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Jiang J, Zhan L, Dai L, Yao X, Qin Y, Zhu Z, Zhang M, Tong W, Wang G. Evaluation of the reliability of MS1-based approach to profile naturally occurring peptides with clinical relevance in urine samples. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022:e9369. [PMID: 35906701 DOI: 10.1002/rcm.9369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/02/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE The profiling of natural urinary peptides is a valuable indicator of kidney condition. While front-end separation limits the speed of peptidomic profiling, MS1-based results suffer from limited peptide coverage and specificity. Clinical studies on chronic kidney disease require an effective strategy to balance the trade-off between identification depth and throughput. METHODS CKD273, a urinary proteome classifier associated with chronic kidney disease, in samples from diabetic nephropathy patients was profiled in parallel using capillary electrophoresis-mass spectrometry (CE-MS), liquid chromatography with mass spectrometry (LC-MS), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Through cross-comparison of results from MS1 of unfractionated peptides and elution-time-resolved MS1 as well as MS/MS in LC- and CE-MS approaches, we evaluated the contribution of false-positive identification to MS1-based identification and quantitation, and analyzed the benefit of front-end separation in terms of accuracy and efficiency. RESULTS In LC- and CE-MS, although MS1 data resulted in higher number of identifications than MS/MS, elution-time-dependent analysis revealed extensive interference by non-CKD273 peptides, which would contribute up to 50% to quantitation if they are not separated from genuine CKD273 peptides. In the absence of separation, MS1 data resulted in lower numbers of identifications and abundance pattern that significantly deviated from those by liquid chromatography with tandem mass spectrometry (LC-MS/MS) or capillary electrophoresis with tandem mass spectrometry (CE-MS/MS). CE showed higher identification efficiency even when less sample was used or achieved faster separation. CONCLUSIONS To ensure the reliability of MS1-based urinary peptide profiling, front-end separation should not be omitted, and elution time should be used in addition to intact mass for identification. Including MS/MS in data acquisition does not compromise the speed or identification number, while benefiting data reliability by providing real-time sequence verification.
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Affiliation(s)
- Jialu Jiang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Lingpeng Zhan
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Liuyan Dai
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Xiaopeng Yao
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Yao Qin
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Zhongqin Zhu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Mei Zhang
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Wenjun Tong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
| | - Guanbo Wang
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
- Biomedical Pioneering Innovation Centre, Peking University, Beijing, China
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Lazari LC, Rosa-Fernandes L, Palmisano G. Identification of Circulating Biomarkers of COVID-19 Using MALDI-TOF Mass Spectrometry. Methods Mol Biol 2022; 2511:175-182. [PMID: 35838960 DOI: 10.1007/978-1-0716-2395-4_13] [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: 06/15/2023]
Abstract
Matrix-assisted laser desorption/ionization source coupled with time-of-flight mass analyzer mass spectrometry (MALDI-TOF MS) is being widely used to obtain proteomic profiles for clinical purposes, as a fast, low-cost, robust, and efficient technique. Here we describe a method for biofluid analysis using MALDI-TOF MS for rapid acquisition of proteomic signatures of COVID-19 infected patients. By using solid-phase extraction, the method allows the analysis of biofluids in less than 15 min.
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Affiliation(s)
- Lucas C Lazari
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, São Paulo, Brazil.
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Lazari LC, Ghilardi FDR, Rosa-Fernandes L, Assis DM, Nicolau JC, Santiago VF, Dalçóquio TF, Angeli CB, Bertolin AJ, Marinho CR, Wrenger C, Durigon EL, Siciliano RF, Palmisano G. Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19. Life Sci Alliance 2021; 4:e202000946. [PMID: 34168074 PMCID: PMC8321665 DOI: 10.26508/lsa.202000946] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 infection poses a global health crisis. In parallel with the ongoing world effort to identify therapeutic solutions, there is a critical need for improvement in the prognosis of COVID-19. Here, we report plasma proteome fingerprinting that predict high (hospitalized) and low-risk (outpatients) cases of COVID-19 identified by a platform that combines machine learning with matrix-assisted laser desorption ionization mass spectrometry analysis. Sample preparation, MS, and data analysis parameters were optimized to achieve an overall accuracy of 92%, sensitivity of 93%, and specificity of 92% in dataset without feature selection. We identified two distinct regions in the MALDI-TOF profile belonging to the same proteoforms. A combination of SDS-PAGE and quantitative bottom-up proteomic analysis allowed the identification of intact and truncated forms of serum amyloid A-1 and A-2 proteins, both already described as biomarkers for viral infections in the acute phase. Unbiased discrimination of high- and low-risk COVID-19 patients using a technology that is currently in clinical use may have a prompt application in the noninvasive prognosis of COVID-19. Further validation will consolidate its clinical utility.
