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Zou W, Yeo SY. Characterization of Animal Protein-Based Binders in Ancient Chinese Wall Paintings Using Atomic Force Microscopy and Fourier Transform Infrared Spectroscopy. APPLIED SPECTROSCOPY 2022; 76:1191-1205. [PMID: 35712890 DOI: 10.1177/00037028221110258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, the topographical characteristics of protein-based binders in ancient Chinese wall paintings and the properties of their sources were investigated and identified. Fifteen samples of protein-based binders (skin glue, bone glue, egg glue, and milk glue) before and after aging and mixing azurite were prepared. Next, the topographical characteristics, adhesive properties, and infrared spectra for each chemical group in the binders were analyzed using atomic force microscopy and attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR), and the sources of various binders were identified using ATR FT-IR and principal component analysis (PCA). Results showed that protein binders such as fish bladder, cow bone, and egg white glue had lower roughness values and good consolidation properties. The most distinctive feature of skin and bone glues before and after aging or mixed with azurite was the stretching vibration peak of CH2 deformation vibration at around 1335 cm-1, while the significant characteristics of egg and milk glue was the C=O stretching vibration in Serine at 1306 cm-1 and C=O stretching vibrations in aspartic acid and glutamic acid at 1416 cm-1. In addition, the significant differences of absorbance peaks were observed in the infrared spectra of various bone, skin, egg, and milk glue samples before and after aging while the spectral differences become insignificant after mixing with azurite. The results of PCA confirmed that egg yolk and ewe's and cow's milk were well differentiated from animal skin and bone glue regardless of whether fresh, aged, or mixed with azurite. In addition, the differences between skin and bone glues were significant, and the various types of bone glue could be also differentiated before and after aging.
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Affiliation(s)
- Weihan Zou
- Department of Architecture, School of Human Settlements and Civil Engineering, 599379Xi'an Jiaotong University, Xi'an, China
| | - Sok Yee Yeo
- Department of Architecture, School of Human Settlements and Civil Engineering, 599379Xi'an Jiaotong University, Xi'an, China
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2
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MALDI-TOF/MS Analysis of Extracellular Vesicles Released by Cancer Cells. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12126149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The direct shedding of extracellular vesicles (EVs) from the plasma membrane is a recognized fundamental method for the intercellular transfer of properties in both physiological and pathological conditions. EVs are classified according to origin, biogenesis, size, content, surface markers, and/or functional properties, and contain various bioactive molecules depending on the physiological state and the type of the cells of origin including lipids, nucleic acids, and proteins. The presence of tumor-derived EVs in body fluids such as blood, ascites, urine, and saliva, together with the important role played in the tumor microenvironment where they intervene at different levels from oncogenesis to metastasis, make EVs a priority target for cancer studies. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) can play a leading role in the analysis and characterization of EVs and their load due to its intrinsic advantages such as high throughput, low sample consumption, speed, the cost-effectiveness of the analysis, and the ease of use. This work reviews the main MALDI-TOF applications for the analysis and characterization of extracellular vesicles in the tumor field.
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Zambonin C, Aresta A. MALDI-TOF/MS Analysis of Non-Invasive Human Urine and Saliva Samples for the Identification of New Cancer Biomarkers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061925. [PMID: 35335287 PMCID: PMC8951187 DOI: 10.3390/molecules27061925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 01/22/2023]
Abstract
Cancer represents a group of heterogeneous diseases that are a leading global cause of death. Even though mortality has decreased in the past thirty years for different reasons, most patients are still diagnosed at the advanced stage, with limited therapeutic choices and poor outcomes. Moreover, the majority of cancers are detected using invasive painful methods, such as endoscopic biopsy, making the development of non-invasive or minimally invasive methods for the discovery and fast detection of specific biomarkers a crucial need. Among body fluids, a valuable non-invasive alternative to tissue biopsy, the most accessible and least invasive are undoubtedly urine and saliva. They are easily retrievable complex fluids containing a large variety of endogenous compounds that may provide information on the physiological condition of the body. The combined analysis of these fluids with matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF/MS), a reliable and easy-to-use instrumentation that provides information with relatively simple sample pretreatments, could represent the ideal option to rapidly achieve fast early stage diagnosis of tumors and their real-time monitoring. On this basis, the present review summarizes the recently reported applications relevant to the MALDI analysis of human urine and saliva samples.
