1
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Bouwmeester R, Richardson K, Denny R, Wilson ID, Degroeve S, Martens L, Vissers JPC. Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling. Talanta 2024; 274:125970. [PMID: 38621320 DOI: 10.1016/j.talanta.2024.125970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and identification of molecules detected in complex mixtures. Here, a novel machine learning (ML) based method for predicting CCS integrating both molecular modeling (MM) and ML methodologies has been devised and shown to be able to accurately predict CCS values for singly charged small molecular weight molecules from a broad range of chemical classes. The model performed favorably compared to existing models, improving compound identifications for isobaric analytes in terms of ranking and assigning identification probability values to the annotation. Furthermore, charge localization was seen to be correlated with CCS prediction accuracy and with gas-phase proton affinity demonstrating the potential to provide a proxy for prediction error based on chemical structural properties. The presented approach and findings represent a further step towards accurate prediction and application of computationally generated CCS values.
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Affiliation(s)
- Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | | | | | - Ian D Wilson
- Computational & Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, United Kingdom
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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2
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King A, Gethings LA, Vissers JPC, Plumb RS, Wilson ID. Increasing coverage of the urinary polar metabolome using ultra high-performance hydrophobic interaction liquid chromatography combined with linear and cyclic travelling wave ion mobility and mass spectrometry. J Chromatogr A 2024; 1714:464537. [PMID: 38157664 DOI: 10.1016/j.chroma.2023.464537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 01/03/2024]
Abstract
The use of HILIC-based separations for the analysis of polar metabolites in metabolic phenotyping studies is well established. Here, we demonstrate the increased coverage of the polar metabolome obtained by travelling wave (TW) ion mobility (IM) instruments combined with HILIC and mass spectrometry (MS) for metabotyping rat and mouse urine samples. Profiling was performed using either a linear TW IM-MS based instrument with a path length of 40 cm or an instrument with a cyclic travelling wave analyser (cIM) with a path length of 95 cm. Due to the added resolution afforded by using both the linear and cyclic IM geometries with MS detection (IM-MS) significant increases in feature count (m/z-tR pairs) were generally obtained compared to HILIC-MS alone. In addition, the use of both linear and cyclic IM-MS improved the quality of the mass spectra obtained as a result of the separation of co-eluting analytes. As would be expected from the increased path length of the cyclic IM-MS instrument compared to the linear device, the largest gains in feature detection were obtained for the HILIC-cIM-MS combination. By increasing the resolution of coeluting components, the cyclic IM-MS instrumentation also provided the largest improvement in the quality of the mass spectral data obtained. When applied to mouse urines obtained from both control and gefitinib-dosed mice, time-related changes were detected in those obtained from the treated animals that were not seen in the controls. Polar metabolites affected by drug administration included, but were not limited to, hypoxanthine, 1,3-dimethyluracil and acetylcarnitine. The changes seen in the relative concentrations of these endogenous metabolites appeared to be related to drug concentrations in the plasma and urine suggesting a pharmacometabodynamic link.
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Affiliation(s)
- Adam King
- Waters Corporation, Stamford Rd, Wilmslow SK9 4AX, United Kingdom
| | - Lee A Gethings
- Waters Corporation, Stamford Rd, Wilmslow SK9 4AX, United Kingdom
| | | | | | - Ian D Wilson
- Division of Systems Medicine, Department of Metabolism Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, United Kingdom.
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3
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Hällqvist J, Lane D, Shapanis A, Davis K, Heywood WE, Doykov I, Śpiewak J, Ghansah N, Keevil B, Gupta P, Jukes-Jones R, Singh R, Foley D, Vissers JPC, Pattison R, Ferries S, Wardle R, Bartlett A, Calton LJ, Anderson L, Razavi M, Pearson T, Pope M, Yip R, Ng LL, Nicholas BI, Bailey A, Noel D, Dalton RN, Heales S, Hopley C, Pitt AR, Barran P, Jones DJL, Mills K, Skipp P, Carling RS. Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use. Clin Chem Lab Med 2023; 61:302-310. [PMID: 36395058 DOI: 10.1515/cclm-2022-1000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
OBJECTIVES During 2020, the UK's Department of Health and Social Care (DHSC) established the Moonshot programme to fund various diagnostic approaches for the detection of SARS-CoV-2, the pathogen behind the COVID-19 pandemic. Mass spectrometry was one of the technologies proposed to increase testing capacity. METHODS Moonshot funded a multi-phase development programme, bringing together experts from academia, industry and the NHS to develop a state-of-the-art targeted protein assay utilising enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS) to capture and detect low levels of tryptic peptides derived from SARS-CoV-2 virus. The assay relies on detection of target peptides, ADETQALPQRK (ADE) and AYNVTQAFGR (AYN), derived from the nucleocapsid protein of SARS-CoV-2, measurement of which allowed the specific, sensitive, and robust detection of the virus from nasopharyngeal (NP) swabs. The diagnostic sensitivity and specificity of LC-MS/MS was compared with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) via a prospective study. RESULTS Analysis of NP swabs (n=361) with a median RT-qPCR quantification cycle (Cq) of 27 (range 16.7-39.1) demonstrated diagnostic sensitivity of 92.4% (87.4-95.5), specificity of 97.4% (94.0-98.9) and near total concordance with RT-qPCR (Cohen's Kappa 0.90). Excluding Cq>32 samples, sensitivity was 97.9% (94.1-99.3), specificity 97.4% (94.0-98.9) and Cohen's Kappa 0.95. CONCLUSIONS This unique collaboration between academia, industry and the NHS enabled development, translation, and validation of a SARS-CoV-2 method in NP swabs to be achieved in 5 months. This pilot provides a model and pipeline for future accelerated development and implementation of LC-MS/MS protein/peptide assays into the routine clinical laboratory.
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Affiliation(s)
- Jenny Hällqvist
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
- UCL Queen Square Institute of Neurology, London, UK
| | - Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- Leicester Diabetes Centre, University of Leicester, Leicester General Hospital, Leicester, UK
| | - Andrew Shapanis
- Centre for Proteomic Research, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Kayleigh Davis
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
| | - Wendy E Heywood
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Ivan Doykov
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Justyna Śpiewak
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Nana Ghansah
- Neurometabolic Unit, National Hospital, London, UK
| | - Brian Keevil
- Department of Biochemistry, Manchester University NHS Trust, Manchester, UK
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rebekah Jukes-Jones
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Raj Singh
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Dominic Foley
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | | | - Rebecca Pattison
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Samantha Ferries
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Robert Wardle
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Amy Bartlett
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Lisa J Calton
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Matt Pope
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Leong L Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | | | - Alistair Bailey
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Dan Noel
- Biological Sciences, University of Southampton, Southampton, UK
| | - R Neil Dalton
- WellChild Laboratory, Evelina London Children's Hospital, London, UK
| | - Simon Heales
- Neurometabolic Unit, National Hospital, London, UK
| | | | - Andrew R Pitt
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Perdita Barran
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Donald J L Jones
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Kevin Mills
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Paul Skipp
- Centre for Proteomic Research, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Rachel S Carling
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
- GKT School Medical Education, Kings College London, London, UK
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4
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Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M. Cov 2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein. Anal Chem 2022; 94:17379-17387. [PMID: 36490367 PMCID: PMC9773173 DOI: 10.1021/acs.analchem.2c01610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pandemic readiness toolbox needs to be extended, targeting different biomolecules, using orthogonal experimental set-ups. Here, we build on our Cov-MS effort using LC-MS, adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma and has increased sensitivity into the attomole range, a 1000-fold improvement compared to direct detection in a matrix. A strong positive correlation was observed with qPCR detection beyond a quantification cycle of 30-31, the level where no live virus can be cultured. The automatable sample preparation and reduced LC dependency allow analysis of up to 500 samples per day per instrument. Importantly, peptide enrichment allows detection of the N protein in pooled samples without sensitivity loss. Easily multiplexed, we detect variants and propose targets for Influenza A and B detection. Thus, the Cov2MS assay can be adapted to test for many different pathogens in pooled samples, providing longitudinal epidemiological monitoring of large numbers of pathogens within a population as an early warning system.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | | | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tessa Van Royen
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Arne Matthys
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | | | - Dominic Foley
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Robert Wardle
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Kevin Wyndham
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Donald Jones
- Leicester Cancer Research Centre, RKCSB, Cardiovascular Research Centre, Glenfield Hospital, University of Leicester, Leicester LE1 7RH, United Kingdom.,John and Lucille van Geest Biomarker Facility, Leicester LE3 9QP, United Kingdom.,The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Level 4, Sandringham Building, Leicester LE1 7RH, United Kingdom
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Geert Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Johannes P C Vissers
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - N Leigh Anderson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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5
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Britt HM, Cragnolini T, Khatun S, Hatimy A, James J, Page N, Williams JP, Hughes C, Denny R, Thalassinos K, Vissers JPC. Evaluation of acquisition modes for semi-quantitative analysis by targeted and untargeted mass spectrometry. Rapid Commun Mass Spectrom 2022; 36:e9308. [PMID: 35353398 PMCID: PMC9287043 DOI: 10.1002/rcm.9308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Analyte quantitation by mass spectrometry underpins a diverse range of scientific endeavors. The fast-growing field of mass spectrometer development has resulted in several targeted and untargeted acquisition modes suitable for these applications. By characterizing the acquisition methods available on an ion mobility (IM)-enabled orthogonal acceleration time-of-flight (oa-ToF) instrument, the optimum modes for analyte semi-quantitation can be deduced. METHODS Serial dilutions of commercial metabolite, peptide, or cross-linked peptide analytes were prepared in matrices of human urine or Escherichia coli digest. Each analyte dilution was introduced into an IM separation-enabled oa-ToF mass spectrometer by reversed-phase liquid chromatography and electrospray ionization. Data were acquired for each sample in duplicate using nine different acquisition modes, including four IM-enabled acquisitions modes, available on the mass spectrometer. RESULTS Five (metabolite) or seven (peptide/cross-linked peptide) point calibration curves were prepared for analytes across each of the acquisition modes. A nonlinear response was observed at high concentrations for some modes, attributed to saturation effects. Two correction methods, one MS1 isotope-correction and one MS2 ion intensity-correction, were applied to address this observation, resulting in an up to twofold increase in dynamic range. By averaging the semi-quantitative results across analyte classes, two parameters, linear dynamic range (LDR) and lower limit of quantification (LLOQ), were determined to evaluate each mode. CONCLUSION A comparison of the acquisition modes revealed that data-independent acquisition and parallel reaction monitoring methods are most robust for semi-quantitation when considering achievable LDR and LLOQ. IM-enabled modes exhibited sensitivity increases, but a simultaneous reduction in dynamic range required correction methods to recover. These findings will assist users in identifying the optimum acquisition mode for their analyte quantitation needs, supporting a diverse range of applications and providing guidance for future acquisition mode developments.