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Affiliation(s)
- Lucas Cardoso Lazari
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - José Carlos Nicolau
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Claudio Rf Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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MALDI Profiling and Applications in Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:27-43. [DOI: 10.1007/978-3-030-15950-4_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Greco V, Piras C, Pieroni L, Ronci M, Putignani L, Roncada P, Urbani A. Applications of MALDI-TOF mass spectrometry in clinical proteomics. Expert Rev Proteomics 2018; 15:683-696. [PMID: 30058389 DOI: 10.1080/14789450.2018.1505510] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.
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Affiliation(s)
- Viviana Greco
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
| | - Cristian Piras
- c Dipartimento di Medicina Veterinaria , Università degli studi di Milano , Milano , Italy
| | - Luisa Pieroni
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy
| | - Maurizio Ronci
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy.,e Department of Medical, Oral and Biotechnological Sciences , University "G. D'Annunzio" of Chieti-Pescara , Chieti , Italy
| | - Lorenza Putignani
- f Unit of Parasitology Bambino Gesù Children's Hospital , IRCCS , Rome , Italy.,g Unit of Human Microbiome , Bambino Gesù Children's Hospital, IRCCS , Rome , Italy
| | - Paola Roncada
- h Dipartimento di Scienze della Salute , Università degli studi "Magna Græcia" di Catanzaro , Catanzaro , Italy
| | - Andrea Urbani
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
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Mateos J, Carneiro I, Corrales F, Elortza F, Paradela A, Del Pino MS, Iloro I, Marcilla M, Mora MI, Valero L, Ciordia S, Fernández V, Fortuño MA, García-Sánchez I, Martínez R, Muñoz MA, Rodriguez C, Doménech N. Multicentric study of the effect of pre-analytical variables in the quality of plasma samples stored in biobanks using different complementary proteomic methods. J Proteomics 2016; 150:109-120. [PMID: 27620695 DOI: 10.1016/j.jprot.2016.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/27/2022]
Abstract
Analytical proteomics has experienced exponential progress in the last decade and can be expected to lead research studies on diagnostic and therapeutic biomarkers in the near future. Because the development of this type of analysis requires the use of a large number of human samples with a minimum of quality requirements, our objective was to identify appropriate indicators for quality control of plasma samples stored in biobanks for research in proteomics. To accomplish this, plasma samples from 100 healthy donors were obtained and processed according to the pre-analytical variables of: a) time delay for the first centrifugation of the original blood sample (4 or 24h) and b) number of freeze/thaw cycles (1, 2 or 3) of the processed plasma samples. The analyses of samples were performed by different and complementary methods such as SPE MALDI-TOF, DIGE, shotgun (iTRAQ, nLC MALDI TOF/TOF) and targeted nLC MS/MS proteomic techniques (SRM). In general, because the distribution of proteins in all samples was found to be very similar, the results shown that delayed processing of blood samples and the number of freeze/thaw cycles has little or no effect on the integrity of proteins in the plasma samples. SIGNIFICANCE The results of the present work indicate that blood proteins in plasma are broadly insensitive to such preanalytical variables as delayed processing or freeze/thaw cycles when analyzed at the peptide level. Although there are other studies related to protein stability of clinical samples with similar results, what is remarkable about our work is the large number of plasma samples examined and that our analyses assessed protein integrity by combining a wide set of complementary proteomic approaches performed at different proteomic platform participating laboratories that all yielded similar results. We believe our study is the most comprehensive performed to date to determine the changes in proteins induced by delayed sample processing and plasma freeze/thaw cycles.