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4
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Ren Y, Yang L, Li M, Wang J, Yan H, Ma N, Liu W, Wang L, Gao X, Gao P, Li T, Liu D. 4210 Da and 1866 Da polypeptides as potential biomarkers of liver disease progression in hepatitis B virus patients. Sci Rep 2021; 11:16982. [PMID: 34417517 PMCID: PMC8379215 DOI: 10.1038/s41598-021-96581-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
HBV infection is recognized as a serious global health problem, and hepatitis B virus infection is a complicated chronic disease leading to liver cirrhosis (LC) and hepatocellular carcinoma (HCC). New biochemical serum markers could be used to advance the diagnosis and prognosis of HBV-associated liver diseases during the progression of chronic hepatitis B into cirrhosis and HCC. We determined whether the 4210 Da and 1866 Da polypeptides are serum metabolite biomarkers of hepatopathy with hepatitis B virus. A total of 570 subjects were divided into five groups: healthy controls, those with natural clearance, and patients with CHB, LC, and HCC. The 1866 Da and 4210 Da polypeptides were measured by Clin-ToF II MALDI-TOF-MS. There were significant differences in 4210 Da and 1866 Da levels among the five groups (P < 0.001). For the differential diagnosis of CHB from normal liver, the areas under the receiver operating characteristic (ROC) curve of 4210 Da and 1866 Da and their combination via logistic regression were 0.961, 0.849 and 0.967. For the differential diagnosis of LC from CHB, the areas under the ROC curve were 0.695, 0.841 and 0.826. For the differential diagnosis of HCC from CHB, the areas under the ROC curve were 0.744, 0.710 and 0.761, respectively. For the differential diagnosis of HCC from LC, the areas under the ROC curve of 4210 Da and 1866 Da were 0.580 and 0.654. The positive rate of 1866 Da was 45.5% and 69.0% in AFP-negative HCC patients and that of 4210 Da was 60.6% 58.6% in AFP-negative HCC patients of the study HCC vs. CHB and HCC vs. LC. The 4210 Da and 1866 Da polypeptide levels were positively correlated with HBV DNA levels (P < 0.001, r = 0.269; P < 0.001, r = 0.285). The 4210 Da and 1866 Da polypeptides had good diagnostic value for the occurrence and progression of HBV-related chronic hepatitis, liver cirrhosis and hepatocellular carcinoma and could serve to accurately guide treatment management and predict clinical outcomes.
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Affiliation(s)
- Yuanyuan Ren
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
- Department of Food Quality and Safety, College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang, 050018, China
| | - Lei Yang
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Man Li
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Jian Wang
- Department of Epidemiology, Hebei North University, Zhangjiakou, 075000, China
| | - Huimin Yan
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, 050021, China
| | - Ning Ma
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Wenxuan Liu
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Liqin Wang
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Xia Gao
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Ping Gao
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Tao Li
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China
| | - Dianwu Liu
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, 050017, China.
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Monopoli A, Nacci A, Cataldi TRI, Calvano CD. Synthesis and Matrix Properties of α-Cyano-5-phenyl-2,4-pentadienic Acid (CPPA) for Intact Proteins Analysis by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Molecules 2020; 25:molecules25246054. [PMID: 33371472 PMCID: PMC7767571 DOI: 10.3390/molecules25246054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/06/2023] Open
Abstract
The effectiveness of a synthesized matrix, α-cyano-5-phenyl-2,4-pentadienic acid (CPPA), for protein analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in complex samples such as foodstuff and bacterial extracts, is demonstrated. Ultraviolet (UV) absorption along with laser desorption/ionization mass spectrometry (LDI-MS) experiments were systematically conducted in positive ion mode under standard Nd:YLF laser excitation with the aim of characterizing the matrix in terms of wavelength absorption and proton affinity. Besides, the results for standard proteins revealed that CPPA significantly enhanced the protein signals, reduced the spot-to-spot variability and increased the spot homogeneity. The CPPA matrix was successful employed to investigate intact microorganisms, milk and seed extracts for protein profiling. Compared to conventional matrices such as sinapinic acid (SA), α-cyano-4-hydroxycinnamic acid (CHCA) and 4-chloro-α-cyanocinnamic acid (CClCA), CPPA exhibited better signal-to-noise (S/N) ratios and a uniform response for most examined proteins occurring in milk, hazelnut and in intact bacterial cells of E. coli. These findings not only provide a reactive proton transfer MALDI matrix with excellent reproducibility and sensitivity, but also contribute to extending the battery of useful matrices for intact protein analysis.
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Affiliation(s)
- Antonio Monopoli
- Agenzia delle Dogane e dei Monopoli, Ufficio delle Dogane di Bari, Corso De Tullio, 70122 Bari, Italy;
| | - Angelo Nacci
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy; (A.N.); (T.R.I.C.)
| | - Tommaso R. I. Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy; (A.N.); (T.R.I.C.)