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Affiliation(s)
- Hannah M. Britt
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUK
| | - Suniya Khatun
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Abubakar Hatimy
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Juliette James
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
| | - Nathanael Page
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- LGC GroupTeddingtonUK
| | | | | | | | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonUK
- Institute of Structural and Molecular Biology, Birkbeck CollegeUniversity of LondonLondonUK
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6
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Connolly JRFB, Munoz-Muriedas J, Lapthorn C, Higton D, Vissers JPC, Webb A, Beaumont C, Dear GJ. Investigation into Small Molecule Isomeric Glucuronide Metabolite Differentiation Using In Silico and Experimental Collision Cross-Section Values. J Am Soc Mass Spectrom 2021; 32:1976-1986. [PMID: 34296869 DOI: 10.1021/jasms.0c00427] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying isomeric metabolites remains a challenging and time-consuming process with both sensitivity and unambiguous structural assignment typically only achieved through the combined use of LC-MS and NMR. Ion mobility mass spectrometry (IMMS) has the potential to produce timely and accurate data using a single technique to identify drug metabolites, including isomers, without the requirement for in-depth interpretation (cf. MS/MS data) using an automated computational pipeline by comparison of experimental collision cross-section (CCS) values with predicted CCS values. An ion mobility enabled Q-Tof mass spectrometer was used to determine the CCS values of 28 (14 isomeric pairs of) small molecule glucuronide metabolites, which were then compared to two different in silico models; a quantum mechanics (QM) and a machine learning (ML) approach to test these approaches. The difference between CCS values within isomer pairs was also assessed to evaluate if the difference was large enough for unambiguous structural identification through in silico prediction. A good correlation was found between both the QM- and ML-based models and experimentally determined CCS values. The predicted CCS values were found to be similar between ML and QM in silico methods, with the QM model more accurately describing the difference in CCS values between isomer pairs. Of the 14 isomeric pairs, only one (naringenin glucuronides) gave a sufficient difference in CCS values for the QM model to distinguish between the isomers with some level of confidence, with the ML model unable to confidently distinguish the studied isomer pairs. An evaluation of analyte structures was also undertaken to explore any trends or anomalies within the data set.
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Affiliation(s)
- John R F B Connolly
- RCSI University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin D02 YN77, Ireland
| | | | - Cris Lapthorn
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David Higton
- Waters Corporation, Stamford Ave, Wilmslow SK9 4AX, United Kingdom
| | | | - Alison Webb
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Claire Beaumont
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gordon J Dear
- GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
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7
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Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, De Spiegeleer B, Judak P, Roels K, De Wilde L, Van Eenoo P, Reyns T, Cherlet M, Dumont E, Debyser G, t'Kindt R, Sandra K, Gupta S, Drouin N, Harms A, Hankemeier T, Jones DJL, Gupta P, Lane D, Lane CS, El Ouadi S, Vincendet JB, Morrice N, Oehrle S, Tanna N, Silvester S, Hannam S, Sigloch FC, Bhangu-Uhlmann A, Claereboudt J, Anderson NL, Razavi M, Degroeve S, Cuypers L, Stove C, Lagrou K, Martens GA, Deforce D, Martens L, Vissers JPC, Dhaenens M. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. JACS Au 2021. [PMID: 34254058 DOI: 10.1101/2020.11.18.20231688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Olivier Tytgat
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
- Department of Life Science Technologies, Imec, 3000 Leuven, Belgium
| | | | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Pathmanaban Ramasamy
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, 1050 Brussels, Belgium
| | - Sigrid Verhelst
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura De Clerck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Corveleyn
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sander Willems
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Nathan Debunne
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Judak
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kris Roels
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Laurie De Wilde
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Van Eenoo
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tim Reyns
- Department of Clinical Chemistry, Ghent University Hospital, 9000 Ghent, Belgium
| | - Marc Cherlet
- Department of Pharmacology, Toxicology, and Biochemistry, Faculty of Veterinary Medicine, Ghent University 9000 Ghent, Belgium
| | - Emmie Dumont
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Griet Debyser
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Koen Sandra
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Surya Gupta
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Amy Harms
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Donald J L Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, U.K., and John and Lucille van Geest Biomarker Facility, Cardiovascular Research Centre, Glenfield Hospital, Leicester LE1 7RH, United Kingdom
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Level 4, Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | - Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Level 4, Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | | | - Said El Ouadi
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | - Nick Morrice
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Stuart Oehrle
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Nikunj Tanna
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Steve Silvester
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Sally Hannam
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | | | | | - N Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Lize Cuypers
- Clinical Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Christophe Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Katrien Lagrou
- Clinical Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Geert A Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | | | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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8
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Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, De Spiegeleer B, Judak P, Roels K, De Wilde L, Van Eenoo P, Reyns T, Cherlet M, Dumont E, Debyser G, t’Kindt R, Sandra K, Gupta S, Drouin N, Harms A, Hankemeier T, Jones DJL, Gupta P, Lane D, Lane CS, El Ouadi S, Vincendet JB, Morrice N, Oehrle S, Tanna N, Silvester S, Hannam S, Sigloch FC, Bhangu-Uhlmann A, Claereboudt J, Anderson NL, Razavi M, Degroeve S, Cuypers L, Stove C, Lagrou K, Martens GA, Deforce D, Martens L, Vissers JPC, Dhaenens M. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. JACS Au 2021; 1:750-765. [PMID: 34254058 PMCID: PMC8230961 DOI: 10.1021/jacsau.1c00048] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 05/03/2023]
Abstract
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Olivier Tytgat
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
- Department
of Life Science Technologies, Imec, 3000 Leuven, Belgium
| | | | - Ralf Gabriels
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Robbin Bouwmeester
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Simon Daled
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Tim Van Den Bossche
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Pathmanaban Ramasamy
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
- Interuniversity
Institute of Bioinformatics in Brussels, ULB/VUB, 1050 Brussels, Belgium
| | - Sigrid Verhelst
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura De Clerck
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Corveleyn
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sander Willems
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Nathan Debunne
- Drug Quality and Registration Group, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration Group, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration Group, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Judak
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kris Roels
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Laurie De Wilde
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Van Eenoo
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tim Reyns
- Department
of Clinical Chemistry, Ghent University
Hospital, 9000 Ghent, Belgium
| | - Marc Cherlet
- Department
of Pharmacology, Toxicology, and Biochemistry, Faculty of Veterinary
Medicine, Ghent University 9000 Ghent, Belgium
| | - Emmie Dumont
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Griet Debyser
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Ruben t’Kindt
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Koen Sandra
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Surya Gupta
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Nicolas Drouin
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic
Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Amy Harms
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic
Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Thomas Hankemeier
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic
Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Donald J. L. Jones
- Leicester
Cancer Research Centre, RKCSB, University of Leicester, U.K., and
John and Lucille van Geest Biomarker Facility, Cardiovascular Research
Centre, Glenfield Hospital, Leicester LE1 7RH, United Kingdom
| | - Pankaj Gupta
- The
Department of Chemical Pathology and Metabolic Diseases, Level 4,
Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | - Dan Lane
- The
Department of Chemical Pathology and Metabolic Diseases, Level 4,
Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | | | - Said El Ouadi
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | - Nick Morrice
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Stuart Oehrle
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Nikunj Tanna
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Steve Silvester
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Sally Hannam
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | | | | | - N. Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Sven Degroeve
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Lize Cuypers
- Clinical
Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Christophe Stove
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Katrien Lagrou
- Clinical
Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Geert A. Martens
- AZ
Delta Medical Laboratories, AZ Delta General
Hospital, 8800 Roeselare, Belgium
| | - Dieter Deforce
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | | | - Maarten Dhaenens
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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9
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Ross JA, Vissers JPC, Nanda J, Stewart GD, Husi H, Habib FK, Hammond DE, Gethings LA. The influence of hypoxia on the prostate cancer proteome. Clin Chem Lab Med 2021; 58:980-993. [PMID: 31940282 DOI: 10.1515/cclm-2019-0626] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
Prostate cancer accounts for around 15% of male deaths in Western Europe and is the second leading cause of cancer death in men after lung cancer. Mounting evidence suggests that prostate cancer deposits exist within a hypoxic environment and this contributes to radio-resistance thus hampering one of the major therapies for this cancer. Recent reports have shown that nitric oxide (NO) donating non-steroidal anti-inflammatory drugs (NSAIDs) reduced tumour hypoxia as well as maintaining a radio-sensitising/therapeutic effect on prostate cancer cells. The aim of this study was to evaluate the impact of hypoxia on the proteome of the prostate and to establish whether NO-NSAID treatment reverted the protein profiles back to their normoxic status. To this end an established hormone insensitive prostate cancer cell line, PC-3, was cultured under hypoxic and normoxic conditions before and following exposure to NO-NSAID in combination with selected other common prostate cancer treatment types. The extracted proteins were analysed by ion mobility-assisted data independent acquisition mass spectrometry (MS), combined with multivariate statistical analyses, to measure hypoxia-induced alterations in the proteome of these cells. The analyses demonstrated that under hypoxic conditions there were well-defined, significantly regulated/differentially expressed proteins primarily involved with structural and binding processes including, for example, TUBB4A, CIRP and PLOD1. Additionally, the exposure of hypoxic cells to NSAID and NO-NSAID agents, resulted in some of these proteins being differentially expressed; for example, both PCNA and HNRNPA1L were down-regulated, corresponding with disruption in the nucleocytoplasmic shuttling process.
