1
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Adair LR, Jones I, Cramer R. Utilizing Precursor Ion Connectivity of Different Charge States to Improve Peptide and Protein Identification in MS/MS Analysis. Anal Chem 2024; 96:985-990. [PMID: 38193749 PMCID: PMC10809226 DOI: 10.1021/acs.analchem.3c03061] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
Tandem mass spectrometry (MS/MS) has become a key method for the structural analysis of biomolecules such as peptides and proteins. A pervasive problem in MS/MS analyses, especially for top-down proteomics, is the occurrence of chimeric spectra, when two or more precursor ions are co-isolated and fragmented, thus leading to complex MS/MS spectra that are populated with fragment ions originating from different precursor ions. This type of convoluted data typically results in low sequence database search scores due to the vast number of mixed-source fragment ions, of which only a fraction originates from a specific precursor ion. Herein, we present a novel workflow that deconvolutes the data of chimeric MS/MS spectra, improving the protein search scores and sequence coverages in database searching and thus providing a more confident peptide and protein identification. Previously misidentified proteins or proteins with insignificant search scores can be correctly and significantly identified following the presented data acquisition and analysis workflow with search scores increasing by a factor of 3-4 for smaller precursor ions (peptides) and >6 for larger precursor ions such as intact ubiquitin and cytochrome C.
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Affiliation(s)
- Lily R. Adair
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, United Kingdom
| | - Ian Jones
- School
of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, United Kingdom
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2
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Lellman S, Reynolds CK, Jones AB, Taylor N, Cramer R. LAP-MALDI MS Profiling and Identification of Potential Biomarkers for the Detection of Bovine Tuberculosis. J Agric Food Chem 2023; 71:13899-13905. [PMID: 37677086 PMCID: PMC10515614 DOI: 10.1021/acs.jafc.3c01879] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Detecting bovine tuberculosis (bTB) primarily relies on the tuberculin skin test, requiring two separate animal handling events with a period of incubation time (normally 3 days) between them. Here, we present the use of liquid atmospheric pressure (LAP)-MALDI for the identification of bTB infection, employing a three-class prediction model that was obtained by supervised linear discriminant analysis (LDA) and tested with bovine mastitis samples as disease-positive controls. Noninvasive collection of nasal swabs was used to collect samples, which were subsequently subjected to a short (<4 h) sample preparation method. Cross-validation of the three-class LDA model from the processed nasal swabs provided a sensitivity of 75.0% and specificity of 90.1%, with an overall classification accuracy of 85.7%. These values are comparable to those for the skin test, showing that LAP-MALDI MS has the potential to provide an alternative single-visit diagnostic platform that can detect bTB within the same day of sampling.
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Affiliation(s)
- Sophie
E. Lellman
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, United Kingdom
| | - Christopher K. Reynolds
- School
of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, United Kingdom
| | - A.K. Barney Jones
- School
of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, United Kingdom
| | - Nick Taylor
- Veterinary
Epidemiology and Economics Research Unit (VEERU), PAN Livestock Services
Ltd, School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, United Kingdom
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3
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Abstract
High-throughput (HTP) mass spectrometry (MS) is a rapidly growing field, with many techniques evolving to accommodate ever increasing sample analysis rates. Many of these techniques, such as AEMS and IR-MALDESI MS, require volumes of at least 20-50 μL for analysis. Here, liquid atmospheric pressure-matrix-assisted laser desorption/ionization (LAP-MALDI) MS is presented as an alternative for ultra-high-throughput analysis of proteins requiring only femtomole quantities of protein in 0.5 μL droplets. By moving a 384-well microtiter sample plate with a high-speed XY-stage actuator, sample acquisition rates of up to 10 samples per second have been achieved at a data acquisition rate of 200 spectra per scan. It is shown that protein mixture solutions with concentrations of ≤2 μM can be analyzed at this speed, while individual protein solutions can be analyzed at concentrations of ≤0.2 μM. Thus, LAP-MALDI MS provides a promising platform for multiplexed HTP protein analysis.