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Affiliation(s)
- Jesús Mateos
- Plataforma de Proteómica, Instituto de Investigación Biomédica (INIBIC), A Coruña, Spain
| | | | - Fernando Corrales
- Centro de Investigación en Medicina Aplicada (CIMA)-UN, Pamplona, Spain
| | - Felix Elortza
- Centro de Investigación Cooperativa en Biociencias CICbioGUNE, Derio, Spain
| | | | | | - Ibon Iloro
- Centro de Investigación Cooperativa en Biociencias CICbioGUNE, Derio, Spain
| | | | - Maria Isabel Mora
- Centro de Investigación en Medicina Aplicada (CIMA)-UN, Pamplona, Spain
| | - Luz Valero
- Universidad de Valencia (UV), Valencia, Spain
| | - Sergio Ciordia
- Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Verónica Fernández
- Biobanco HCB-IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | | | - Clara Rodriguez
- Biobanco Vasco/Centro Vasco de Transfusiones, Barakaldo, Spain
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Hammarström B, Nilson B, Laurell T, Nilsson J, Ekström S. Acoustic Trapping for Bacteria Identification in Positive Blood Cultures with MALDI-TOF MS. Anal Chem 2014; 86:10560-7. [DOI: 10.1021/ac502020f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Björn Hammarström
- Department
of Biomedical Engineering, Lund University, 221 00 Lund, Sweden
| | - Bo Nilson
- Clinical
Microbiology, Labmedicin, Region Skåne, 221 85 Lund, Sweden
- Department
of Laboratory Medicine, Division of Medicinal Microbiology, Lund University, SE-223 62 Lund, Sweden
| | - Thomas Laurell
- Department
of Biomedical Engineering, Lund University, 221 00 Lund, Sweden
- Department
of Biomedical Engineering, Dongguk University, Jung-gu, Seoul 100-715, Korea
| | - Johan Nilsson
- Department
of Biomedical Engineering, Lund University, 221 00 Lund, Sweden
| | - Simon Ekström
- Department
of Biomedical Engineering, Lund University, 221 00 Lund, Sweden
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8
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Nicolardi S, Velstra B, Mertens BJ, Bonsing B, Mesker WE, Tollenaar RA, Deelder AM, van der Burgt YE. Ultrahigh resolution profiles lead to more detailed serum peptidome signatures of pancreatic cancer. TRANSLATIONAL PROTEOMICS 2014. [DOI: 10.1016/j.trprot.2013.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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9
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Dudley E. MALDI Profiling and Applications in Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:33-58. [DOI: 10.1007/978-3-319-06068-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Tissue biomarkers of breast cancer and their association with conventional pathologic features. Br J Cancer 2013; 108:351-60. [PMID: 23299531 PMCID: PMC3566809 DOI: 10.1038/bjc.2012.552] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: Tissue protein expression profiling has the potential to detect new biomarkers to improve breast cancer (BC) diagnosis, staging, and prognostication. This study aimed to identify tissue proteins that differentiate breast cancer tissue from healthy breast tissue using protein chip mass spectrometry and to examine associations with conventional pathological features. Methods: To develop a training model, 82 BC and 82 adjacent unaffected tissue (AT) samples were analysed on cation-exchange protein chips by time-of-flight mass spectrometry. For validation, 89 independent BC and AT sample pairs were analysed. Results: From the protein peaks that were differentially expressed between BC and AT by univariate analysis, binary logistic regression yielded two peaks that together classified BC and AT with a ROC area under the curve of 0.92. Two proteins, ubiquitin and S100P (in a novel truncated form), were identified by liquid chromatography/tandem mass spectrometry and validated by immunoblotting and reactive-surface protein chip immunocapture. The combined marker panel was positively associated with high histologic grade, larger tumour size, lymphovascular invasion, ER and PR positivity, and HER2 overexpression, suggesting that it may be associated with a HER2-enriched molecular subtype of breast cancer. Conclusion: This independently validated protein panel may be valuable in the classification and prognostication of breast cancer patients.