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Affiliation(s)
- James A Ross
- Tissue Injury and Repair Group, University of Edinburgh, Edinburgh, UK
| | | | - Jyoti Nanda
- Tissue Injury and Repair Group, University of Edinburgh, Edinburgh, UK.,Prostate Research Group, University of Edinburgh, Edinburgh, UK
| | - Grant D Stewart
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Fouad K Habib
- Tissue Injury and Repair Group, University of Edinburgh, Edinburgh, UK.,Prostate Research Group, University of Edinburgh, Edinburgh, UK
| | - Dean E Hammond
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
| | - Lee A Gethings
- Waters Corporation, Wilmslow, UK.,Manchester Institute of Biotechnology, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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10
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Higton D, Palmer ME, Vissers JPC, Mullin LG, Plumb RS, Wilson ID. Use of Cyclic Ion Mobility Spectrometry (cIM)-Mass Spectrometry to Study the Intramolecular Transacylation of Diclofenac Acyl Glucuronide. Anal Chem 2021; 93:7413-7421. [PMID: 33984239 DOI: 10.1021/acs.analchem.0c04487] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
1-β-O-Acyl-glucuronides (AGs) are common metabolites of carboxylic acid-containing xenobiotics, including, e.g., many nonsteroidal anti-inflammatory drugs (NSAIDs). They are of concern to regulatory authorities because of the association of these metabolites with the hepatotoxicity that has resulted in drug withdrawal. One factor in assessing the potential risk posed by AGs is the rate of transacylation of the biosynthetic 1-β-O-acyl form to the 2-, 3-, and 4-O-acyl isomers. While transacylation can be measured using 1H NMR spectroscopy or liquid chromatography-mass spectrometry (LC-MS), the process can be time consuming and involve significant method development. The separation of these positional isomers by ion mobility spectrometry (IMS) has the potential to allow their rapid analysis, but conventional instruments lacked the resolving power to do this. Prediction of the collision cross section (CCS) using a machine learning model suggested that greater IMS resolution might be of use in this area. Cyclic IMS was evaluated for separating mixtures of isomeric AGs of diclofenac and was compared with a conventional ultraperformance liquid chromatography (UPLC)-MS method as a means for studying transacylation kinetics. The resolution of isomeric AGs was not seen using a conventional traveling wave IMS device; however, separation was seen after several passes around a cyclic IMS. The cyclic IMS enabled the degradation of the 1-β-O-acyl-isomer to be analyzed much more rapidly than by LC-MS. The ability of cyclic IMS to monitor the rate of AG transacylation at different pH values, without the need for a prior chromatographic separation, should allow high-throughput, real-time, monitoring of these types of reactions.
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Affiliation(s)
- David Higton
- Waters Corporation, Stamford Road, Wilmslow SK9 4AX, U.K
| | | | | | | | - Robert S Plumb
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Ian D Wilson
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, U.K
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11
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Broeckling CD, Yao L, Isaac G, Gioioso M, Ianchis V, Vissers JPC. Application of Predicted Collisional Cross Section to Metabolome Databases to Probabilistically Describe the Current and Future Ion Mobility Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:661-669. [PMID: 33539078 DOI: 10.1021/jasms.0c00375] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Metabolomics is a powerful phenotyping platform with potential for high-throughput analyses. The primary technology for metabolite profiling is mass spectrometry. In recent years, the coupling of mass spectrometry with ion mobility spectrometry (IMS) has offered the promise of faster analysis time and greater resolving power. Our understanding of the potential impact of IMS on the field of metabolomics is limited by availability of comprehensive experimental data. In this analysis, we use a probabilistic approach to enumerate the strengths and limitations, the present and future, of this technology. This is accomplished through use of "model" metabolomes, predicted physicochemical properties, and probabilistic descriptions of resolving power. This analysis advances our understanding of the importance of orthogonality in resolving (separation) dimensions, describes the impact of the metabolome composition on resolution demands, and offers a system resolution landscape that may serve to guide practitioners in the coming years.
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Affiliation(s)
- Corey D Broeckling
- Analytical Resources Core, Bioanalysis and Omics Center, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Linxing Yao
- Analytical Resources Core, Bioanalysis and Omics Center, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Giorgis Isaac
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Marisa Gioioso
- Waters Corporation, Milford, Massachusetts 01757, United States
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12
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Vissers JPC, McCullagh M. An Analytical Perspective on Protein Analysis and Discovery Proteomics by Ion Mobility-Mass Spectrometry. Methods Mol Biol 2020; 2084:161-178. [PMID: 31729660 DOI: 10.1007/978-1-0716-0030-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ion mobility combined with mass spectrometry (IM-MS) is a powerful technique for the analysis of biomolecules and complex mixtures. This chapter reviews the current state-of-the-art in ion mobility technology and its application to biology, protein analysis, and quantitative discovery proteomics in particular, from an analytical perspective. IM-MS can be used as a technique to separate mixtures, to determine structural information (rotationally averaged cross-sectional area) and to enhance MS duty cycle and sensitivity. Moreover, IM-MS is ideally suited for hyphenating with liquid chromatography, or other front-end separation techniques such as, GC, microcolumn LC, capillary electrophoresis, and direct analysis, including MALDI and DESI, providing an semiorthogonal layer of separation, which affords the more unambiguous and confident detection of a wide range of analytes. To illustrate these enhancements, as well as recent developments, the principle of in-line IM separation and hyphenation to orthogonal acceleration time-of-flight mass spectrometers are discussed, in addition to the enhancement of biophysical MS-based analysis using typical proteomics and related application examples.
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13
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Jacobsen MD, Beynon RJ, Gethings LA, Claydon AJ, Langridge JI, Vissers JPC, Brown AJP, Hammond DE. Specificity of the osmotic stress response in Candida albicans highlighted by quantitative proteomics. Sci Rep 2018; 8:14492. [PMID: 30262823 PMCID: PMC6160413 DOI: 10.1038/s41598-018-32792-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/13/2018] [Indexed: 11/18/2022] Open
Abstract
Stress adaptation is critical for the survival of microbes in dynamic environments, and in particular, for fungal pathogens to survive in and colonise host niches. Proteomic analyses have the potential to significantly enhance our understanding of these adaptive responses by providing insight into post-transcriptional regulatory mechanisms that contribute to the outputs, as well as testing presumptions about the regulation of protein levels based on transcript profiling. Here, we used label-free, quantitative mass spectrometry to re-examine the response of the major fungal pathogen of humans, Candida albicans, to osmotic stress. Of the 1,262 proteins that were identified, 84 were down-regulated in response to 1M NaCl, reflecting the decrease in ribosome biogenesis and translation that often accompanies stress. The 64 up-regulated proteins included central metabolic enzymes required for glycerol synthesis, a key osmolyte for this yeast, as well as proteins with functions during stress. These data reinforce the view that adaptation to salt stress involves a transient reduction in ribosome biogenesis and translation together with the accumulation of the osmolyte, glycerol. The specificity of the response to salt stress is highlighted by the small proportion of quantified C. albicans proteins (5%) whose relative elevated abundances were statistically significant.
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Affiliation(s)
- Mette D Jacobsen
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, United Kingdom
| | - Lee A Gethings
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Amy J Claydon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L697ZB, United Kingdom
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Johannes P C Vissers
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom.
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, United Kingdom.
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14
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Parkinson E, Aleksic M, Cubberley R, Kaur-Atwal G, Vissers JPC, Skipp P. Determination of Protein Haptenation by Chemical Sensitizers Within the Complexity of the Human Skin Proteome. Toxicol Sci 2018; 162:429-438. [PMID: 29267982 PMCID: PMC5889026 DOI: 10.1093/toxsci/kfx265] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Skin sensitization associated with the development of allergic contact dermatitis occurs via a number of specific key events at the cellular level. The molecular initiating event (MIE), the first in the sequence of these events, occurs after exposure of the skin to an electrophilic chemical, causing the irreversible haptenation of proteins within skin. Characterization of this MIE is a key step in elucidating the skin sensitization adverse outcome pathway and is essential to providing parameters for mathematical models to predict the capacity of a chemical to cause sensitization. As a first step to addressing this challenge, we have exposed complex protein lysates from a keratinocyte cell line and human skin tissue with a range of well characterized sensitizers, including dinitrochlorobenzene, 5-chloro-2-methylisothiazol-3-one, cinnamaldehyde, and the non (or weak) sensitizer 6-methyl coumarin. Using a novel stable isotope labeling approach combined with ion mobility-assisted data independent mass spectrometry (HDMSE), we have characterized the haptenome for these sensitizers. Although a significant proportion of highly abundant proteins were haptenated, we also observed the haptenation of low abundant proteins by all 3 of the chemical sensitizers tested, indicating that within a complex protein background, protein abundance is not the sole determinant driving haptenation, highlighting a relationship to tertiary protein structure and the amino acid specificity of these chemical sensitizers and sensitizer potency.