- Centro Interdipartimentale di Ricerca S.M.A.R.T., 70126 Bari, Italy
| | - Cosima D. Calvano
- Centro Interdipartimentale di Ricerca S.M.A.R.T., 70126 Bari, Italy
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via Orabona, 70126 Bari, Italy
- Correspondence:
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6
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Padoan A, Basso D, Zambon CF, Prayer-Galetti T, Arrigoni G, Bozzato D, Moz S, Zattoni F, Bellocco R, Plebani M. MALDI-TOF peptidomic analysis of serum and post-prostatic massage urine specimens to identify prostate cancer biomarkers. Clin Proteomics 2018; 15:23. [PMID: 30065622 PMCID: PMC6060548 DOI: 10.1186/s12014-018-9199-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/16/2018] [Indexed: 12/25/2022] Open
Abstract
Background Lower urinary tract symptoms (LUTS) and prostate specific antigen-based parameters seem to have only a limited utility for the differential diagnosis of prostate cancer (PCa). MALDI-TOF/MS peptidomic profiling could be a useful diagnostic tool for biomarker discovery, although reproducibility issues have limited its applicability until now. The current study aimed to evaluate a new MALDI-TOF/MS candidate biomarker. Methods Within- and between-subject variability of MALDI-TOF/MS-based peptidomic urine and serum analyses were evaluated in 20 and 15 healthy donors, respectively. Normalizations and approaches for accounting below limit of detection (LOD) values were utilized to enhance reproducibility, while Monte Carlo experiments were performed to verify whether measurement error can be dealt with LOD data. Post-prostatic massage urine and serum samples from 148 LUTS patients were analysed using MALDI-TOF/MS. Regression-calibration and simulation and extrapolation methods were used to derive the unbiased association between peptidomic features and PCa. Results Although the median normalized peptidomic variability was 24.9%, the within- and between-subject variability showed that median normalization, LOD adjustment, and log2 data transformation were the best combination in terms of reliability; in measurement error conditions, intraclass correlation coefficient was a reliable estimate when the LOD/2 was substituted for below LOD values. In the patients studied, 43 peptides were shared by the urine and serum, and several features were found to be associated with PCa. Only few serum features, however, show statistical significance after the multiple testing procedures were completed. Two serum fragmentation patterns corresponded to the complement C4-A. Conclusions MALDI-TOF/MS serum peptidome profiling was more efficacious with respect to post-prostatic massage urine analysis in discriminating PCa. Electronic supplementary material The online version of this article (10.1186/s12014-018-9199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Padoan
- 1Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padua, Italy
| | - Daniela Basso
- 1Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padua, Italy
| | | | - Tommaso Prayer-Galetti
- 3Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padua, Italy
| | - Giorgio Arrigoni
- 2Department of Biomedical Sciences, University of Padova, Padua, Italy.,4Proteomic Center, University of Padova, Padua, Italy
| | - Dania Bozzato
- 1Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padua, Italy
| | - Stefania Moz
- 1Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padua, Italy
| | - Filiberto Zattoni
- 3Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padua, Italy
| | - Rino Bellocco
- 5Department of Statistics and Quantitative Methods, University of Milano-Bicocca, Milan, Italy.,6Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institute, Stockholm, Sweden
| | - Mario Plebani
- 1Department of Medicine-DIMED, University of Padova, Via Giustiniani 2, 35128 Padua, Italy
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7
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Panderi I, Yakirevich E, Papagerakis S, Noble L, Lombardo K, Pantazatos D. Differentiating tumor heterogeneity in formalin-fixed paraffin-embedded (FFPE) prostate adenocarcinoma tissues using principal component analysis of matrix-assisted laser desorption/ionization imaging mass spectral data. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:160-170. [PMID: 27791282 DOI: 10.1002/rcm.7776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/25/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Many patients with adenocarcinoma of the prostate present with advanced and metastatic cancer at the time of diagnosis. There is an urgent need to detect biomarkers that will improve the diagnosis and prognosis of this disease. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is playing a key role in cancer research and it can be useful to unravel the molecular profile of prostate cancer biopsies. METHODS MALDI imaging data sets are highly complex and their interpretation requires the use of multivariate statistical methods. In this study, MALDI-IMS technology, sequential principal component analysis (PCA) and two-dimensional (2-D) peak distribution tests were employed to investigate tumor heterogeneity in formalin-fixed paraffin-embedded (FFPE) prostate cancer biopsies. RESULTS Multivariate statistics revealed a number of mass ion peaks obtained from different tumor regions that were distinguishable from the adjacent normal regions within a given specimen. These ion peaks have been used to generate ion images and visualize the difference between tumor and normal regions. Mass peaks at m/z 3370, 3441, 3447 and 3707 exhibited stronger ion signals in the tumor regions. CONCLUSIONS This study reports statistically significant mass ion peaks unique to tumor regions in adenocarcinoma of the prostate and adds to the clinical utility of MALDI-IMS for analysis of FFPE tissue at a molecular level that supersedes all other standard histopathologic techniques for diagnostic purposes used in the current clinical practice. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Irene Panderi
- Brown University, Warren Alpert Medical School, COBRE Center for Cancer Research, Rhode Island Hospital, Providence, RI, USA
- National and Kapodistrian University of Athens, Department of Pharmacy, Division of Pharmaceutical Chemistry, Laboratory of Pharmaceutical Analysis, Athens, Greece
| | - Evgeny Yakirevich
- Brown University, Warren Alpert Medical School, Department of Pathology, Rhode Island Hospital, Providence, RI, USA
| | - Silvana Papagerakis
- University of Michigan Comprehensive Cancer Center, School of Medicine, Department of Periodontics and Oral Medicine, Division of Oral Pathology/Medicine/Radiology, Ann Arbor, MI, USA
| | - Lelia Noble
- Brown University, Warren Alpert Medical School, COBRE Center for Cancer Research, Rhode Island Hospital, Providence, RI, USA
| | - Kara Lombardo
- Brown University, Warren Alpert Medical School, Department of Pathology, Rhode Island Hospital, Providence, RI, USA
| | - Dionysios Pantazatos
- Brown University, Warren Alpert Medical School, COBRE Center for Cancer Research, Rhode Island Hospital, Providence, RI, USA
- Weill Cornell Medical College, Division of Infectious Diseases, Transplantation-Oncology Infectious Disease Program, New York, NY, USA
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8
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Gałęzowska G, Cieszynska-Semenowicz M, Okrągła E, Szychowska K, Wolska L. Progress in Analytical Techniques for Determination of Urine Components. SEPARATION AND PURIFICATION REVIEWS 2017. [DOI: 10.1080/15422119.2017.1281826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Grażyna Gałęzowska