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Boccardi C, Rocchiccioli S, Cecchettini A, Mercatanti A, Citti L. An automated plasma protein fractionation design: high-throughput perspectives for proteomic analysis. BMC Res Notes 2012; 5:612. [PMID: 23116412 PMCID: PMC3517536 DOI: 10.1186/1756-0500-5-612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/26/2012] [Indexed: 01/17/2023] Open
Abstract
Background Human plasma, representing the most complete record of the individual phenotype, is an appealing sample for proteomics analysis in clinical applications. Up to today, the major obstacle in a proteomics study of plasma is the large dynamic range of protein concentration and the efforts of many researchers focused on the resolution of this important drawback. Findings In this study, proteins from pooled plasma samples were fractionated according to their chemical characteristics on a home-designed SPE automated platform. The resulting fractions were digested and further resolved by reversed-phase liquid chromatography coupled with MALDI TOF/TOF mass spectrometry. A total of 712 proteins were successfully identified until a concentration level of ng/mL. Pearson correlation coefficient was used to test reproducibility. Conclusions Our multidimensional fractionation approach reduced the analysis time (2 days are enough to process 16 plasma samples filling a 96-well plate) over the conventional gel-electrophoresis or multi-LC column based methods. The robotic processing, avoiding contaminants or lack of sample handling skill, promises highly reproducible specimen analyses (more than 85% Pearson correlation). The automated platform here presented is flexible and easily modulated changing fractioning elements or detectors.
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Affiliation(s)
- Claudia Boccardi
- Institute of Clinical Physiology-CNR, Via Moruzzi 1, 56124 Pisa, Italy
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Savino R, Paduano S, Preianò M, Terracciano R. The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci 2012. [PMID: 23203042 PMCID: PMC3509558 DOI: 10.3390/ijms131113926] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets.
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Affiliation(s)
- Rocco Savino
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Græcia", Catanzaro, University Campus, Europa Avenue, 88100 Catanzaro, Italy.
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Zhong DN, Ning QY, Wu JZ, Zang N, Wu JL, Hu DF, Luo SY, Huang AC, Li LL, Li GJ. Comparative proteomic profiles indicating genetic factors may involve in hepatocellular carcinoma familial aggregation. Cancer Sci 2012; 103:1833-8. [PMID: 22726459 DOI: 10.1111/j.1349-7006.2012.02368.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/03/2012] [Accepted: 06/14/2012] [Indexed: 12/23/2022] Open
Abstract
Familial aggregation of hepatocellular carcinoma (HCC), the third leading cause of cancer death worldwide, has shown to be a common phenomenon. We investigated the association between the genetic background and HCC familial aggregation. Serum samples were collected from HCC family members and normal control family members for screening the differentially expressed protein peaks with the approach of surface-enhanced laser desorption ionization time-of-flight mass spectrometry. Potential genetically associated protein peaks were selected and further identified by matrix assisted laser desorption ionization-time of flight mass spectrometry. A panel of six protein peaks (m/z 6432.94, 8478.35, 9381.91, 17284.67, 17418.34, and 18111.04) were speculated to reflect the genetic susceptibility of HCC familial aggregation. Three of them (m/z 6432.94, 8478.35, and 9381.91) were selected to identify as the candidate proteins. Nine identified proteins, including mostly apolipoprotein family (ApoA1, ApoA2, ApoC3, ApoE) and serum amyloid A protein (SAA), were found overexpressed in the multiple HCC cases family members. The comparative proteomic profiles have suggested that genetic factors ought to be taken into account for familial aggregation of HCC.
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Affiliation(s)
- Da-Ni Zhong
- Department of Infectious Diseases, First Affiliated Hospital, Guangxi Medical University, Nanning, China
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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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Penno MAS, Colegate SM, Michalski WP, Hoffmann P. Detection and measurement of carbohydrate deficient transferrin in serum using immuno-capture mass spectrometry: diagnostic applications for annual ryegrass toxicity and corynetoxin exposure. Res Vet Sci 2011; 93:611-7. [PMID: 21963292 DOI: 10.1016/j.rvsc.2011.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 08/15/2011] [Accepted: 08/27/2011] [Indexed: 10/17/2022]
Abstract
The neurological livestock disease annual ryegrass toxicity (ARGT) is caused by the ingestion of the naturally occurring glycolipid toxins - the corynetoxins. Corynetoxins also threaten human health as potential contaminants of the food supply. Presently, there are no routine diagnostic tests for corynetoxins-exposure in humans or livestock. Chronic ingestion of corynetoxins has been modeled in rats exposed to dietary tunicamycins for 12 months and carbohydrate deficient transferrin (CDT) has been previously identified as a candidate disease biomarker. Here, the technique of immuno-capture mass spectrometry (icMS) was used to evaluate serum levels of CDT, discriminating between control and tunicamycins-exposed rats with 85% accuracy. The icMS approach is based on the combination of specific transferrin enrichment with functionalized magnetic beads and automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). With no other clinically-relevant diagnostic tests available icMS could be readily adapted for high-throughput clinical assessment of corynetoxins-exposure in humans or livestock.