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Affiliation(s)
- Bob Challen
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, U.K
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, U.K
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4
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Challen B, Cramer R. Advances in ionisation techniques for mass spectrometry-based omics research. Proteomics 2022; 22:e2100394. [PMID: 35709387 DOI: 10.1002/pmic.202100394] [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: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022]
Abstract
Omics analysis by mass spectrometry (MS) is a vast field, with proteomics, metabolomics and lipidomics dominating recent research by exploiting biological MS ionisation techniques. Traditional MS ionisation techniques such as electrospray ionisation have limitations in analyte-specific sensitivity, modes of sampling and throughput, leading to many researchers investigating new ionisation methods for omics research. In this review, we examine the current landscape of these new ionisation techniques, divided into the three groups of (electro)spray-based, laser-based and other miscellaneous ionisation techniques. Due to the wide range of new developments, this review can only provide a starting point for further reading on each ionisation technique, as each have unique benefits, often for specialised applications, which promise beneficial results for different areas in the omics world.
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Affiliation(s)
- Bob Challen
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
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5
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Krenkel H, Brown J, Richardson K, Hoyes E, Morris M, Cramer R. Ultrahigh-Throughput Sample Analysis Using Liquid Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2022; 94:4141-4145. [PMID: 35234449 PMCID: PMC9385107 DOI: 10.1021/acs.analchem.1c05614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Indexed: 11/28/2022]
Abstract
![]()
Mass
spectrometry (MS) allows for automated analysis of complex
samples at high resolution without the need for labeling/derivatization.
Liquid atmospheric pressure matrix-assisted laser desorption/ionization
(LAP-MALDI) enables rapid sample preparation and MS analysis using
microtiter-plate formats and high-performing mass spectrometers. We
present a step change in high-speed, large-scale MS sample analysis
of peptides at 20 samples/s and an enzymatic assay at 40 samples/s,
i.e., an order of magnitude faster than current MS platforms. LAP-MALDI
requires only low amounts of sample volume (<2 μL), of which
only a fraction (<1%) is typically consumed, and allows for multiplexing
and high-speed MS/MS analysis, demonstrated at ∼10 samples/s.
Its high ion signal stability and similarity to electrospray ionization
enables CVs below 10% and the analysis of multiply charged peptide
ions at these extreme speeds. LAP-MALDI MS fulfills the speed requirements
for large-scale population diagnostics and compound screening with
the potential of analyzing >1 million samples per day.
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Affiliation(s)
- Henriette Krenkel
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, U.K
| | - Jeffery Brown
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | | | - Emmy Hoyes
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6DX, U.K
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6
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Piras C, Hale OJ, Reynolds CK, Jones AKB, Taylor N, Morris M, Cramer R. LAP-MALDI MS coupled with machine learning: an ambient mass spectrometry approach for high-throughput diagnostics. Chem Sci 2022; 13:1746-1758. [PMID: 35282613 PMCID: PMC8826629 DOI: 10.1039/d1sc05171g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/17/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
Large-scale population screening for early and accurate detection of disease is a key objective for future diagnostics. Ideally, diagnostic tests that achieve this goal are also cost-effective, fast and easily adaptable to new diseases with the potential of multiplexing. Mass spectrometry (MS), particularly MALDI MS profiling, has been explored for many years in disease diagnostics, most successfully in clinical microbiology but less in early detection of diseases. Here, we present liquid atmospheric pressure (LAP)-MALDI MS profiling as a rapid, large-scale and cost-effective platform for disease analysis. Using this new platform, two different types of tests exemplify its potential in early disease diagnosis and response to therapy. First, it is shown that LAP-MALDI MS profiling detects bovine mastitis two days before its clinical manifestation with a sensitivity of up to 70% and a specificity of up to 100%. This highly accurate, pre-symptomatic detection is demonstrated by using a large set of milk samples collected weekly over six months from approximately 500 dairy cows. Second, the potential of LAP-MALDI MS in antimicrobial resistance (AMR) detection is shown by employing the same mass spectrometric setup and similarly simple sample preparation as for the early detection of mastitis.