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Affiliation(s)
- Erika Parkinson
- Centre for Biological Sciences
- Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Maja Aleksic
- Safety & Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | - Richard Cubberley
- Safety & Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook MK44 1LQ, UK
| | | | | | - Paul Skipp
- Centre for Biological Sciences
- Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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15
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Juvvadi PR, Moseley MA, Hughes CJ, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Geromanos SJ, Wildgoose J, Richardson K, Langridge JI, Vissers JPC, Steinbach WJ. Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs. J Proteome Res 2017; 17:780-793. [PMID: 29251506 DOI: 10.1021/acs.jproteome.7b00499] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcineurin is a critical cell-signaling protein that orchestrates growth, stress response, virulence, and antifungal drug resistance in several fungal pathogens. Blocking calcineurin signaling increases the efficacy of several currently available antifungals and suppresses drug resistance. We demonstrate the application of a novel scanning quadrupole DIA method for the analysis of changes in the proteins coimmunoprecipitated with calcineurin during therapeutic antifungal drug treatments of the deadly human fungal pathogen Aspergillus fumigatus. Our experimental design afforded an assessment of the precision of the method as demonstrated by peptide- and protein-centric analysis from eight replicates of the study pool QC samples. Two distinct classes of clinically relevant antifungal drugs that are guideline recommended for the treatment of invasive "aspergillosis" caused by Aspergillus fumigatus, the azoles (voriconazole) and the echinocandins (caspofungin and micafungin), which specifically target the fungal plasma membrane and the fungal cell wall, respectively, were chosen to distinguish variations occurring in the proteins coimmunoprecipitated with calcineurin. Novel potential interactors were identified in response to the different drug treatments that are indicative of the possible role for calcineurin in regulating these effectors. Notably, treatment with voriconazole showed increased immunoprecipitation of key proteins involved in membrane ergosterol biosynthesis with calcineurin. In contrast, echinocandin (caspofungin or micafungin) treatments caused increased immunoprecipitation of proteins involved in cell-wall biosynthesis and septation. Furthermore, abundant coimmunoprecipitation of ribosomal proteins with calcineurin occurred exclusively in echinocandins treatment, indicating reprogramming of cellular growth mechanisms during different antifungal drug treatments. While variations in the observed calcineurin immunoprecipitated proteins may also be due to changes in their expression levels under different drug treatments, this study suggests an important role for calcineurin-dependent cellular mechanisms in response to antifungal treatment of A. fumigatus that warrants future studies.
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Affiliation(s)
- Praveen R Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Sarah Lennon
- Waters Corporation , Wilmslow SK9 4AX, United Kingdom
| | - Simon R Perkins
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | | | | | | | | | - William J Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center , Durham, North Carolina 27710, United States
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16
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Moseley MA, Hughes CJ, Juvvadi PR, Soderblom EJ, Lennon S, Perkins SR, Thompson JW, Steinbach WJ, Geromanos SJ, Wildgoose J, Langridge JI, Richardson K, Vissers JPC. Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization. J Proteome Res 2017; 17:770-779. [PMID: 28901143 DOI: 10.1021/acs.jproteome.7b00464] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel data-independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of complex biological samples. The principle of the scanning quadrupole DIA method is discussed, and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semiquantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterized human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publicly available data that used similar chromatographic conditions but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with >90% overlap of the detected proteins.
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Affiliation(s)
- M Arthur Moseley
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | | | - Praveen R Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Sarah Lennon
- Waters Corporation , Wilmslow SK9 4AX, United Kingdom
| | - Simon R Perkins
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 3BX, United Kingdom
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource Center for Genomic and Computational Biology, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - William J Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center , Durham, North Carolina 27710, United States.,Department of Molecular Genetics and Microbiology, Duke University Medical Center , Durham, North Carolina 27710, United States
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17
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Gethings LA, Richardson K, Wildgoose J, Lennon S, Jarvis S, Bevan CL, Vissers JPC, Langridge JI. Lipid profiling of complex biological mixtures by liquid chromatography/mass spectrometry using a novel scanning quadrupole data-independent acquisition strategy. Rapid Commun Mass Spectrom 2017; 31:1599-1606. [PMID: 28703389 DOI: 10.1002/rcm.7941] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE A novel data-independent acquisition method is detailed that incorporates a scanning quadrupole in front of an orthogonal acceleration time-of-flight (TOF) mass analyser. This approach is described and the attributes are compared and contrasted to other DIA approaches. METHODS Specific application of the method to both targeted and untargeted lipidomic identification strategies is discussed, with data from both shotgun and LC separated lipidomics experiments presented. RESULTS The benefits of the fast quadrupole scanning technique are highlighted, and include improvements in speed and specificity for complex mixtures providing high quality qualitative and quantitative data. CONCLUSIONS In particular the high specificity afforded by the scanning quadrupole improves qualitative information for lipid identification.
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Affiliation(s)
| | | | | | - Sarah Lennon
- Waters Corporation, Stamford Avenue, Wilmslow, UK
| | - Sheba Jarvis
- Department of Surgery and Cancer, Imperial College, London, UK
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18
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Williams BJ, Ciavarini SJ, Devlin C, Cohn SM, Xie R, Vissers JPC, Martin LB, Caswell A, Langridge JI, Geromanos SJ. Multi-mode acquisition (MMA): An MS/MS acquisition strategy for maximizing selectivity, specificity and sensitivity of DIA product ion spectra. Proteomics 2017; 16:2284-301. [PMID: 27296928 DOI: 10.1002/pmic.201500492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/16/2016] [Accepted: 06/10/2016] [Indexed: 01/08/2023]
Abstract
In proteomics studies, it is generally accepted that depth of coverage and dynamic range is limited in data-directed acquisitions. The serial nature of the method limits both sensitivity and the number of precursor ions that can be sampled. To that end, a number of data-independent acquisition (DIA) strategies have been introduced with these methods, for the most part, immune to the sampling issue; nevertheless, some do have other limitations with respect to sensitivity. The major limitation with DIA approaches is interference, i.e., MS/MS spectra are highly chimeric and often incapable of being identified using conventional database search engines. Utilizing each available dimension of separation prior to ion detection, we present a new multi-mode acquisition (MMA) strategy multiplexing both narrowband and wideband DIA acquisitions in a single analytical workflow. The iterative nature of the MMA workflow limits the adverse effects of interference with minimal loss in sensitivity. Qualitative identification can be performed by selected ion chromatograms or conventional database search strategies.
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Affiliation(s)
| | | | | | | | - Rong Xie
- Waters Corporation, Milford, MA, USA
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19
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Markmann S, Krambeck S, Hughes CJ, Mirzaian M, Aerts JMFG, Saftig P, Schweizer M, Vissers JPC, Braulke T, Damme M. Quantitative Proteome Analysis of Mouse Liver Lysosomes Provides Evidence for Mannose 6-phosphate-independent Targeting Mechanisms of Acid Hydrolases in Mucolipidosis II. Mol Cell Proteomics 2017; 16:438-450. [PMID: 28062798 DOI: 10.1074/mcp.m116.063636] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/24/2016] [Indexed: 01/01/2023] Open
Abstract
The efficient receptor-mediated targeting of soluble lysosomal proteins to lysosomes requires the modification with mannose 6-phosphate (M6P) residues. Although the absence of M6P results in misrouting and hypersecretion of lysosomal enzymes in many cells, normal levels of lysosomal enzymes have been reported in liver of patients lacking the M6P-generating phosphotransferase (PT). The identity of lysosomal proteins depending on M6P has not yet been comprehensively analyzed. In this study we purified lysosomes from liver of PT-defective mice and 67 known soluble lysosomal proteins were identified that illustrated quantitative changes using an ion mobility-assisted data-independent label-free LC-MS approach. After validation of various differentially expressed lysosomal components by Western blotting and enzyme activity assays, the data revealed a small number of lysosomal proteins depending on M6P, including neuraminidase 1, cathepsin F, Npc2, and cathepsin L, whereas the majority reach lysosomes by alternative pathways. These data were compared with findings on cultured hepatocytes and liver sinusoid endothelial cells isolated from the liver of wild-type and PT-defective mice. Our findings show that the relative expression, targeting efficiency and lysosomal localization of lysosomal proteins tested in cultured hepatic cells resemble their proportion in isolated liver lysosomes. Hypersecretion of newly synthesized nonphosphorylated lysosomal proteins suggest that secretion-recapture mechanisms contribute to maintain major lysosomal functions in liver.
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Affiliation(s)
- Sandra Markmann
- From the ‡Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,§Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Svenja Krambeck
- From the ‡Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,§Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | | | - Mina Mirzaian
- ¶Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Johannes M F G Aerts
- ¶Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - Paul Saftig
- ‖Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany
| | - Michaela Schweizer
- **Morphology Unit, Center for Molecular Neurobiology ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Thomas Braulke
- From the ‡Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
| | - Markus Damme
- ‖Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, 24098 Kiel, Germany;
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20
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Kramer G, Wegdam W, Donker-Koopman W, Ottenhoff R, Gaspar P, Verhoek M, Nelson J, Gabriel T, Kallemeijn W, Boot RG, Laman JD, Vissers JPC, Cox T, Pavlova E, Moran MT, Aerts JM, van Eijk M. Elevation of glycoprotein nonmetastatic melanoma protein B in type 1 Gaucher disease patients and mouse models. FEBS Open Bio 2016; 6:902-13. [PMID: 27642553 PMCID: PMC5011488 DOI: 10.1002/2211-5463.12078] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/18/2016] [Accepted: 04/27/2016] [Indexed: 12/23/2022] Open
Abstract
Gaucher disease is caused by inherited deficiency of lysosomal glucocerebrosidase. Proteome analysis of laser‐dissected splenic Gaucher cells revealed increased amounts of glycoprotein nonmetastatic melanoma protein B (gpNMB). Plasma gpNMB was also elevated, correlating with chitotriosidase and CCL18, which are established markers for human Gaucher cells. In Gaucher mice, gpNMB is also produced by Gaucher cells. Correction of glucocerebrosidase deficiency in mice by gene transfer or pharmacological substrate reduction reverses gpNMB abnormalities. In conclusion, gpNMB acts as a marker for glucosylceramide‐laden macrophages in man and mouse and gpNMB should be considered as candidate biomarker for Gaucher disease in treatment monitoring.
