-266. [PMID: 32938022 DOI: 10.1039/c0ay00414f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Citrullination is a post-translational modification of proteins which deiminates arginine, increasing the mass by 0.98 Da. Protein citrullination is a known biomarker for multiple sclerosis and a potential biomarker for rheumatoid arthritis. Collision-induced dissociation (CID) tandem mass spectrometry of citrullinated peptides produces a dominant neutral loss of isocyanic acid (HNCO, -43 Da) from the deiminated arginine amino acid side-chain. Here we show that the loss of isocyanic acid in CID can be used as a trigger for targeted analysis by supplemental activation electron transfer dissociation (saETD). Unlike CID, post-translational modifications (PTMs) are retained on peptide backbone fragments produced by saETD, improving the confidence in assignment of both peptide sequence and PTM site. The method is demonstrated for four synthetic peptides spiked into complex trypsin-digested saliva samples and a commercial six protein tryptic mixture. In contrast to CID alone, the neutral-loss triggered ETD approach results in high confidence identification of three of the four peptides, including an unexpected disulfide-bound dimer, and zero false positives.
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Affiliation(s)
- Andrew J Creese
- School of Dentistry, Periodontal Research Group, University of Birmingham, St Chads Queensway, Birmingham, B4 6NN, UK
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Melissa M Grant
- School of Dentistry, Periodontal Research Group, University of Birmingham, St Chads Queensway, Birmingham, B4 6NN, UK
| | - Iain L C Chapple
- School of Dentistry, Periodontal Research Group, University of Birmingham, St Chads Queensway, Birmingham, B4 6NN, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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