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Affiliation(s)
- Cristian Piras
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6DX UK +44 (0)118 378 4550.,Department of Health Sciences, "Magna Græcia University" of Catanzaro Campus Universitario "Salvatore Venuta" Viale Europa 88100 Catanzaro Italy
| | - Oliver J Hale
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6DX UK +44 (0)118 378 4550
| | - Christopher K Reynolds
- School of Agriculture, Policy and Development, University of Reading Whiteknights Reading RG6 6EU UK
| | - A K Barney Jones
- School of Agriculture, Policy and Development, University of Reading Whiteknights Reading RG6 6EU UK
| | - Nick Taylor
- Veterinary Epidemiology and Economics Research Unit (VEERU), PAN Livestock Services Ltd, School of Agriculture, Policy and Development, University of Reading Whiteknights Reading RG6 6EU UK
| | | | - Rainer Cramer
- Department of Chemistry, University of Reading Whiteknights Reading RG6 6DX UK +44 (0)118 378 4550
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7
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Piras C, Hale OJ, Reynolds CK, Jones AK, Taylor N, Morris M, Cramer R. Speciation and milk adulteration analysis by rapid ambient liquid MALDI mass spectrometry profiling using machine learning. Sci Rep 2021; 11:3305. [PMID: 33558627 PMCID: PMC7870811 DOI: 10.1038/s41598-021-82846-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/18/2021] [Indexed: 11/09/2022] Open
Abstract
Growing interest in food quality and traceability by regulators as well as consumers demands advances in more rapid, versatile and cost-effective analytical methods. Milk, as most food matrices, is a heterogeneous mixture composed of metabolites, lipids and proteins. One of the major challenges is to have simultaneous, quantitative detection (profiling) of this panel of biomolecules to gather valuable information for assessing food quality, traceability and safety. Here, for milk analysis, atmospheric pressure matrix-assisted laser desorption/ionization employing homogenous liquid sample droplets was used on a Q-TOF mass analyzer. This method has the capability to produce multiply charged proteinaceous ions as well as highly informative profiles of singly charged lipids/metabolites. In two examples, this method is coupled with user-friendly machine-learning software. First, rapid speciation of milk (cow, goat, sheep and camel) is demonstrated with 100% classification accuracy. Second, the detection of cow milk as adulterant in goat milk is shown at concentrations as low as 5% with 92.5% sensitivity and 94.5% specificity.
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Affiliation(s)
- Cristian Piras
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6DX, UK
- Department of Health Sciences, "Magna Græcia University" of Catanzaro, Campus Universitario "Salvatore Venuta" Viale Europa, 88100, Catanzaro, Italy
| | - Oliver J Hale
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6DX, UK
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher K Reynolds
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6EU, UK
| | - A K Jones
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6EU, UK
| | - Nick Taylor
- Veterinary Epidemiology and Economics Research Unit (VEERU) & PAN Livestock Services Ltd, School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6EU, UK
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow, SK9 4AX, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6DX, UK.
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8
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Hale OJ, Ryumin P, Brown JM, Morris M, Cramer R. Production and analysis of multiply charged negative ions by liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 2021; 35 Suppl 1:e8246. [PMID: 30067883 PMCID: PMC7757204 DOI: 10.1002/rcm.8246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 05/08/2023]
Abstract
RATIONALE Liquid atmospheric pressure matrix-assisted laser desorption/ionisation (AP-MALDI) has been shown to enable the production of electrospray ionisation (ESI)-like multiply charged analyte ions with little sample consumption and long-lasting, robust ion yield for sensitive analysis by mass spectrometry (MS). Previous reports have focused on positive ion production. Here, we report an initial optimisation of liquid AP-MALDI for ESI-like negative ion production and its application to the analysis of peptides/proteins, DNA and lipids. METHODS The instrumentation employed for this study is identical to that of earlier liquid AP-MALDI MS studies for positive analyte ion production with a simple non-commercial AP ion source that is attached to a Waters Synapt G2-Si mass spectrometer and incorporates a heated ion transfer tube. The preparation of liquid MALDI matrices is similar to positive ion mode analysis but has been adjusted for negative ion mode by changing the chromophore to 3-aminoquinoline and 9-aminoacridine for further improvements. RESULTS For DNA, liquid AP-MALDI MS analysis benefited from switching to 9-aminoacridine-based MALDI samples and the negative ion mode, increasing the number of charges by up to a factor of 2 and the analyte ion signal intensities by more than 10-fold compared with the positive ion mode. The limit of detection was recorded at around 10 fmol for ATGCAT. For lipids, negative ion mode analysis provided a fully orthogonal set of detected lipids. CONCLUSIONS Negative ion mode is a sensitive alternative to positive ion mode in liquid AP-MALDI MS analysis. In particular, the analysis of lipids and DNA benefited from the complementarity of the detected lipid species and the vastly greater DNA ion signal intensities in negative ion mode.