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Affiliation(s)
- Gertjan Kramer
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands; European Molecular Biology Laboratory Germany
| | - Wouter Wegdam
- Department of Gynecology Academic Medical Center Amsterdam The Netherlands
| | - Wilma Donker-Koopman
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Roelof Ottenhoff
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Paulo Gaspar
- Organelle Biogenesis & Function Group Instituto de Investigação e Inovação em Saúde (I3S) Porto Portugal; Institute of Molecular and Cell Biology (IBMC) Universidade do Porto Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS) Universidade do Porto Portugal
| | - Marri Verhoek
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Jessica Nelson
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Tanit Gabriel
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Wouter Kallemeijn
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Rolf G Boot
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Jon D Laman
- Department of Neuroscience University Medical Center Groningen The Netherlands
| | | | - Timothy Cox
- Department of Internal Medicine Addenbrooke's Hospital Cambridge UK
| | - Elena Pavlova
- Department of Internal Medicine Addenbrooke's Hospital Cambridge UK
| | | | - Johannes M Aerts
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Marco van Eijk
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands; Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
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21
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Mbasu RJ, Heaney LM, Molloy BJ, Hughes CJ, Ng LL, Vissers JPC, Langridge JI, Jones DJL. Advances in quadrupole and time-of-flight mass spectrometry for peptide MRM based translational research analysis. Proteomics 2016; 16:2206-20. [PMID: 27214876 DOI: 10.1002/pmic.201500500] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/30/2016] [Accepted: 05/04/2016] [Indexed: 11/06/2022]
Abstract
The application of unit resolution tandem quadrupole and high-resolution orthogonal acceleration ToF mass spectrometers for the quantitation and translational analysis of proteolytic peptides is described. The MS platforms were contrasted in terms of sensitivity and linear response. Moreover, the selectivity of the platforms was investigated and the effect on quantitative precision studied. Chromatographic LC conditions, including gradient length and configuration, were investigated with respect to speed/throughput, while minimizing isobaric interferences, thereby providing information with regard to practical sample cohort size limitations of LC-MS for large cohort experiments. In addition to these fundamental analytical performance metrics, precision and linear dynamic ranges were also studied. An LC-MS configuration that encompasses the best combination of throughput and analytical accuracy for translational studies was chosen, despite the MS platforms giving similar quantitative performance, and instances were identified where alternative combinations were found to be beneficial. This configuration was utilized to demonstrate that proteolytically digested nondepleted samples from heart failure patients could be classified with good discriminative power using a subset of proteins previously suggested as candidate biomarkers for cardiovascular diseases.
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Affiliation(s)
- Richard J Mbasu
- Department of Cancer Studies, RKCSB, University of Leicester, Leicester, UK.,Department of Cardiovascular Sciences, NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Liam M Heaney
- Department of Cardiovascular Sciences, NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | | | | | - Leong L Ng
- Department of Cardiovascular Sciences, NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | | | | | - Donald J L Jones
- Department of Cancer Studies, RKCSB, University of Leicester, Leicester, UK.,Department of Cardiovascular Sciences, NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
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22
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Kramer G, Woolerton Y, van Straalen JP, Vissers JPC, Dekker N, Langridge JI, Beynon RJ, Speijer D, Sturk A, Aerts JMFG. Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. PLoS One 2015; 10:e0140097. [PMID: 26474480 PMCID: PMC4608811 DOI: 10.1371/journal.pone.0140097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/22/2015] [Indexed: 12/28/2022] Open
Abstract
Background Quantitative proteomic analysis with mass spectrometry holds great promise for simultaneously quantifying proteins in various biosamples, such as human plasma. Thus far, studies addressing the reproducible measurement of endogenous protein concentrations in human plasma have focussed on targeted analyses employing isotopically labelled standards. Non-targeted proteomics, on the other hand, has been less employed to this end, even though it has been instrumental in discovery proteomics, generating large datasets in multiple fields of research. Results Using a non-targeted mass spectrometric assay (LCMSE), we quantified abundant plasma proteins (43 mg/mL—40 ug/mL range) in human blood plasma specimens from 30 healthy volunteers and one blood serum sample (ProteomeXchange: PXD000347). Quantitative results were obtained by label-free mass spectrometry using a single internal standard to estimate protein concentrations. This approach resulted in quantitative results for 59 proteins (cut off ≥11 samples quantified) of which 41 proteins were quantified in all 31 samples and 23 of these with an inter-assay variability of ≤ 20%. Results for 7 apolipoproteins were compared with those obtained using isotope-labelled standards, while 12 proteins were compared to routine immunoassays. Comparison of quantitative data obtained by LCMSE and immunoassays showed good to excellent correlations in relative protein abundance (r = 0.72–0.96) and comparable median concentrations for 8 out of 12 proteins tested. Plasma concentrations of 56 proteins determined by LCMSE were of similar accuracy as those reported by targeted studies and 7 apolipoproteins quantified by isotope-labelled standards, when compared to reference concentrations from literature. Conclusions This study shows that LCMSE offers good quantification of relative abundance as well as reasonable estimations of concentrations of abundant plasma proteins.
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Affiliation(s)
- Gertjan Kramer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
| | - Yvonne Woolerton
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jan P. van Straalen
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Nick Dekker
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Robert J. Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Auguste Sturk
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
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23
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Abstract
Data set description: This data set is composed by label-free alternate-scanning LC-MS/MS proteomics analysis human and Wistar rat pancreatic islet endocrine cells. The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat). From these mass spectrometry data, 'relative molar amount units' between cell types and across species were calculated. Biological relevance: These data provide a quantitative view on the unfractionated proteomes of human and rat beta and alpha cells. It is likely biased towards the proteins with higher molar abundance, relating to core functional pathways, but also includes several proteins with an islet-enriched expression. The quality of the cell preps is state-of-the-art, and the label-free quantitation is both precise and accurate, allowing detailed quantitative analysis.
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Affiliation(s)
- B Brackeva
- B-Probe, Diabetes Research Center, Vrije Universiteit Brussel (VUB), Belgium ; Department of Clinical Chemistry and Radio-immunology, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - G Kramer
- Department of Medical Biochemistry, Academisch Medisch Centrum, Amsterdam, The Netherlands
| | | | - G A Martens
- B-Probe, Diabetes Research Center, Vrije Universiteit Brussel (VUB), Belgium ; Department of Clinical Chemistry and Radio-immunology, Universitair Ziekenhuis Brussel, Brussels, Belgium
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24
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Sedic M, Gethings LA, Vissers JPC, Shockcor JP, McDonald S, Vasieva O, Lemac M, Langridge JI, Batinić D, Pavelić SK. Label-free mass spectrometric profiling of urinary proteins and metabolites from paediatric idiopathic nephrotic syndrome. Biochem Biophys Res Commun 2014; 452:21-6. [PMID: 25150443 DOI: 10.1016/j.bbrc.2014.08.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 08/04/2014] [Indexed: 01/20/2023]
Abstract
Idiopathic nephrotic syndrome (INS) is caused by renal diseases that increase the permeability of the glomerular filtration barrier without evidence of a specific systemic cause. The aim of the present work was to reveal inherent molecular features of INS in children using combined urinary proteomics and metabolomics profiling. In this study, label-free mass spectrometric analysis of urinary proteins and small molecule metabolites was carried out in 12 patients with INS versus 12 sex- and age-matched control subjects with normal renal function. Integration and biological interpretation of obtained results were carried out by Ingenuity IPA software. Validation of obtained proteomics data was carried out by Western blot method. Proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000765. This study indicates for the first time that paediatric INS is associated with up-regulation of afamin, hydroxyphenylacetate and uridine, and concomitant down-regulation in glutamine and phenylalanine levels, and many of these molecular species were previously shown to be involved in oxidative stress. Further studies in larger patient population are underway to investigate the role of oxidative stress in renal injury in paediatric INS.
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Affiliation(s)
- Mirela Sedic
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Lee A Gethings
- Waters Corporation, MS Technologies, Manchester, United Kingdom
| | | | | | | | - Olga Vasieva
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, United Kingdom
| | - Maja Lemac
- Division of Nephrology, Department of Pediatrics, Zagreb University Hospital Centre, Zagreb, Croatia
| | | | - Danica Batinić
- Division of Nephrology, Department of Pediatrics, Zagreb University Hospital Centre, Zagreb, Croatia
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25
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Helm D, Vissers JPC, Hughes CJ, Hahne H, Ruprecht B, Pachl F, Grzyb A, Richardson K, Wildgoose J, Maier SK, Marx H, Wilhelm M, Becher I, Lemeer S, Bantscheff M, Langridge JI, Kuster B. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics. Mol Cell Proteomics 2014; 13:3709-15. [PMID: 25106551 DOI: 10.1074/mcp.m114.041038] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A.
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Affiliation(s)
- Dominic Helm
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | - Hannes Hahne
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Benjamin Ruprecht
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Fiona Pachl
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | | | - Stefan K Maier
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Harald Marx
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Mathias Wilhelm
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | - Simone Lemeer
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | | | | | - Bernhard Kuster
- From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany; ‖Center for Integrated Protein Science Munich, Germany
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26
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Alberio T, McMahon K, Cuccurullo M, Gethings LA, Lawless C, Zibetti M, Lopiano L, Vissers JPC, Fasano M. Verification of a Parkinson’s Disease Protein Signature in T-Lymphocytes by Multiple Reaction Monitoring. J Proteome Res 2014; 13:3554-61. [DOI: 10.1021/pr401142p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Tiziana Alberio
- Division
of Biomedical Sciences, Department of Theoretical and Applied Sciences, University of Insubria. Via Luciano Manara 7, Busto
Arsizio I-21052, Italy
- Center
of Neuroscience, University of Insubria, Via Alberto da Giussano 12, Busto Arsizio I-21052, Italy
| | - Kelly McMahon
- Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | | | - Lee A. Gethings
- Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - Craig Lawless
- Faculty
of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Maurizio Zibetti
- Department
of Neuroscience, University of Torino, Via Cherasco 15, Torino I-10126, Italy
| | - Leonardo Lopiano
- Department
of Neuroscience, University of Torino, Via Cherasco 15, Torino I-10126, Italy
| | | | - Mauro Fasano
- Division
of Biomedical Sciences, Department of Theoretical and Applied Sciences, University of Insubria. Via Luciano Manara 7, Busto
Arsizio I-21052, Italy
- Center
of Neuroscience, University of Insubria, Via Alberto da Giussano 12, Busto Arsizio I-21052, Italy
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27
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Williams JP, Pringle S, Richardson K, Gethings L, Vissers JPC, De Cecco M, Houel S, Chakraborty AB, Yu YQ, Chen W, Brown JM. Characterisation of glycoproteins using a quadrupole time-of-flight mass spectrometer configured for electron transfer dissociation. Rapid Commun Mass Spectrom 2013; 27:2383-2390. [PMID: 24097394 DOI: 10.1002/rcm.6684] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Electron transfer dissociation (ETD) within ion trapping mass spectrometers has proven to be a useful tool for the characterisation of post-translational modifications. In this study, we describe the implementation of ETD upon a modified quadrupole time-of-flight (Q-ToF) system and methods for the analysis of glycoproteins. METHODS Liquid chromatography electrospray ionisation mass spectrometry (LC/ESI-MS) was performed using a hybrid quadrupole/ion mobility/oa-ToF mass spectrometer equipped with ETD functionality. 1,4-Dicyanobenzene reagent anions necessary for the ETD reaction were generated from a glow discharge region located within the ESI source block. ETD reactions occurred in the stacked ring travelling wave ion guide (located after the quadrupole mass filter and prior to the oa-ToF mass analyser). LC/ETD was performed upon 'super-charged' tryptic glycopeptide ions produced from the recombinant monoclonal antibody trastuzumab. LC/ETD was also performed on ions from the smaller glycopeptides obtained from erythropoietin. RESULTS ETD performed upon the quadruply 'super-charged' N-linked glycopeptide ions of trastuzumab and the triply charged O-linked glycopeptide ions of erythropoietin provided both glycosylation site assignments and full sequence information, respectively. Tandem mass (MS/MS) spectra employing collision-induced dissociation (CID) were dominated by oxonium product ions hampering full peptide sequence characterisation. CONCLUSIONS LC/ETD on the Q-ToF system proved effective at characterising a number of different N-linked glyco-forms of the tryptic peptide, EEQYNSTYR, from trastuzumab as well as glyco-forms from the O-linked tryptic peptide, EASIPPDAASAAPLR, from erythropoietin. The data demonstrates that the glycopeptide site heterogeneity of trastuzumab and erythropoietin can be accurately characterised. In addition, the post-column mixing of the super-charging reagent, m-NBA, is an effective method to increase the precursor ion charge state and to improve ETD reaction efficiency.
