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Chen R, Fulton KM, Twine SM, Li J. IDENTIFICATION OF MHC PEPTIDES USING MASS SPECTROMETRY FOR NEOANTIGEN DISCOVERY AND CANCER VACCINE DEVELOPMENT. MASS SPECTROMETRY REVIEWS 2021; 40:110-125. [PMID: 31875992 DOI: 10.1002/mas.21616] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunotherapy with neoantigens presented by major histocompatibility complex (MHC) is one of the most promising approaches in cancer treatment. Using this approach, cancer vaccines can be designed to target tumor-specific mutations that are not found in normal tissues. Clinical trials have demonstrated an increased immune response and eradication of tumors after injecting synthetic peptides selected from the immunopeptidome. Although the sequence of MHC binding peptides can be predicted from genome sequencing and prediction algorithms, this approach results in large numbers of predicted peptides, requiring the confirmation by mass spectrometry (MS) analysis. Identification of MHC peptides by direct MS analysis of immunopeptidome is accurate and sensitive, with tens of thousands of unique peptides potentially identified from either cancer cell line or tumor tissue. Peptides with mutations can also be identified with patient-specific protein databases constructed from genome or transcriptome sequencing data. MS analysis also enables the characterization of the post-translational modifications (PTMs) of those antigens that cannot be predicted. Moreover, PTMs were found to be more efficient in triggering an immune response. In addition to reviewing recent advances in the identification of neoantigens using MS, the techniques for cancer vaccine candidate selection and formulation, vaccine delivery systems, and the potential for use in combination with other therapeutics are also discussed. It is anticipated that MS-based techniques will play an important role in future cancer vaccine development. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:110-125, 2021.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
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Chen R, Stupak J, Williamson S, Twine SM, Li J. Online porous graphic carbon chromatography coupled with tandem mass spectrometry for post-translational modification analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1240-1247. [PMID: 31034685 DOI: 10.1002/rcm.8459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Porous graphic carbon chromatography (PGC) has a different mechanism in the retention of tryptic peptides compared with reversed-phase chromatography and in this study we show that coupling PGC with tandem mass spectrometry offer advantages for the quantitation of phosphorylation stoichiometry and characterization of site-specific glycosylation. METHODS Digests of protein standards (horse myoglobin, bovine fetuin and β-casein) were analyzed with a capillary liquid chromatography/tandem mass spectrometry (LC/MS/MS) system by coupling an Agilent 1100 HPLC system to a Synapt G2-Si HDMS (Waters). Peptides were separated using a HyperCarb PGC column (300 μm i.d. × 100 mm) packed with 3 μm particles. MS/MS data were collected in data-dependent mode and three MS/MS scans were acquired after the full MS scan. RAW data were transformed to .mgf by PLGS (Waters) and searched against the Swissprot database by Mascot. Chromatograms and MS/MS spectra of identified compounds were extracted with Masslynx (Waters) and imported to Origin for analysis. Glycan composition and peptide sequence were manually annotated. RESULTS PGC/MS/MS enabled accurate quantitation of the stoichiometry of specific phosphorylation sites from β-casein by efficient separation of the phosphopeptide and its non-phosphorylated counterpart, which cannot be achieved by reversed-phase chromatography. PGC/MS/MS also enabled comprehensive characterization of protein sialoglycosylation as isomeric glycopeptides with different combinations of α2-3- and α2-6-linked sialic acids can be separated and the ratios of each combination were verified by exoglycosidase digestion. CONCLUSIONS PGC has demonstrated superior separation of peptides with phosphorylation and glycosylation and can be used as an alternative in the proteomic characterization of post-translational modifications (PTMs) by polar groups.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jacek Stupak
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Sam Williamson
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
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Wang M, Liu L, Yin Z, Lu Y. Comparison of two online extraction systems and development of the online SPE-HPLC-DAD method to simultaneously determine ten β-amino alcohol drugs in plasma. RSC Adv 2018; 8:5816-5821. [PMID: 35539588 PMCID: PMC9078181 DOI: 10.1039/c7ra13276j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/26/2018] [Indexed: 11/21/2022] Open
Abstract
Multiple comparisons of two online pretreatment systems were conducted, which provided a reference for choosing a suitable solution.