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Affiliation(s)
- Oliver J Hale
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Pavel Ryumin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Jeffery M Brown
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
- Waters Corporation, Stamford Avenue, Wilmslow, SK9 4AX, UK
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow, SK9 4AX, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
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9
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Castelletto V, Seitsonen J, Ruokolainen J, Piras C, Cramer R, Edwards-Gayle CJC, Hamley IW. Peptide nanotubes self-assembled from leucine-rich alpha helical surfactant-like peptides. Chem Commun (Camb) 2020; 56:11977-11980. [PMID: 33033814 DOI: 10.1039/d0cc04299d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The designed arginine-rich surfactant-like peptide R3L12 (arginine3-leucine12) is shown to form a remarkable diversity of self-assembled nanostructures in aqueous solution, depending on pH, including nanotubes, mesh-like tubular networks in three-dimensions and square planar arrays in two-dimensions. These structures are built from α-helical antiparallel coiled-coil peptide dimers arranged perpendicular to the nanotube axis, in a "cross-α" nanotube structure. The aggregation behavior is rationalized based on the effects of dimensionality, and the balance of hydrophobic and electrostatic interactions. The nanotube and nanomesh structures display arginine at high density on their surfaces, which may be valuable for future applications.
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Affiliation(s)
- Valeria Castelletto
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
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10
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Piras C, Ceniti C, Hartmane E, Costanzo N, Morittu VM, Roncada P, Britti D, Cramer R. Rapid Liquid AP-MALDI MS Profiling of Lipids and Proteins from Goat and Sheep Milk for Speciation and Colostrum Analysis. Proteomes 2020; 8:proteomes8030020. [PMID: 32825579 PMCID: PMC7564146 DOI: 10.3390/proteomes8030020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Rapid profiling of the biomolecular components of milk can be useful for food quality assessment and for food fraud detection. Differences in commercial value and availability of milk from specific species are often the reasons for the illicit and fraudulent sale of milk whose species origin is wrongly declared. In this study, a fast, MS-based speciation method is presented to distinguish sheep from goat milk and sheep colostrum at different phases. Using liquid atmospheric pressure (AP)-matrix-assisted laser desorption/ionisation (MALDI) MS, it was possible to classify samples of goat and sheep milk with 100% accuracy in one minute of data acquisition per sample. Moreover, an accuracy of 98% was achieved in classifying pure sheep milk samples and sheep milk samples containing 10% goat milk. Evaluating colostrum quality and postnatal stages represents another possible application of this technology. Classification of sheep colostrum samples that were collected within 6 hours after parturition and 48 hours later was achieved with an accuracy of 84.4%. Our data show that substantial changes in the lipid profile can account for the accurate classification of colostrum collected at the early and late time points. This method applied to the analysis of protein orthologs of different species can, as in this case, allow unequivocal speciation analysis.
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Affiliation(s)
- Cristian Piras
- Department of Chemistry, University of Reading, Reading RG6 6DX, UK; (C.P.); (E.H.)
| | - Carlotta Ceniti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, I-88100 Catanzaro, Italy; (C.C.); (N.C.); (V.M.M.); (P.R.); (D.B.)
| | - Evita Hartmane
- Department of Chemistry, University of Reading, Reading RG6 6DX, UK; (C.P.); (E.H.)
| | - Nicola Costanzo
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, I-88100 Catanzaro, Italy; (C.C.); (N.C.); (V.M.M.); (P.R.); (D.B.)
| | - Valeria Maria Morittu
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, I-88100 Catanzaro, Italy; (C.C.); (N.C.); (V.M.M.); (P.R.); (D.B.)
| | - Paola Roncada
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, I-88100 Catanzaro, Italy; (C.C.); (N.C.); (V.M.M.); (P.R.); (D.B.)
| | - Domenico Britti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, I-88100 Catanzaro, Italy; (C.C.); (N.C.); (V.M.M.); (P.R.); (D.B.)
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Reading RG6 6DX, UK; (C.P.); (E.H.)