- Department of Environment Toxicology, Faculty of Health Science, Medical University of Gdansk, Gdansk, Poland
| | | | - Emilia Okrągła
- Department of Environment Toxicology, Faculty of Health Science, Medical University of Gdansk, Gdansk, Poland
| | - Katarzyna Szychowska
- Department of Environment Toxicology, Faculty of Health Science, Medical University of Gdansk, Gdansk, Poland
| | - Lidia Wolska
- Department of Environment Toxicology, Faculty of Health Science, Medical University of Gdansk, Gdansk, Poland
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9
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Yeung RSM, Albani S, Feldman BM, Mellins E, Prakken B, Wedderburn LR. Enhancing translational research in paediatric rheumatology through standardization. Nat Rev Rheumatol 2016; 12:684-690. [PMID: 27652504 DOI: 10.1038/nrrheum.2016.156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The past decade has seen many successes in translational rheumatology, from dramatic improvements in outcomes brought about by novel biologic therapies, to the discovery of new monogenic inflammatory disorders. Advances in molecular medicine, combined with progress towards precision care, provide an excellent opportunity to accelerate the translation of biological understanding to the bedside. However, although the field of rheumatology is a leader in the standardization of data collection and measures of disease activity, it lags behind in standardization of biological sample collection and assay performance. Uniform approaches are necessary for robust collaborative research, particularly in rare diseases. Standardization is also critical to increase reproducibility between centres, a prerequisite for clinical implementation of translational research. This Perspectives article emphasizes the need for standardization and implementation of best practices, presented in the context of lessons learned from international biorepository networks.
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Affiliation(s)
- Rae S M Yeung
- Department of Paediatrics, Division of Rheumatology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; and at the Department of Immunology and the Institute of Medical Science, University of Toronto Faculty of Medicine, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Salvatore Albani
- Duke-National University of Singapore Graduate Medical School, 8 College Road, 169857, Singapore
| | - Brian M Feldman
- Department of Paediatrics and Institute of Medical Science, University of Toronto Faculty of Medicine, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; the Division of Rheumatology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada; and at the Institute of Health Policy Management and Evaluation, The Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, Ontario M5T 3M7, Canada
| | - Elizabeth Mellins
- Department of Pediatrics and the Stanford Program in Immunology, Stanford University, 300 Pasteur Drive, Stanford, California 94305, USA
| | - Berent Prakken
- Department of Immunology, University Medical Centre, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Lucy R Wedderburn
- Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
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10
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Challenges in biomarker discovery with MALDI-TOF MS. Clin Chim Acta 2016; 458:84-98. [PMID: 27134187 DOI: 10.1016/j.cca.2016.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Abstract
MALDI-TOF MS technique is commonly used in system biology and clinical studies to search for new potential markers associated with pathological conditions. Despite numerous concerns regarding a sample preparation or processing of complex data, this strategy is still recognized as a popular tool and its awareness has risen in the proteomic community over the last decade. In this review, we present comprehensive application of MALDI mass spectrometry with special focus on profiling research. We also discuss major advantages and disadvantages of universal sample preparation methods such as micro-SPE columns, immunodepletion or magnetic beads, and we show the potential of nanostructured materials in capturing low molecular weight subproteomes. Furthermore, as the general protocol considerably affects spectra quality and interpretation, an alternative solution for improved ion detection, including hydrophobic constituents, data processing and statistical analysis is being considered in up-to-date profiling pattern. In conclusion, many reports involving MALDI-TOF MS indicated highly abundant proteins as valuable indicators, and at the same time showed the inaccuracy of available methods in the detection of low abundant proteome that is the most interesting from the clinical perspective. Therefore, the analytical aspects of sample preparation methods should be standardized to provide a reproducible, low sample handling and credible procedure.
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11
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Preianò M, Maggisano G, Lombardo N, Montalcini T, Paduano S, Pelaia G, Savino R, Terracciano R. Influence of storage conditions on MALDI-TOF MS profiling of gingival crevicular fluid: Implications on the role of S100A8 and S100A9 for clinical and proteomic based diagnostic investigations. Proteomics 2016; 16:1033-45. [DOI: 10.1002/pmic.201500328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/08/2015] [Accepted: 12/22/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Mariaimmacolata Preianò
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro Italy
| | - Giuseppina Maggisano
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro Italy
| | - Nicola Lombardo
- Department of Medical and Surgical Sciences; University “Magna Graecia”; Catanzaro Italy
| | - Tiziana Montalcini
- Department of Medical and Surgical Sciences; University “Magna Graecia”; Catanzaro Italy
| | - Sergio Paduano
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro Italy
| | - Girolamo Pelaia
- Department of Medical and Surgical Sciences; University “Magna Graecia”; Catanzaro Italy
| | - Rocco Savino
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro Italy
| | - Rosa Terracciano
- Department of Health Sciences; Laboratory of Mass Spectrometry and Proteomics; University “Magna Graecia”; Catanzaro Italy
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12
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Gopal J, Muthu M, Chun SC, Wu HF. State-of-the-art nanoplatform-integrated MALDI-MS impacting resolutions in urinary proteomics. Proteomics Clin Appl 2015; 9:469-81. [PMID: 25736343 DOI: 10.1002/prca.201400182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/26/2014] [Accepted: 02/26/2015] [Indexed: 12/17/2022]
Abstract
Urine proteomics has become a subject of interest, since it has led to a number of breakthroughs in disease diagnostics. Urine contains information not only from the kidney and the urinary tract but also from other organs, thus urinary proteome analysis allows for identification of biomarkers for both urogenital and systemic diseases. The following review gives a brief overview of the analytical techniques that have been in practice for urinary proteomics. MALDI-MS technique and its current application status in this area of clinical research have been discussed. The review comments on the challenges facing the conventional MALDI-MS technique and the upgradation of this technique with the introduction of nanotechnology. This review projects nano-based techniques such as nano-MALDI-MS, surface-assisted laser desorption/ionization, and nanostructure-initiator MS as the platforms that have the potential in trafficking MALDI-MS from the lab to the bedside.