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28
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Thalassinos K, Vissers JPC, Tenzer S, Levin Y, Thompson JW, Daniel D, Mann D, DeLong MR, Moseley MA, America AH, Ottens AK, Cavey GS, Efstathiou G, Scrivens JH, Langridge JI, Geromanos SJ. Design and application of a data-independent precursor and product ion repository. J Am Soc Mass Spectrom 2012; 23:1808-1820. [PMID: 22847389 DOI: 10.1007/s13361-012-0416-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 05/09/2012] [Accepted: 05/13/2012] [Indexed: 06/01/2023]
Abstract
The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.
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29
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Richardson K, Denny R, Hughes C, Skilling J, Sikora J, Dadlez M, Manteca A, Jung HR, Jensen ON, Redeker V, Melki R, Langridge JI, Vissers JPC. A probabilistic framework for peptide and protein quantification from data-dependent and data-independent LC-MS proteomics experiments. OMICS 2012; 16:468-82. [PMID: 22871168 DOI: 10.1089/omi.2012.0019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A probability-based quantification framework is presented for the calculation of relative peptide and protein abundance in label-free and label-dependent LC-MS proteomics data. The results are accompanied by credible intervals and regulation probabilities. The algorithm takes into account data uncertainties via Poisson statistics modified by a noise contribution that is determined automatically during an initial normalization stage. Protein quantification relies on assignments of component peptides to the acquired data. These assignments are generally of variable reliability and may not be present across all of the experiments comprising an analysis. It is also possible for a peptide to be identified to more than one protein in a given mixture. For these reasons the algorithm accepts a prior probability of peptide assignment for each intensity measurement. The model is constructed in such a way that outliers of any type can be automatically reweighted. Two discrete normalization methods can be employed. The first method is based on a user-defined subset of peptides, while the second method relies on the presence of a dominant background of endogenous peptides for which the concentration is assumed to be unaffected. Normalization is performed using the same computational and statistical procedures employed by the main quantification algorithm. The performance of the algorithm will be illustrated on example data sets, and its utility demonstrated for typical proteomics applications. The quantification algorithm supports relative protein quantification based on precursor and product ion intensities acquired by means of data-dependent methods, originating from all common isotopically-labeled approaches, as well as label-free ion intensity-based data-independent methods.
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30
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Rivers J, Hughes C, McKenna T, Woolerton Y, Vissers JPC, Langridge JI, Beynon RJ. Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library. PLoS One 2011; 6:e28902. [PMID: 22205978 PMCID: PMC3242751 DOI: 10.1371/journal.pone.0028902] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 11/16/2011] [Indexed: 12/04/2022] Open
Abstract
Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method.
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Affiliation(s)
- Jenny Rivers
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Chris Hughes
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - Thérèse McKenna
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - Yvonne Woolerton
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Johannes P. C. Vissers
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - James I. Langridge
- Waters Corporation MS Technologies Centre, Atlas Park, Wythenshawe, Manchester, United Kingdom
| | - Robert J. Beynon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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31
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Redeker V, Hughes C, Savistchenko J, Vissers JPC, Melki R. Qualitative and quantitative multiplexed proteomic analysis of complex yeast protein fractions that modulate the assembly of the yeast prion Sup35p. PLoS One 2011; 6:e23659. [PMID: 21931608 PMCID: PMC3172207 DOI: 10.1371/journal.pone.0023659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 07/22/2011] [Indexed: 01/25/2023] Open
Abstract
Background The aggregation of the baker's yeast prion Sup35p is at the origin of the transmissible [PSI+] trait. We and others have shown that molecular chaperones modulate Sup35p aggregation. However, other protein classes might be involved in [PSI+] formation. Results We designed a functional proteomic study that combines two techniques to identify modulators of Sup35p aggregation and describe the changes associated to [PSI+] formation. The first allows measuring the effect of fractionated Saccharomyces cerevisiae cytosolic extracts from [PSI+] and [psi−] yeast cells on Sup35p assembly. The second is a multiplex qualitative and quantitative comparison of protein composition of active and inactive fractions using a gel-free and label-free LC-MS approach. We identify changes in proteins involved in translation, folding, degradation, oxido-reduction and metabolic processes. Conclusion Our functional proteomic study provides the first inventory list of over 300 proteins that directly or indirectly affect Sup35p aggregation and [PSI+] formation. Our results highlight the complexity of the cellular changes accompanying [PSI+] formation and pave the way for in vitro studies aimed to document the effect of individual and/or combinations of proteins identified here, susceptible of affecting Sup35p assembly.
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Affiliation(s)
- Virginie Redeker
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- * E-mail: (VR); (RM)
| | - Chris Hughes
- Waters Corporation, Atlas Park, Manchester, United Kingdom
| | - Jimmy Savistchenko
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | | | - Ronald Melki
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- * E-mail: (VR); (RM)
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32
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Sedic M, Kraljevic Pavelic S, Cindric M, Vissers JPC, Peronja M, Josic D, Cuk M, Fumic K, Pavelic K, Baric I. Plasma biomarker identification in S-adenosylhomocysteine hydrolase deficiency. Electrophoresis 2011; 32:1970-5. [PMID: 21732553 DOI: 10.1002/elps.201000556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/07/2011] [Accepted: 02/07/2011] [Indexed: 11/09/2022]
Abstract
S-Adenosylhomocysteine hydrolase (AHCY) deficiency is a rare congenital disorder in methionine metabolism clinically characterized by white matter atrophy, delayed myelination, slowly progressive myopathy, retarded psychomotor development and mildly active chronic hepatitis. In the present study, we utilized a comparative proteomics strategy based on 2-DE/MALDI-MS and LC/ESI-MS to analyze plasma proteins from three AHCY-deficient patients prior to and after receiving dietary treatment designed to alleviate disease symptoms. Obtained results revealed candidate biomarkers for the detection of myopathy specifically associated with AHCY deficiency, such as carbonic anhydrase 3, creatine kinase, and thrombospondin 4. Several proteins mediating T-cell activation and function were identified as well, including attractin and diacylglycerol kinase α. Further validation and functional analysis of identified proteins with clinical value would ensure that these biomarkers make their way into routine diagnosis and management of AHCY deficiency.