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Affiliation(s)
- M A S Penno
- Adelaide Proteomics Centre, University of Adelaide, Adelaide, South Australia 5005, Australia
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16
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Shrivas K, Wu HF. Multifunctional nanoparticles composite for MALDI-MS: Cd2+-doped carbon nanotubes with CdS nanoparticles as the matrix, preconcentrating and accelerating probes of microwave enzymatic digestion of peptides and proteins for direct MALDI-MS analysis. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1452-1460. [PMID: 21053343 DOI: 10.1002/jms.1861] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
For the first time, we utilized multifunctional nanoparticles composite (NPs composite) for matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis of peptides and proteins. Multiwalled carbon nanotubes doped with Cd(2+) ions and modified with cadmium sulfide NPs were synthesized by a chemical reduction method at room temperature. The multifunctional NPs composite applied for the analysis of peptides and microwave-digested proteins in the atmospheric pressure matrix-assisted laser desorption/ionization ion-trap and MALDI time-of-flight (TOF) mass spectrometry (MS) was successfully demonstrated. The maximum detection sensitivity for peptides in MALDI-MS was achieved by the adsorption of negatively charged peptides onto the surfaces of NP composite through electrostatic interactions. The optimal conditions of peptide mixtures were obtained at 20 min of incubation time using 1 mg of NPs composite when the pH of the sample solution was kept higher than the pI values of peptides. The potentiality of the NP composite in the preconcentration of peptides was compared with that of the individual NP by calculating the preconcentration factors (PF) and found that the NPs composite showed a 4-6 times of PF than the other NPs. In addition, the NPs composite was also applied as heat-absorbing materials for efficient microwave tryptic digestion of cytochrome c and lysozyme from milk protein in MALDI-TOF-MS analysis. We believe that the use of NPs composite technique would be an efficient and powerful preconcentrating tool for MALDI-MS for the study of proteome research.
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Affiliation(s)
- Kamlesh Shrivas
- Department of Chemistry, National Sun Yat-Sen University, 70, Lien-Hai Road, Kaohsiung 80424, Taiwan
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18
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Abstract
OBJECTIVE To establish new biomarkers for accurate diagnosis of pancreatic cancer (PC) using a standardized serum peptidome profiling and compare the results with those from the tumor marker, CA 19-9. METHODS Serum samples from 102 patients (55 with chronic pancreatitis and 47 with PC) and 56 healthy controls were collected and analyzed following a protocol that was rigorously designed to prevent preanalytical variation. Serum peptides were extracted using immobilized copper ion chromatography on a robotic platform. Mass spectra were acquired by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry on an Autoflex II spectrometer (Bruker Daltonics, Bremen, Germany). Statistical analysis was performed using the Clinprotools 2.2 software (Bruker Daltonics) and the SPSS 15.0 software (SPSS Inc, Chicago, Ill). RESULTS Standardized peptidome profiling showed a median coefficient of variation of 11.6% calculated using all the extracted peptides and negligible influence of sex and age on peptidome profiles. The diagnostic sensitivity was 89.9%, and the diagnostic specificity was 92.7%, using 2 serum features and CA 19-9 serum concentration. Healthy controls were differentiated from patients with PC and chronic pancreatitis, with the use of 3 features of the peptidome (diagnostic sensitivity, 98.2%; diagnostic specificity, 97.1%). CONCLUSIONS Standardized serum peptidome profiling could be a useful tool to improve biochemical diagnosis of PC in combination with the classic tumor marker, CA 19-9.