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Affiliation(s)
- Judy Gopal
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Manikandan Muthu
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Se-Chul Chun
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University and Academia Sinica, Kaohsiung, Taiwan.,Center for Nanosciences and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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13
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Manard BT, Jones SMH, Marcus RK. Capillary-channeled polymer (C-CP) fibers for the rapid extraction of proteins from urine matrices prior to detection with MALDI-MS. Proteomics Clin Appl 2015; 9:522-30. [PMID: 25450308 DOI: 10.1002/prca.201400081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/10/2014] [Accepted: 11/25/2014] [Indexed: 11/07/2022]
Abstract
PURPOSE While MS is a powerful tool for biomarker determinations, the high salt content and the small molecules present in urine poses incredible challenges. Separation/extraction methods must be employed for the isolation of target species at relevant concentrations. Micropipette tips packed with capillary-channeled polymer (C-CP) fibers are employed for the SPE of proteins from a synthetic and a certified urine matrix. EXPERIMENTAL DESIGN Extractions are performed utilizing a very simple centrifugation method to spin-down species through the C-CP fiber tips. Proteins adsorb to the hydrophobic polypropylene fibers and are eluted in a solvent suitable for MALDI-MS analysis. Figures of merit are determined for representative compounds β2-microglobulin, retinol binding protein, and transferrin. RESULTS The optimum protein processing included a 100 μL aqueous rinse and an elution solvent composition was 10 μL of 55:45 ACN:water (with triflouroacetic acid). MALDI-MS responses for the target proteins are improved from nondetectable levels to eventually yield LOD ranging from 5 to 180 nM in 1 μL aliquots. CONCLUSION AND CLINICAL RELEVANCE C-CP fiber tips offer a plethora of advantages including low materials costs, high throughput, microvolume processing, and the determination of sub-nanogram quantities of analyte; allowing determination of biomarkers that are otherwise undetectable in urine matrices.
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Affiliation(s)
| | - Sarah M H Jones
- Department of Chemistry, Clemson University, Clemson, SC, USA
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14
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Hepburn S, Cairns DA, Jackson D, Craven RA, Riley B, Hutchinson M, Wood S, Smith MW, Thompson D, Banks RE. An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis. Proteomics Clin Appl 2015; 9:507-21. [PMID: 25400092 PMCID: PMC4964914 DOI: 10.1002/prca.201400079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/20/2014] [Accepted: 11/10/2014] [Indexed: 11/24/2022]
Abstract
Purpose We have examined the impact of sample processing time delay, temperature, and the addition of protease inhibitors (PIs) on the urinary proteome and peptidome, an important aspect of biomarker studies. Experimental design Ten urine samples from patients with varying pathologies were each divided and PIs added to one‐half, with aliquots of each then processed and frozen immediately, or after a delay of 6 h at 4°C or room temperature (20–22°C), effectively yielding 60 samples in total. Samples were then analyzed by 2D‐PAGE, SELDI‐TOF‐MS, and immunoassay. Results Interindividual variability in profiles was the dominant feature in all analyses. Minimal changes were observed by 2D‐PAGE as a result of delay in processing, temperature, or PIs and no changes were seen in IgG, albumin, β2‐microglobulin, or α1‐microglobulin measured by immunoassay. Analysis of peptides showed clustering of some samples by presence/absence of PIs but the extent was very patient‐dependent with most samples showing minimal effects. Conclusions and clinical relevance The extent of processing‐induced changes and the benefit of PI addition are patient‐ and sample‐dependent. A consistent processing methodology is essential within a study to avoid any confounding of the results.
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Affiliation(s)
- Sophie Hepburn
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK.,Department of Blood Sciences, The General Infirmary, Leeds, UK
| | - David A Cairns
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | | | - Rachel A Craven
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Beverley Riley
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Michelle Hutchinson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Steven Wood
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Matthew Welberry Smith
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK.,Department of Renal Medicine, St James's University Hospital, Leeds, UK
| | - Douglas Thompson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK.,Department of Blood Sciences, The General Infirmary, Leeds, UK
| | - Rosamonde E Banks
- Clinical and Biomedical Proteomics Group, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
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15
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Cho YT, Su H, Wu WJ, Wu DC, Hou MF, Kuo CH, Shiea J. Biomarker Characterization by MALDI-TOF/MS. Adv Clin Chem 2015; 69:209-54. [PMID: 25934363 DOI: 10.1016/bs.acc.2015.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.