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Affiliation(s)
- Man Wang
- College of Pharmacy
- Nankai University
- Tianjin 300071
- PR China
- State Key Laboratory of Medicinal Chemical Biology
| | - Lei Liu
- College of Pharmacy
- Nankai University
- Tianjin 300071
- PR China
| | - Zheng Yin
- College of Pharmacy
- Nankai University
- Tianjin 300071
- PR China
- State Key Laboratory of Medicinal Chemical Biology
| | - Yaxin Lu
- College of Pharmacy
- Nankai University
- Tianjin 300071
- PR China
- State Key Laboratory of Medicinal Chemical Biology
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Minshull TC, Cole J, Dockrell DH, Read RC, Dickman MJ. Analysis of histone post translational modifications in primary monocyte derived macrophages using reverse phase×reverse phase chromatography in conjunction with porous graphitic carbon stationary phase. J Chromatogr A 2016; 1453:43-53. [PMID: 27260198 PMCID: PMC4906248 DOI: 10.1016/j.chroma.2016.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/12/2016] [Accepted: 05/03/2016] [Indexed: 02/07/2023]
Abstract
A two dimensional-liquid chromatography (2D-LC) based approach was developed for the identification and quantification of histone post translational modifications in conjunction with mass spectrometry analysis. Using a bottom-up strategy, offline 2D-LC was developed using reverse phase chromatography. A porous graphitic carbon stationary phase in the first dimension and a C18 stationary phase in the second dimension interfaced with mass spectrometry was used to analyse global levels of histone post translational modifications in human primary monocyte-derived macrophages. The results demonstrated that 84 different histone peptide proteoforms, with modifications at 18 different sites including combinatorial marks were identified, representing an increase in the identification of histone peptides by 65% and 51% compared to two different 1D-LC approaches on the same mass spectrometer. The use of the porous graphitic stationary phase in the first dimension resulted in efficient separation of histone peptides across the gradient, with good resolution and is orthogonal to the online C18 reverse phase chromatography. Overall, more histone peptides were identified using the 2D-LC approach compared to conventional 1D-LC approaches. In addition, a bioinformatic pipeline was developed in-house to enable the high throughput efficient and accurate quantification of fractionated histone peptides. The automation of a section of the downstream analysis pipeline increased the throughput of the 2D-LC-MS/MS approach for the quantification of histone post translational modifications.
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Affiliation(s)
- Thomas C Minshull
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom; Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, United Kingdom; Sheffield Teaching Hospitals, United Kingdom
| | - Joby Cole
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom; Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, United Kingdom; Sheffield Teaching Hospitals, United Kingdom
| | - David H Dockrell
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, United Kingdom; Sheffield Teaching Hospitals, United Kingdom
| | - Robert C Read
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine and Institute for Life Sciences, University of Southampton, NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton SO166YD, United Kingdom
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom.
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Ortiz-Almirall X, Pena-Abaurrea M, Jobst K, Reiner E. Nontargeted Analysis of Persistent Organic Pollutants by Mass Spectrometry and GC×GC. APPLICATIONS OF TIME-OF-FLIGHT AND ORBITRAP MASS SPECTROMETRY IN ENVIRONMENTAL, FOOD, DOPING, AND FORENSIC ANALYSIS 2016. [DOI: 10.1016/bs.coac.2016.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Fan Y, Shen G, Li P, Xi X, Wu H, Tian H, Lu Y, Yin Z. A simple and automated online SPE-LC-MS/MS method for simultaneous determination of olanzapine, fluoxetine and norfluoxetine in human plasma and its application in therapeutic drug monitoring. RSC Adv 2015. [DOI: 10.1039/c5ra02489g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An integration of sample pretreatment automation using online SPE technique could provide an easy to use, efficient, sensitive and high quality methods for TDM.