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Nicolardi S, Palmblad M, Dalebout H, Bladergroen M, Tollenaar RAEM, Deelder AM, van der Burgt YEM. Quality control based on isotopic distributions for high-throughput MALDI-TOF and MALDI-FTICR serum peptide profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1515-1525. [PMID: 20541438 DOI: 10.1016/j.jasms.2010.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 04/23/2010] [Accepted: 05/06/2010] [Indexed: 05/29/2023]
Abstract
In this study, we have implemented a new quality control (QC) parameter for peptide profiling based on isotopic distributions. This QC parameter is an objective measure and facilitates automatic sorting of large numbers of peptide spectra. Peptides in human serum samples were enriched using reversed-phase C(18)-functionalized magnetic beads using a high-throughput robotic platform. High-resolution MALDI-TOF and ultrahigh resolution MALDI-FTICR mass spectra were obtained and a workflow was developed for automated analysis and evaluation of these profiles. To this end, the isotopic distributions of multiple peptides were quantified from both MALDI-TOF and MALDI-FTICR spectra. Odd peptide isotope distributions in TOF spectra could be rationalized from ultrahigh resolution FTICR spectra that showed overlap of different peptides. The comparison of isotope patterns with estimated polyaveragine distributions was used to calculate a QC value for each single mass spectrum. Sorting these QC values enabled the best MALDI spectrum to be selected from replicate spots. Moreover, using this approach spectra containing high intensities of polymers or other contaminants and lacking peptides of interest can be efficiently removed from a clinical dataset. In general, this method simplifies the exclusion of low quality spectra from further statistical analysis.
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Affiliation(s)
- Simone Nicolardi
- Department of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, Leiden, The Netherlands
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20
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Magni F, Van Der Burgt YEM, Chinello C, Mainini V, Gianazza E, Squeo V, Deelder AM, Kienle MG. Biomarkers discovery by peptide and protein profiling in biological fluids based on functionalized magnetic beads purification and mass spectrometry. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2010; 8 Suppl 3:s92-7. [PMID: 20606758 PMCID: PMC2897205 DOI: 10.2450/2010.015s] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Fulvio Magni
- Department of Experimental Medicine, University of Milano-Bicocca, Monza, Italy.
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21
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Williams D, Ackloo S, Zhu P, Bowden P, Evans KR, Addison CL, Lock C, Marshall JG. Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides. Anal Bioanal Chem 2009; 396:1223-47. [PMID: 20033139 DOI: 10.1007/s00216-009-3345-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 11/30/2022]
Abstract
The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography-electrospray ionization-tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.
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Affiliation(s)
- Declan Williams
- Department of Chemistry and Biology, Faculty of Engineering and Applied Science, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
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22
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Meltretter J, Birlouez-Aragon I, Becker CM, Pischetsrieder M. Assessment of heat treatment of dairy products by MALDI-TOF-MS. Mol Nutr Food Res 2009; 53:1487-95. [DOI: 10.1002/mnfr.200900008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Gámez-Pozo A, Sánchez-Navarro I, Nistal M, Calvo E, Madero R, Díaz E, Camafeita E, de Castro J, López JA, González-Barón M, Espinosa E, Fresno Vara JÁ. MALDI profiling of human lung cancer subtypes. PLoS One 2009; 4:e7731. [PMID: 19890392 PMCID: PMC2767501 DOI: 10.1371/journal.pone.0007731] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 10/08/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Proteomics is expected to play a key role in cancer biomarker discovery. Although it has become feasible to rapidly analyze proteins from crude cell extracts using mass spectrometry, complex sample composition hampers this type of measurement. Therefore, for effective proteome analysis, it becomes critical to enrich samples for the analytes of interest. Despite that one-third of the proteins in eukaryotic cells are thought to be phosphorylated at some point in their life cycle, only a low percentage of intracellular proteins is phosphorylated at a given time. METHODOLOGY/PRINCIPAL FINDINGS In this work, we have applied chromatographic phosphopeptide enrichment techniques to reduce the complexity of human clinical samples. A novel method for high-throughput peptide profiling of human tumor samples, using Parallel IMAC and MALDI-TOF MS, is described. We have applied this methodology to analyze human normal and cancer lung samples in the search for new biomarkers. Using a highly reproducible spectral processing algorithm to produce peptide mass profiles with minimal variability across the samples, lineal discriminant-based and decision tree-based classification models were generated. These models can distinguish normal from tumor samples, as well as differentiate the various non-small cell lung cancer histological subtypes. CONCLUSIONS/SIGNIFICANCE A novel, optimized sample preparation method and a careful data acquisition strategy is described for high-throughput peptide profiling of small amounts of human normal lung and lung cancer samples. We show that the appropriate combination of peptide expression values is able to discriminate normal lung from non-small cell lung cancer samples and among different histological subtypes. Our study does emphasize the great potential of proteomics in the molecular characterization of cancer.