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Affiliation(s)
- Yi-Tzu Cho
- Department of Cosmetic Applications and Management, Yuh-Ing Junior College of Health Care & Management, Kaohsiung, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Jeng Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chao-Hung Kuo
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Padoan A, Basso D, La Malfa M, Zambon CF, Aiyetan P, Zhang H, Di Chiara A, Pavanello G, Bellocco R, Chan DW, Plebani M. Reproducibility in urine peptidome profiling using MALDI-TOF. Proteomics 2015; 15:1476-85. [DOI: 10.1002/pmic.201400253] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 10/09/2014] [Accepted: 12/15/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Andrea Padoan
- Department of Medicine-DIMED; University of Padova; Padova Italy
| | - Daniela Basso
- Department of Medicine-DIMED; University of Padova; Padova Italy
| | - Marco La Malfa
- Department of Medicine-DIMED; University of Padova; Padova Italy
| | | | - Paul Aiyetan
- Department of Pathology; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Hui Zhang
- Department of Pathology; Johns Hopkins University School of Medicine; Baltimore MD USA
| | | | | | - Rino Bellocco
- Department of Statistics and Quantitative Methods; University of Milano-Bicocca; Milano Italy
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute; Stockholm Sweden
| | - Daniel W. Chan
- Department of Pathology; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Mario Plebani
- Department of Medicine-DIMED; University of Padova; Padova Italy
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17
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Ammerlaan W, Trezzi JP, Mathay C, Hiller K, Betsou F. Method Validation for Preparing Urine Samples for Downstream Proteomic and Metabolomic Applications. Biopreserv Biobank 2014; 12:351-7. [DOI: 10.1089/bio.2014.0013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Jean-Pierre Trezzi
- Integrated BioBank of Luxemburg (IBBL), Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), Luxembourg
| | - Conny Mathay
- Integrated BioBank of Luxemburg (IBBL), Luxembourg
| | - Karsten Hiller
- Luxembourg Centre for Systems Biomedicine (LCSB), Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxemburg (IBBL), Luxembourg
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18
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Proteomics and diabetic nephropathy: what have we learned from a decade of clinical proteomics studies? J Nephrol 2014; 27:221-8. [PMID: 24567069 DOI: 10.1007/s40620-014-0044-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/15/2013] [Indexed: 02/02/2023]
Abstract
Diabetic nephropathy (DN) has become the most frequent cause of chronic kidney disease worldwide due to the constant increase of the incidence of type 2 diabetes mellitus in developed and developing countries. The understanding of the pathophysiological mechanisms of human diseases through a large-scale characterization of the protein content of a biological sample is the key feature of the proteomics approach to the study of human disease. We discuss the main results of over 10 years of tissue and urine proteomics studies applied to DN in order to understand how far we have come and how far we still have to go before obtaining a full comprehension of the molecular mechanisms involved in the pathogenesis of DN and identifying reliable biomarkers for accurate management of patients.
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19
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Wang RQ, Druckenmüller K, Elbers G, Guenther K, Croué JP. Analysis of aquatic-phase natural organic matter by optimized LDI-MS method. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:154-160. [PMID: 24464543 DOI: 10.1002/jms.3321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/26/2013] [Accepted: 11/30/2013] [Indexed: 06/03/2023]
Abstract
The composition and physiochemical properties of aquatic-phase natural organic matter (NOM) are most important problems for both environmental studies and water industry. Laser desorption/ionization (LDI) mass spectrometry facilitated successful examinations of NOM, as humic and fulvic acids in NOM are readily ionized by the nitrogen laser. In this study, hydrophobic NOMs (HPO NOMs) from river, reservoir and waste water were characterized by this technique. The effect of analytical variables like concentration, solvent composition and laser energy was investigated. The exact masses of small molecular NOM moieties in the range of 200-1200 m/z were determined in reflectron mode. In addition, spectra of post-source-decay experiments in this range showed that some compounds from different natural NOMs had the same fragmental ions. In the large mass range of 1200-15,000 Da, macromolecules and their aggregates were found in HPO NOMs from natural waters. Highly humic HPO exhibited mass peaks larger than 8000 Da. On the other hand, the waste water and reservoir water mainly had relatively smaller molecules of about 2000 Da. The LDI-MS measurements indicated that highly humic river waters were able to form large aggregates and membrane foulants, while the HPO NOMs from waste water and reservoir water were unlikely to form large aggregates.
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Affiliation(s)
- Ren-Qi Wang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China; Water Desalination and Reuse Center (WDRC), 4700 King Abdullah University of Science and Technology, Kingdom of Saudi Arabia
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20
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Classical MALDI-MS versus CE-based ESI-MS proteomic profiling in urine for clinical applications. Bioanalysis 2014; 6:247-66. [DOI: 10.4155/bio.13.313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human urine is an attractive and informative biofluid for medical diagnosis, which has been shown to reflect the (patho)-physiology of not only the urogenital system, but also others such as the cardiovascular system. For this reason, many studies have concentrated on the study of the urine proteome, aiming to find relevant biomarkers that could be applied in a clinical setting. However, this goal can only be achieved after reliable quantitative and qualitative analysis of the urinary proteome. In the last two decades, MS-based platforms have evolved to become indispensable tools for biomarker research. In this review, we will present and compare two of the most clinically relevant analytical platforms that have been used for the study of the urinary proteome, namely CE-based ESI-MS and classical MALDI-MS. These platforms, although not directly comparable, have been extensively used in proteomic profiling and therefore their comparison is fundamentally relevant to this field.