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Affiliation(s)
- Yiran Fan
- College of Pharmacy
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Guanghu Shen
- Tianjin AnDing Hospital
- Tianjin 300222
- P. R. China
| | - Ping Li
- College of Pharmacy
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Xiaonan Xi
- College of Pharmacy
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Haiting Wu
- College of Pharmacy
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Hongjun Tian
- Tianjin AnDing Hospital
- Tianjin 300222
- P. R. China
| | - Yaxin Lu
- College of Pharmacy
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
| | - Zheng Yin
- College of Pharmacy
- State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071
- P. R. China
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Zhao Y, Szeto SSW, Kong RPW, Law CH, Li G, Quan Q, Zhang Z, Wang Y, Chu IK. Online two-dimensional porous graphitic carbon/reversed phase liquid chromatography platform applied to shotgun proteomics and glycoproteomics. Anal Chem 2014; 86:12172-9. [PMID: 25393709 DOI: 10.1021/ac503254t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel fully automatable two-dimensional liquid chromatography (2DLC) platform has been integrated into a modified commercial off-the-shelf LC instrument, incorporating porous graphitic carbon (PGC) separation and conventional low-pH reversed-phase (RP) separation for both proteomics and N-glycomics analyses; the dual-trap column configuration of this platform offers desirable high-throughput analyses with almost no idle time, in addition to a miniaturized setup and simplified operation. The total run time per analysis was only 19 h when using eight PGC fractions for unattended large-scale qualitative and quantitative proteomic analyses; the identification of 2678 nonredundant proteins and 11,984 unique peptides provided one of the most comprehensive proteome data sets for primary cerebellar granule neurons (CGNs). The effect of pH on the PGC column was investigated for the first time to improve the hydrophobic peptide coverage; the performance of the optimized system was first benchmarked using tryptic digests of Saccharomyces cerevisiae cell lysates and then evaluated through duplicate analyses of Macaca fascicularis cerebral cortex lysates using isobaric tags for relative and absolute quantitation (iTRAQ) technology. An additional plug-and-play PGC module functioned in a complementary manner to recover unretained hydrophilic solutes from the low-pH RP column; synchronization of the fractionations between the PGC-RP system and the PGC module facilitated simultaneous analyses of hydrophobic and hydrophilic compounds from a single sample injection event. This methodology was applied to perform, for the first time, detailed glycomics analyses of Macaca fascicularis plasma, resulting in the identification of a total 130 N-glycosylated plasma proteins, 705 N-glycopeptides, and 254 N-glycosylation sites.
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Affiliation(s)
- Yun Zhao
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
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Liu L, Wen Y, Liu K, Sun L, Lu Y, Yin Z. Simultaneous determination of a broad range of cardiovascular drugs in plasma with a simple and efficient extraction/clean up procedure and chromatography-mass spectrometry analysis. RSC Adv 2014. [DOI: 10.1039/c4ra01045k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A simple, easy to use and efficient method was described for simultaneous determination of ten cardiovascular drugs with a broad range of physicochemical properties in rat plasma via online SPE and HPLC-MS/MS.
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Affiliation(s)
- Lei Liu
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071, PR China
| | - Yabin Wen
- College of Life Science
- Nankai University
- Tianjin 300071, PR China
| | - Kangning Liu
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071, PR China
| | - Liang Sun
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071, PR China
| | - Yaxin Lu
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071, PR China
| | - Zheng Yin
- College of Pharmacy & State Key Laboratory of Elemento-Organic Chemistry
- Nankai University
- Tianjin 300071, PR China
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On-line solid phase extraction–liquid chromatography, with emphasis on modern bioanalysis and miniaturized systems. J Pharm Biomed Anal 2014; 87:120-9. [DOI: 10.1016/j.jpba.2013.05.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/24/2022]
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