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Affiliation(s)
- Angelo Gámez-Pozo
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Iker Sánchez-Navarro
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Manuel Nistal
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Unidad de Proteómica, Madrid, Spain
| | - Rosario Madero
- Unidad de Bioestadística, Hospital Universitario La Paz, Madrid, Spain
| | - Esther Díaz
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Unidad de Proteómica, Madrid, Spain
| | - Javier de Castro
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Juan Antonio López
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Unidad de Proteómica, Madrid, Spain
| | - Manuel González-Barón
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Enrique Espinosa
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Laboratory of Molecular Pathology and Oncology, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
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24
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Penno MAS, Ernst M, Hoffmann P. Optimal preparation methods for automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling of low molecular weight proteins and peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2656-2662. [PMID: 19630030 DOI: 10.1002/rcm.4167] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mass spectrometry (MS) profiling of the proteome and peptidome for disease-associated patterns is a new concept in clinical diagnostics. The technique, however, is highly sensitive to external sources of variation leading to potentially unacceptable numbers of false positive and false negative results. Before MS profiling can be confidently implemented in a medical setting, standard experimental methods must be developed that minimize technical variance. Past studies of variance have focused largely on pre-analytical variation (i.e., sample collection, handling, etc.). Here, we examined how factors at the analytical stage including the matrix and solid-phase extraction influence MS profiling. Firstly, a standard peptide/protein sample was measured automatically by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS across five consecutive days using two different preparation methods, dried droplet and sample/matrix, of four types of matrix: alpha-cyano-4-hydroxycinnamic acid (HCCA), sinapinic acid (SA), 2,5-dihydroxybenzoic acid (DHB) and 2,5-dihydroxyacetophenone (DHAP). The results indicated that the matrix preparation greatly influenced a number of key parameters of the spectra including repeatability (within-day variability), reproducibility (inter-day variability), resolution, signal strength, background intensity and detectability. Secondly, an investigation into the variance associated with C8 magnetic bead extraction of the standard sample prior to automated MS profiling demonstrated that the process did not adversely affect these same parameters. In fact, the spectra were generally more robust following extraction. Thirdly, the best performing matrix preparations were evaluated using C8 magnetic bead extracted human plasma. We conclude that the DHAP prepared according to the dried-droplet method is the most appropriate matrix to use when performing automated MS profiling.
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Affiliation(s)
- Megan A S Penno
- Adelaide Proteomics Centre, University of Adelaide, Adelaide, South Australia, Australia.
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25
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Sakaeda T, Yamamori M, Kuwahara A, Nishiguchi K. Pharmacokinetics and pharmacogenomics in esophageal cancer chemoradiotherapy. Adv Drug Deliv Rev 2009; 61:388-401. [PMID: 19135108 DOI: 10.1016/j.addr.2008.10.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2008] [Accepted: 10/30/2008] [Indexed: 12/15/2022]
Abstract
Esophageal cancer is one of the most lethal malignancies. Surgical resection of the tumor from the primary site has been the standard treatment, especially for localized squamous cell carcinoma, but considerable clinical efforts during the last decade have resulted in novel courses of treatment. These options include chemoradiotherapy, consisting of a continuous infusion of 5-fluorouracil (5-FU), cisplatin (CDDP), and concurrent radiation. Given the substantial inter- and/or intra-individual variation in clinical outcome, future improvements will likely require the incorporation of a novel anticancer drug, pharmacokinetically guided administration of CDDP or 5-FU, and identification of potential responders by patient genetic profiling prior to treatment. In this review, the latest information on incidence, risk factors, biomarkers, therapeutic strategies, and the pharmacokinetically guided or genotype-guided administration of CDDP and 5-FU is summarized for future individualization of esophageal cancer treatment.