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Affiliation(s)
- Mirela Sedic
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
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33
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Colucci-D'Amato L, Farina A, Vissers JPC, Chambery A. Quantitative neuroproteomics: classical and novel tools for studying neural differentiation and function. Stem Cell Rev Rep 2011; 7:77-93. [PMID: 20352529 DOI: 10.1007/s12015-010-9136-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience ("neuroproteomics") are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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34
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Röwer C, Vissers JPC, Koy C, Kipping M, Hecker M, Reimer T, Gerber B, Thiesen HJ, Glocker MO. Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue. Anal Bioanal Chem 2009; 395:2443-56. [PMID: 19876624 DOI: 10.1007/s00216-009-3187-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 09/18/2009] [Accepted: 09/23/2009] [Indexed: 11/26/2022]
Abstract
As more and more alternative treatments become available for breast carcinoma, there is a need to stratify patients and individual molecular information seems to be suitable for this purpose. In this study, we applied label-free protein quantitation by nanoscale LC-MS and investigated whether this approach could be used for defining a proteome signature for invasive ductal breast carcinoma. Tissue samples from healthy breast and tumor were collected from three patients. Protein identifications were based on LC-MS peptide fragmentation data which were obtained simultaneously to the quantitative information. Hereby, an invasive ductal breast carcinoma proteome signature was generated which contains 60 protein entries. The on-column concentrations for osteoinductive factor, vimentin, GAP-DH, and NDKA are provided as examples. These proteins represent distinctive gene ontology groups of differentially expressed proteins and are discussed as risk markers for primary tumor pathogenesis. The developed methodology has been found well applicable in a clinical environment in which standard operating procedures can be kept; a prerequisite for the definition of molecular parameter sets that shall be capable for stratification of patients.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Chromatography, Liquid/methods
- Computational Biology
- Female
- Humans
- Immunoenzyme Techniques
- Nanotechnology
- Proteome/analysis
- Proteomics/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, University of Rostock, 18055, Rostock, Germany
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35
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Geromanos SJ, Vissers JPC, Silva JC, Dorschel CA, Li GZ, Gorenstein MV, Bateman RH, Langridge JI. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009; 9:1683-95. [PMID: 19294628 DOI: 10.1002/pmic.200800562] [Citation(s) in RCA: 384] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The detection, correlation, and comparison of peptide and product ions from a data independent LC-MS acquisition strategy with data dependent LC-MS/MS is described. The data independent mode of acquisition differs from an LC-MS/MS data acquisition since no ion transmission window is applied with the first mass analyzer prior to collision induced disassociation. Alternating the energy applied to the collision cell, between low and elevated energy, on a scan-to-scan basis, provides accurate mass precursor and associated product ion spectra from every ion above the LOD of the mass spectrometer. The method therefore provides a near 100% duty cycle, with an inherent increase in signal intensity due to the fact that both precursor and product ion data are collected on all isotopes of every charge-state across the entire chromatographic peak width. The correlation of product to precursor ions, after deconvolution, is achieved by using reconstructed retention time apices and chromatographic peak shapes. Presented are the results from the comparison of a simple four protein mixture, in the presence and absence of an enzymatically digested protein extract from Escherichia coli. The samples were run in triplicate by both data dependant analysis (DDA) LC-MS/MS and data-independent, alternate scanning LC-MS. The detection and identification of precursor and product ions from the combined DDA search results of the four protein mixture were used for comparison to all other data. Each individual set of data-independent LC-MS data provides a more comprehensive set of detected ions than the combined peptide identifications from the DDA LC-MS/MS experiments. In the presence of the complex E. coli background, over 90% of the monoisotopic masses from the combined LC-MS/MS identifications were detected at the appropriate retention time. Moreover, the fragmentation pattern and number of associated elevated energy product ions in each replicate experiment was found to be very similar to the DDA identifications. In the case of the corresponding individual DDA LC-MS/MS experiment, 43% of the possible detectable peptides of interest were identified. The presented data illustrates that the time-aligned data from data-independent alternate scanning LC-MS experiments is highly comparable to the data obtained via DDA. The obtained information can therefore be effectively and correctly deconvolved to correlate product ions with parent precursor ions. The ability to generate precursor-product ion tables from this information and subsequently identify the correct parent precursor peptide will be illustrated in a companion manuscript.
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36
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Li GZ, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 2009; 9:1696-719. [DOI: 10.1002/pmic.200800564] [Citation(s) in RCA: 444] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Chambery A, Vissers JPC, Langridge JI, Lonardo E, Minchiotti G, Ruvo M, Parente A. Qualitative and Quantitative Proteomic Profiling of Cripto−/− Embryonic Stem Cells by Means of Accurate Mass LC−MS Analysis. J Proteome Res 2009; 8:1047-58. [DOI: 10.1021/pr800485c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Enza Lonardo
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Gabriella Minchiotti
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Menotti Ruvo
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
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38
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Chambery A, Colucci-D’Amato L, Vissers JPC, Scarpella S, Langridge JI, Parente A. Proteomic Profiling of Proliferating and Differentiated Neural mes-c-myc A1 Cell Line from Mouse Embryonic Mesencephalon by LC−MS. J Proteome Res 2008; 8:227-38. [DOI: 10.1021/pr800454n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Luca Colucci-D’Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Simona Scarpella
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
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39
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Donoghue PM, Hughes C, Vissers JPC, Langridge JI, Dunn MJ. Nonionic detergent phase extraction for the proteomic analysis of heart membrane proteins using label-free LC-MS. Proteomics 2008; 8:3895-905. [PMID: 18712767 DOI: 10.1002/pmic.200800116] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Heart diseases resulting in heart failure are among the leading causes of morbidity and mortality in the Western world and can result from either systemic disease (e.g., hypertensive heart disease, ischemic heart disease) or specific heart muscle disease (e.g., dilated cardiomyopathy/DCM). Subproteome analysis of such disease subsets affords a reduction in sample complexity, potentially revealing biomarkers of cardiac failure that would otherwise remain undiscovered in proteome wide studies. Label-free nanoscale LC-MS has been applied in this study to validate a Triton X-114-based phase enrichment method for cardiac membrane proteins. Annotation of the subcellular location combined with GRAVY score analysis indicates a clear separation between soluble and membrane-bound proteins with an enrichment of over 62% for this protein subset. LC-MS allowed confident identification and annotation of hydrophobic proteins in this control sample pilot study and demonstrates the power of the proposed technique to extract integral membrane-bound proteins. This approach should be applicable to a wider scale study of disease-associated changes in the cardiac membrane subproteome.
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Affiliation(s)
- Pamela M Donoghue
- Proteome Research Centre, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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Vissers JPC, Langridge JI, Aerts JMFG. Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol Cell Proteomics 2007; 6:755-66. [PMID: 17293593 DOI: 10.1074/mcp.m600303-mcp200] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Novel approaches for the qualitative and quantitative proteomics analysis by nanoscale LC-MS applied to the study of protein expression response in depleted and undepleted serum of Gaucher patients undergoing enzyme replacement therapy are presented. Particular emphasis is given to the method reproducibility of these LC-MS experiments without the use of isotopic labels. The level of chitotriosidase, an established Gaucher biomarker, was assessed by means of an absolute concentration determination technique for alternate scanning LC-MS generated data. Disease associated proteins, including fibrinogens, complement cascade proteins, and members of the high density lipoprotein serum content, were recognized by various clustering methods and sorting and intensity profile grouping of identified peptides. Condition-unique LC-MS protein signatures could be generated utilizing the measured serum protein concentrations and are presented for all investigated conditions. The clustering results of the study were also used as input for gene ontology searches to determine the correlation between the molecular functions of the identified peptides and proteins.
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America AHP, Cordewener JHG, van Geffen MHA, Lommen A, Vissers JPC, Bino RJ, Hall RD. Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC-MS. Proteomics 2006; 6:641-53. [PMID: 16372275 DOI: 10.1002/pmic.200500034] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A method for high-resolution proteomics analyses of complex protein mixtures is presented using multidimensional HPLC coupled to MS (MDLC-MS). The method was applied to identify proteins that are differentially expressed during fruit ripening of tomato. Protein extracts from red and green tomato fruits were digested by trypsin. The resulting highly complex peptide mixtures were separated by strong cation exchange chromatography (SCX), and subsequently analyzed by RP nano-LC coupled to quadrupole-TOF MS. For detailed quantitative comparison, triplicate RP-LC-MS runs were performed for each SCX fraction. The resulting data sets were analyzed using MetAlign software for noise and data reduction, multiple alignment and statistical variance analysis. For each RP-LC-MS chromatogram, up to 7000 mass components were detected. Peak intensity data were compared by multivariate and statistical analysis. This revealed a clear separation between the green and red tomato samples, and a clear separation of the different SCX fractions. MS/MS spectra were collected using the data-dependent acquisition mode from a selected set of differentially detected peptide masses, enabling the identification of proteins that were differentially expressed during ripening of tomato fruits. Our approach is a highly sensitive method to analyze proteins in complex mixtures without the need of isotope labeling.
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Abstract
Relative quantification methods have dominated the quantitative proteomics field. There is a need, however, to conduct absolute quantification studies to accurately model and understand the complex molecular biology that results in proteome variability among biological samples. A new method of absolute quantification of proteins is described. This method is based on the discovery of an unexpected relationship between MS signal response and protein concentration: the average MS signal response for the three most intense tryptic peptides per mole of protein is constant within a coefficient of variation of less than +/-10%. Given an internal standard, this relationship is used to calculate a universal signal response factor. The universal signal response factor (counts/mol) was shown to be the same for all proteins tested in this study. A controlled set of six exogenous proteins of varying concentrations was studied in the absence and presence of human serum. The absolute quantity of the standard proteins was determined with a relative error of less than +/-15%. The average MS signal responses of the three most intense peptides from each protein were plotted against their calculated protein concentrations, and this plot resulted in a linear relationship with an R(2) value of 0.9939. The analyses were applied to determine the absolute concentration of 11 common serum proteins, and these concentrations were then compared with known values available in the literature. Additionally within an unfractionated Escherichia coli lysate, a subset of identified proteins known to exist as functional complexes was studied. The calculated absolute quantities were used to accurately determine their stoichiometry.
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Amme S, Rutten T, Melzer M, Sonsmann G, Vissers JPC, Schlesier B, Mock HP. A proteome approach defines protective functions of tobacco leaf trichomes. Proteomics 2005; 5:2508-18. [PMID: 15984042 DOI: 10.1002/pmic.200401274] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Indexed: 11/09/2022]
Abstract
The leaf surface of most terrestrial plants is covered with plant hairs called trichomes. These epidermal appendages are thought to contribute to many aspects of plant defense against biotic and abiotic stresses in a variety of species. Trichome development has been intensively studied in Arabidopsis, and the phytochemical composition of trichomes was analyzed in a number of plant species. However, comparatively little is known of the proteins expressed. We therefore initiated a proteome approach to better define the cellular mechanisms operating in plant trichomes using two-dimensional gel electrophoresis to separate proteins of whole leaves and isolated trichomes. Tobacco was chosen due to the presence of glandular trichomes involved in the secretion of defense compounds. Comparative image analysis of the protein patterns indicated a number of spots, which were highly enriched in trichomes relative to leaves. These spots were excised for identification by mass spectrometry. The results showed that among the proteins specifically enriched in trichomes, the components of stress defense responses were strongly represented. The high expression of stress-related proteins was verified by Western blotting. Superoxide dismutase isoforms were additionally analyzed by activity staining. Our results demonstrate feasibility of the proteome approach to elucidate the cell biology of plant trichomes.