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21
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Di Girolamo F, Lante I, Muraca M, Putignani L. The Role of Mass Spectrometry in the "Omics" Era. CURR ORG CHEM 2013; 17:2891-2905. [PMID: 24376367 PMCID: PMC3873040 DOI: 10.2174/1385272817888131118162725] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/06/2013] [Accepted: 09/06/2013] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS) is one of the key analytical technology on which the emerging ''-omics'' approaches are based. It may provide detection and quantization of thousands of proteins and biologically active metabolites from a tissue, body fluid or cell culture working in a ''global'' or ''targeted'' manner, down to ultra-trace levels. It can be expected that the high performance of MS technology, coupled to routine data handling, will soon bring fruit in the request for a better understanding of human diseases, leading to new molecular biomarkers, hence affecting drug targets and therapies. In this review, we focus on the main advances in the MS technologies, influencing genomics, transcriptomics, proteomics, lipidomics and metabolomics fields, up to the most recent MS applications to meta-omic studies.
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Affiliation(s)
- Francesco Di Girolamo
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Isabella Lante
- Laboratory Medicine, San Camillo Hospital, Viale Vittorio Veneto 18, 31100, Treviso, Italy
| | - Maurizio Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Lorenza Putignani
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
- Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
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22
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Flatley B, Malone P, Cramer R. MALDI mass spectrometry in prostate cancer biomarker discovery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:940-9. [PMID: 23831156 DOI: 10.1016/j.bbapap.2013.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/23/2013] [Accepted: 06/20/2013] [Indexed: 01/14/2023]
Abstract
Matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry (MS) is a highly versatile and sensitive analytical technique, which is known for its soft ionisation of biomolecules such as peptides and proteins. Generally, MALDI MS analysis requires little sample preparation, and in some cases like MS profiling it can be automated through the use of robotic liquid-handling systems. For more than a decade now, MALDI MS has been extensively utilised in the search for biomarkers that could aid clinicians in diagnosis, prognosis, and treatment decision making. This review examines the various MALDI-based MS techniques like MS imaging, MS profiling and proteomics in-depth analysis where MALDI MS follows fractionation and separation methods such as gel electrophoresis, and how these have contributed to prostate cancer biomarker research. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Brian Flatley
- Department of Chemistry, University of Reading, Reading, UK; Urology Research Department, Royal Berkshire Hospital, Reading, UK
| | - Peter Malone
- Urology Research Department, Royal Berkshire Hospital, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Reading, UK.
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23
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Two classifiers based on serum peptide pattern for prediction of HBV-induced liver cirrhosis using MALDI-TOF MS. BIOMED RESEARCH INTERNATIONAL 2013; 2013:814876. [PMID: 23509784 PMCID: PMC3590609 DOI: 10.1155/2013/814876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/09/2013] [Indexed: 01/16/2023]
Abstract
Chronic infection with hepatitis B virus (HBV) is associated with the majority of cases of liver cirrhosis (LC) in China. Although liver biopsy is the reference method for evaluation of cirrhosis, it is an invasive procedure with inherent risk. The aim of this study is to discover novel noninvasive specific serum biomarkers for the diagnosis of HBV-induced LC. We performed bead fractionation/MALDI-TOF MS analysis on sera from patients with LC. Thirteen feature peaks which had optimal discriminatory performance were obtained by using support-vector-machine-(SVM-) based strategy. Based on the previous results, five supervised machine learning methods were employed to construct classifiers that discriminated proteomic spectra of patients with HBV-induced LC from those of controls. Here, we describe two novel methods for prediction of HBV-induced LC, termed LC-NB and LC-MLP, respectively. We obtained a sensitivity of 90.9%, a specificity of 94.9%, and overall accuracy of 93.8% on an independent test set. Comparisons with the existing methods showed that LC-NB and LC-MLP held better accuracy. Our study suggests that potential serum biomarkers can be determined for discriminating LC and non-LC cohorts by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. These two classifiers could be used for clinical practice in HBV-induced LC assessment.