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Affiliation(s)
- Toshiyuki Sakaeda
- Center for Integrative Education of Pharmacy Frontier, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
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26
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Lancashire LJ, Lemetre C, Ball GR. An introduction to artificial neural networks in bioinformatics--application to complex microarray and mass spectrometry datasets in cancer studies. Brief Bioinform 2009; 10:315-29. [PMID: 19307287 DOI: 10.1093/bib/bbp012] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Applications of genomic and proteomic technologies have seen a major increase, resulting in an explosion in the amount of highly dimensional and complex data being generated. Subsequently this has increased the effort by the bioinformatics community to develop novel computational approaches that allow for meaningful information to be extracted. This information must be of biological relevance and thus correlate to disease phenotypes of interest. Artificial neural networks are a form of machine learning from the field of artificial intelligence with proven pattern recognition capabilities and have been utilized in many areas of bioinformatics. This is due to their ability to cope with highly dimensional complex datasets such as those developed by protein mass spectrometry and DNA microarray experiments. As such, neural networks have been applied to problems such as disease classification and identification of biomarkers. This review introduces and describes the concepts related to neural networks, the advantages and caveats to their use, examples of their applications in mass spectrometry and microarray research (with a particular focus on cancer studies), and illustrations from recent literature showing where neural networks have performed well in comparison to other machine learning methods. This should form the necessary background knowledge and information enabling researchers with an interest in these methodologies, but not necessarily from a machine learning background, to apply the concepts to their own datasets, thus maximizing the information gain from these complex biological systems.
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Affiliation(s)
- Lee J Lancashire
- Clinical and Experimental Pharmacology, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK.
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27
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Callesen AK, Madsen JS, Vach W, Kruse TA, Mogensen O, Jensen ON. Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 2009; 9:1428-41. [DOI: 10.1002/pmic.200800382] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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28
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Meltretter J, Schmidt A, Humeny A, Becker CM, Pischetsrieder M. Analysis of the peptide profile of milk and its changes during thermal treatment and storage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:2899-906. [PMID: 18419126 DOI: 10.1021/jf073479o] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this study a new method was developed for analysis of the low molecular weight protein fraction of milk, allowing a simple and fast overview of the peptide profile of various milk samples. For this purpose, immobilized metal affinity chromatography (IMAC) was coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). By this technique, two major peptides in milk could be identified as fragments of alpha-s1-casein. During heat treatment of raw milk, five new peptides were generated, the origin of which could be assigned to the casein fraction. Storage experiments with extended shelf life milk at 4 degrees C did not show any changes in the peptide profile, whereas in ultra high temperature milk stored at room temperature, one peptide increased significantly, which was identified as the N-terminus of alpha-s1-casein. The peptide was assumed to be formed in an enzymatic reaction, which was confirmed in a storage experiment with sterilized milk. Analyses of different commercially available milk samples confirmed the results obtained with the heated and stored milk. Furthermore, differences in the peptide profiles of the samples, probably due to different cow breeds or lactation stages, were observed. These results establish IMAC prior to MALDI-TOF-MS as a valid tool for the rapid analysis of the peptide profile of milk.
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Affiliation(s)
- Jasmin Meltretter
- Department of Chemistry and Pharmacy, Emil-Fischer-Center, University of Erlangen-Nuremberg, Schuhstrasse 19, 91052 Erlangen, Germany.
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29
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Callesen AK, Vach W, Jørgensen PE, Cold S, Tan Q, dePont Christensen R, Mogensen O, Kruse TA, Jensen ON, Madsen JS. Combined Experimental and Statistical Strategy for Mass Spectrometry Based Serum Protein Profiling for Diagnosis of Breast Cancer: A Case-Control Study. J Proteome Res 2008; 7:1419-26. [DOI: 10.1021/pr7007576] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anne K. Callesen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Werner Vach
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Per E. Jørgensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Søren Cold
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Qihua Tan
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - René dePont Christensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Ole Mogensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Torben A. Kruse
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Ole N. Jensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Jonna S. Madsen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
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