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Affiliation(s)
- Steffen Amme
- Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Gagnaire V, Piot M, Camier B, Vissers JPC, Jan G, Léonil J. Survey of bacterial proteins released in cheese: a proteomic approach. Int J Food Microbiol 2004; 94:185-201. [PMID: 15193805 DOI: 10.1016/j.ijfoodmicro.2004.01.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2003] [Revised: 11/28/2003] [Accepted: 01/20/2004] [Indexed: 11/16/2022]
Abstract
During the ripening of Emmental cheese, the bacterial ecosystem confers its organoleptic characteristics to the evolving curd both by the action of the living cells, and through the release of numerous proteins, including various types of enzymes into the cheese when the cells lyse. In Emmental cheese these proteins can be released from thermophilic lactic acid bacteria used as starters like Lactobacillus helveticus, Lb delbruecki subsp. lactis and Streptococcus salivarius subsp. thermophilus and ripening bacteria such as Propionibacterium freudenreichii. The aim of this study was to obtain a proteomic view of the different groups of proteins within the cheese using proteomic tools to create a reference map. A methodology was therefore developed to reduce the complexity of cheese matrix prior to 2D-PAGE analysis. The aqueous phase of cheese was prefractionated by size exclusion chromatography, bacterial and milk proteins were separated and subsequently characterised by mass spectrometry, prior to peptide mass fingerprint and sequence homology database search. Five functional groups of proteins were identified involved in: (i) proteolysis, (ii) glycolysis, (iii) stress response, (iv) DNA and RNA repair and (v) oxidoreduction. The results revealed stress responses triggered by thermophilic lactic acid bacteria and Propionibacterium strains at the end of ripening. Information was also obtained regarding the origin and nature of the peptidases released into the cheese, thus providing a greater understanding of casein degradation mechanisms during ripening. Different peptidases arose from St thermophilus and Lb helveticus, suggesting that streptococci are involved in peptide degradation in addition to the proteolytic activity of lactobacilli.
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Affiliation(s)
- Valérie Gagnaire
- INRA, Laboratoire de Recherche et de Technologie laitière, 65 rue de Saint Brieuc, 35042 Rennes Cedex, France.
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Leverrier P, Vissers JPC, Rouault A, Boyaval P, Jan G. Mass spectrometry proteomic analysis of stress adaptation reveals both common and distinct response pathways in Propionibacterium freudenreichii. Arch Microbiol 2004; 181:215-30. [PMID: 14730419 DOI: 10.1007/s00203-003-0646-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2003] [Revised: 12/04/2003] [Accepted: 12/10/2003] [Indexed: 10/26/2022]
Abstract
Microorganisms used in food technology and probiotics are exposed to technological and digestive stresses, respectively. Traditionally used as Swiss-type cheese starters, propionibacteria also constitute promising human probiotics. Stress tolerance and cross-protection in Propionibacterium freudenreichii were thus examined after exposure to heat, acid, or bile salts stresses. Adapted cells demonstrated acquired homologous tolerance. Cross-protection between bile salts and heat adaptation was demonstrated. By contrast, bile salts pretreatment sensitized cells to acid challenge and vice versa. Surprisingly, heat and acid responses did not present significant cross-protection in P. freudenreichii. During adaptations, important changes in cellular protein synthesis were observed using two-dimensional electrophoresis. While global protein synthesis decreased, several proteins were overexpressed during stress adaptations. Thirty-four proteins were induced by acid pretreatment, 34 by bile salts pretreatment, and 26 by heat pretreatment. Six proteins are common to all stresses and represent general stress-response components. Among these polypeptides, general stress chaperones, and proteins involved in energetic metabolism, oxidative stress response, or SOS response were identified. These results bring new insight into the tolerance of P. freudenreichii to heat, acid, and bile salts, and should be taken into consideration in the development of probiotic preparations.
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Affiliation(s)
- Pauline Leverrier
- Laboratoire de Recherches de Technologie Laitière, Institut National de la Recherche Agronomique, 65 rue de St Brieuc, 35042 Rennes cedex, France
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van den Burg HA, Spronk CAEM, Boeren S, Kennedy MA, Vissers JPC, Vuister GW, de Wit PJGM, Vervoort J. Binding of the AVR4 elicitor of Cladosporium fulvum to chitotriose units is facilitated by positive allosteric protein-protein interactions: the chitin-binding site of AVR4 represents a novel binding site on the folding scaffold shared between the invertebrate and the plant chitin-binding domain. J Biol Chem 2004; 279:16786-96. [PMID: 14769793 DOI: 10.1074/jbc.m312594200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The attack of fungal cell walls by plant chitinases is an important plant defense response to fungal infection. Anti-fungal activity of plant chitinases is largely restricted to chitinases that contain a noncatalytic, plant-specific chitin-binding domain (ChBD) (also called Hevein domain). Current data confirm that the race-specific elicitor AVR4 of the tomato pathogen Cladosporium fulvum can protect fungi against plant chitinases, which is based on the presence of a novel type of ChBD in AVR4 that was first identified in invertebrates. Although these two classes of ChBDs (Hevein and invertebrate) are sequentially unrelated, they share structural homology. Here, we show that the chitin-binding sites of these two classes of ChBDs have different topologies and characteristics. The K(D), DeltaH, and DeltaS values obtained for the interaction between AVR4 and chito-oligomers are comparable with those obtained for Hevein. However, the binding site of AVR4 is larger than that of Hevein, i.e. AVR4 interacts strictly with chitotriose, whereas Hevein can also interact with the monomer N-acetylglucosamine. Moreover, binding of additional AVR4 molecules to chitin occurs through positive cooperative protein-protein interactions. By this mechanism AVR4 is likely to effectively shield chitin on the fungal cell wall, preventing the cell wall from being degraded by plant chitinases.
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Affiliation(s)
- Harrold A van den Burg
- Laboratorie of Biochemistry, Wageningen University, NL-6703 HA Wageningen, The Netherlands
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Bobeldijk I, Stoks PGM, Vissers JPC, Emke E, van Leerdam JA, Muilwijk B, Berbee R, Noij THM. Surface and wastewater quality monitoring: combination of liquid chromatography with (geno)toxicity detection, diode array detection and tandem mass spectrometry for identification of pollutants. J Chromatogr A 2002; 970:167-81. [PMID: 12350091 DOI: 10.1016/s0021-9673(02)00398-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of unknown water pollutants with liquid chromatography and tandem mass spectrometry (LC-MS-MS) is often more complex and time consuming than identification with gas chromatography and mass spectrometry (GC-MS). In order to focus the identification effort on relevant compounds, unknown peaks need to be selected carefully. Based on its frequency of occurrence in the LC-Diode Array Detection (LC-DAD) chromatograms of surface and infiltrated waters, an unknown peak was selected for identification with LC-MS-MS. This compound was identified as hexamethoxymethylmelamine (HMMM), a chemical often used in the coating industry. This is the first time the presence of this chemical in surface waters has been reported. In addition to HMMM, two other structurally related compounds were found to be present in the investigated surface water. A standard mixture of HMMM and its by-products did not exhibit (geno)toxicity under the test conditions applied in this study. In another example, a genotoxic fraction of an industrial wastewater was isolated and examined by LC-MS-MS using a modern quadrupole-orthogonal acceleration-time-of-flight mass spectrometer (Q-TOF). Four compounds were detected. The structures of two compounds present are proposed to be 9-amino-2-hydroxy-acridine and 9-hydroxy-acridine-N-oxide or its structural isomer dihydroxy-acridine. Confirmation with standards could not be carried out, as pure compounds are not available. The other two compounds (structural isomers) could not be identified based on the data available within this study.
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Affiliation(s)
- I Bobeldijk
- Kwa Water Research, Nieuwegein, The Netherlands.
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Bateman RH, Carruthers R, Hoyes JB, Jones C, Langridge JI, Millar A, Vissers JPC. A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J Am Soc Mass Spectrom 2002; 13:792-803. [PMID: 12148804 DOI: 10.1016/s1044-0305(02)00420-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A tandem quadrupole time-of-flight (Q-TOF) mass spectrometer has been programmed such that phosphorylated peptides can automatically be discovered and identified in a way similar to that of the use of precursor ion or neutral loss scanning, but without the need to scan the quadrupole mass filter. Instead, the method capitalizes on the innate capability of the Q-TOF to record mass spectra and product ion spectra quickly, with good sensitivity and with good mass accuracy. Alternate mass spectra, with and without fragmentation, are recorded at high and low collision energy with the quadrupole operating in wideband mode. The method of analysis is both compatible with and dependant on liquid chromatography for separation of complex mixtures. The method has been demonstrated by searching for the neutral loss of 98 Da (H3PO4) from phosphoserine and phosphothreonine residues, or for the phosphorylated immonium ion at m/z 216 from phosphotyrosine. The method also incorporates acquisition of the product ion spectrum from any candidate precursor ions, thereby allowing confirmation of the neutral loss or product ion and providing additional sequence information to assist identification of the protein and assign the site of phosphorylation.
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Affiliation(s)
- R H Bateman
- Micromass Ltd., Wythenshawe, Manchester, UK.
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Abstract
A variable flow "peak trapping" liquid chromatography (LC) interface has been developed for the coupling of nanoscale LC to electrospray ionization mass spectrometry (ESI-MS). The presented peak trapping LC interface allows for the extended analysis time of co-eluting compounds and has been employed for the identification of proteins via tandem mass spectrometry (MS/MS). The variable flow process can be controlled either manually or in a completely automated manner where the mass spectrometer status determines the status of the variable flow interface. When the mass spectrometer operates in MS survey mode, the interface is operated in a so-called "high-flow" mode. Alternatively, the interface is operated in a "low-flow" mode during MS/MS analysis. In the "high-flow" mode of the variable flow process the column flow rate is typically around 200 nL/min, whereas in the "low-flow" mode the column effluent is introduced into the source of the mass spectrometer at 25 nL/min. In addition to the flow reduction during MS/MS analysis, the gradient is paused to preserve the peptide separation on the analytical nanoscale LC column. The performance of the variable flow nanoscale LC/MS/MS interface is demonstrated by the automated analysis of standard peptide mixtures and protein digests utilizing variable flow, data-dependent scanning MS/MS techniques, and automated database searching.
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Vissers JPC, Claessens HA, Laven J, Cramers CA. Colloid Chemical Aspects of Slurry Packing Techniques in Microcolumn Liquid Chromatography. Anal Chem 2002. [DOI: 10.1021/ac00109a032] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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