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Cho YT, Su H, Huang TL, Chen HC, Wu WJ, Wu PC, Wu DC, Shiea J. Matrix-assisted laser desorption ionization/time-of-flight mass spectrometry for clinical diagnosis. Clin Chim Acta 2013; 415:266-75. [DOI: 10.1016/j.cca.2012.10.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 10/16/2012] [Indexed: 01/01/2023]
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25
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Proteomics study on the hepatoprotective effects of traditional Chinese medicine formulae Yin-Chen-Hao-Tang by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. J Pharm Biomed Anal 2012; 75:173-9. [PMID: 23262417 DOI: 10.1016/j.jpba.2012.11.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/12/2012] [Accepted: 11/15/2012] [Indexed: 11/20/2022]
Abstract
Proteomics can bring breakthroughs in the study of traditional Chinese medicine (TCM). Yin-Chen-Hao-Tang (YCHT), a famous TCM formulae, has been used to alleviate various types of liver injury. However, the underlying mechanisms and drug targets of YCHT associated with the hepatic injury are largely unknown. To identify the possible target proteins of YCHT, two-dimensional gel electrophoresis (2-DE)-based proteomics was performed and proteins altered after YCHT treatment were identified by MALDI-TOF/TOF-MS. Interestingly, 15 modulated proteins were identified, out of which 7 were found to be significantly altered by YCHT. YCHT treatment caused a statistically significant down-regulation of zinc finger protein 407, haptoglobin, macroglobulin, alpha-1-antitrypsin; significant up-regulation of transthyretin, vitamin D-binding protein, and prothrombin, appear to be involved in metabolism, energy generation, chaperone, antioxidation, signal transduction, protein folding and apoptosis. Finally, interaction network from 7 differentially expressed protein to the signal-related proteins was established using bioinformatic analysis. Of note, these signal-related proteins could be included in a network together with 7 proteins through direct interaction or only one intermediate partner. Functional pathway analysis suggested that these proteins were closely related in the protein-protein interaction network and the modulation of multiple vital physiological pathways. Thus, our data will help to understand the molecular mechanisms of hepatoprotective effects of YCHT.
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Guinan T, Ronci M, Kobus H, Voelcker NH. Rapid detection of illicit drugs in neat saliva using desorption/ionization on porous silicon. Talanta 2012; 99:791-8. [DOI: 10.1016/j.talanta.2012.07.029] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/08/2012] [Accepted: 07/09/2012] [Indexed: 12/18/2022]
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Jiang H, Wang XH, Yu XM, Zheng ZG. Detection and Prognostic Analysis of Serum Protein Expression in Esophageal Squamous Cell Cancer. Asian Pac J Cancer Prev 2012; 13:1579-82. [DOI: 10.7314/apjcp.2012.13.4.1579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Romero-Pastor J, Navas N, Kuckova S, Rodríguez-Navarro A, Cardell C. Collagen-based proteinaceous binder-pigment interaction study under UV ageing conditions by MALDI-TOF-MS and principal component analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:322-330. [PMID: 22431458 DOI: 10.1002/jms.2966] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This study focuses on acquiring information on the degradation process of proteinaceous binders due to ultra violet (UV) radiation and possible interactions owing to the presence of historical mineral pigments. With this aim, three different paint model samples were prepared according to medieval recipes, using rabbit glue as proteinaceus binders. One of these model samples contained only the binder, and the other two were prepared by mixing each of the pigments (cinnabar or azurite) with the binder (glue tempera model samples). The model samples were studied by applying Principal Component Analysis (PCA) to their mass spectra obtained with Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). The complementary use of Fourier Transform Infrared Spectroscopy to study conformational changes of secondary structure of the proteinaceous binder is also proposed. Ageing effects on the model samples after up to 3000 h of UV irradiation were periodically analyzed by the proposed approach. PCA on MS data proved capable of identifying significant changes in the model samples, and the results suggested different aging behavior based on the pigment present. This research represents the first attempt to use this approach (PCA on MALDI-TOF-MS data) in the field of Cultural Heritage and demonstrates the potential benefits in the study of proteinaceous artistic materials for purposes of conservation and restoration.
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Affiliation(s)
- Julia Romero-Pastor
- Department of Mineralogy and Petrology, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
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Bateson H, Saleem S, Loadman PM, Sutton CW. Use of matrix-assisted laser desorption/ionisation mass spectrometry in cancer research. J Pharmacol Toxicol Methods 2011; 64:197-206. [DOI: 10.1016/j.vascn.2011.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/18/2011] [Accepted: 04/08/2011] [Indexed: 02/04/2023]
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30
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Bateson H, Saleem S, Loadman PM, Sutton CW. Use of matrix-assisted laser desorption/ionisation mass spectrometry in cancer research. J Pharmacol Toxicol Methods 2011; 64:197-206. [DOI: https:/doi.org/10.1016/j.vascn.2011.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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31
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The application of SELDI-TOF-MS in clinical diagnosis of cancers. J Biomed Biotechnol 2011; 2011:245821. [PMID: 21687541 PMCID: PMC3114543 DOI: 10.1155/2011/245821] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/30/2011] [Indexed: 12/24/2022] Open
Abstract
Cancer diagnosis is important, and the early diagnosis of cancers could predict a more successful treatment. The proteomic studies emerged to be useful in combined analyses of samples from patients and provide more accurate diagnosis when compared to the single-factor-based diagnosis. In recent years, cancer detection with surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS) is flourishing and brought significant progress in this area. This paper summarizes some recent results with this technique for cancer diagnosis.
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Lim MD, Dickherber A, Compton CC. Before you analyze a human specimen, think quality, variability, and bias. Anal Chem 2010; 83:8-13. [PMID: 21114268 DOI: 10.1021/ac1018974] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Personalized medicine requires capabilities to detect and measure health-associated biomarkers with increasingly specific and sensitive methods, putting analytical chemists at the front lines of translational research. Analytical scientists must be upstream in the experimental design process because the analysis of a biospecimen (tissue, blood, etc.) presents technical and experimental design complexities. (To listen to a podcast about this feature, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).
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Affiliation(s)
- Mark David Lim
- AAAS Science and Technology Policy Fellowship Program and National Cancer Institute, National Institutes of Health, USA
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