- Correspondence: ; Tel.: +44-118-378-4550
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11
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Cramer R. High-speed Analysis of Large Sample Sets - How Can This Key Aspect of the Omics Be Achieved? Mol Cell Proteomics 2020; 19:1760-1766. [PMID: 32796012 DOI: 10.1074/mcp.p120.001997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/21/2020] [Revised: 07/29/2020] [Indexed: 01/25/2023] Open
Abstract
High-speed analysis of large (prote)omics sample sets at the rate of thousands or millions of samples per day on a single platform has been a challenge since the beginning of proteomics. For many years, ESI-based MS methods have dominated proteomics because of their high sensitivity and great depth in analyzing complex proteomes. However, despite improvements in speed, ESI-based MS methods are fundamentally limited by their sample introduction, which excludes off-line sample preparation/fractionation because of the time required to switch between individual samples/sample fractions, and therefore being dependent on the speed of on-line sample preparation methods such as liquid chromatography. Laser-based ionization methods have the advantage of moving from one sample to the next without these limitations, being mainly restricted by the speed of modern sample stages, i.e. 10 ms or less between samples. This speed matches the data acquisition speed of modern high-performing mass spectrometers whereas the pulse repetition rate of the lasers (>1 kHz) provides a sufficient number of desorption/ionization events for successful ion signal detection from each sample at the above speed of the sample stages. Other advantages of laser-based ionization methods include the generally higher tolerance to sample additives and contamination compared with ESI MS, and the contact-less and pulsed nature of the laser used for desorption, reducing the risk of cross-contamination. Furthermore, new developments in MALDI have expanded its analytical capabilities, now being able to fully exploit high-performing hybrid mass analyzers and their strengths in sensitivity and MS/MS analysis by generating an ESI-like stable yield of multiply charged analyte ions. Thus, these new developments and the intrinsically high speed of laser-based methods now provide a good basis for tackling extreme sample analysis speed in the omics.
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Affiliation(s)
- Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK.
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12
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Scollo E, Neville DC, Oruna-Concha MJ, Trotin M, Umaharan P, Sukha D, Kalloo R, Cramer R. Proteomic and peptidomic UHPLC-ESI MS/MS analysis of cocoa beans fermented using the Styrofoam-box method. Food Chem 2020; 316:126350. [DOI: 10.1016/j.foodchem.2020.126350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 11/26/2022]
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13
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Krenkel H, Hartmane E, Piras C, Brown J, Morris M, Cramer R. Advancing Liquid Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Toward Ultrahigh-Throughput Analysis. Anal Chem 2020; 92:2931-2936. [PMID: 31967792 PMCID: PMC7145281 DOI: 10.1021/acs.analchem.9b05202] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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] [Indexed: 12/14/2022]
Abstract
Label-free high-throughput screening using mass spectrometry has the potential to provide rapid large-scale sample analysis at a speed of more than one sample per second. Such speed is important for compound library, assay and future clinical screening of millions of samples within a reasonable time frame. Herein, we present a liquid atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) setup for high-throughput large-scale sample analysis (>5 samples per second) for three substance classes (peptides, antibiotics, and lipids). Liquid support matrices (LSM) were used for the analysis of standard substances as well as complex biological fluids (milk). Throughput and analytical robustness were mainly dependent on the complexity of the sample composition and the current limitations of the commercial hardware. However, the ultimate limits of liquid AP-MALDI in sample throughput can be conservatively estimated to be beyond 10-20 samples per second. This level of analytical speed is highly competitive compared with other label-free MS methods, including electrospray ionization and solid state MALDI, as well as MS methods using multiplexing by labeling, which in principle can also be used in combination with liquid AP-MALDI MS.
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Affiliation(s)
- Henriette Krenkel
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Evita Hartmane
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Cristian Piras
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Jeffery Brown
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom.,Waters Corporation , Stamford Avenue , Wilmslow SK9 4AX , United Kingdom
| | - Michael Morris
- Waters Corporation , Stamford Avenue , Wilmslow SK9 4AX , United Kingdom
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
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14
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Scollo E, Neville DC, Oruna-Concha MJ, Trotin M, Cramer R. UHPLC–MS/MS analysis of cocoa bean proteomes from four different genotypes. Food Chem 2020; 303:125244. [DOI: 10.1016/j.foodchem.2019.125244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 01/01/2023]
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15
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Lellman SE, Cramer R. Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. ACTA ACUST UNITED AC 2019; 58:930-938. [DOI: 10.1515/cclm-2019-0908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Abstract
Background
In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.
Methods
Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.
Results
Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.
Conclusions
Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.
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Affiliation(s)
- Sophie E. Lellman
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
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16
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Hutchinson JA, Hamley IW, Edwards-Gayle CJC, Castelletto V, Piras C, Cramer R, Kowalczyk R, Seitsonen J, Ruokolainen J, Rambo RP. Melanin production by tyrosinase activity on a tyrosine-rich peptide fragment and pH-dependent self-assembly of its lipidated analogue. Org Biomol Chem 2019; 17:4543-4553. [PMID: 30994696 DOI: 10.1039/c9ob00550a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We investigate the self-assembly of a palmitoylated (C16-chain at the N terminus) peptide fragment in comparison to the unlipidated peptide EELNRYY, a fragment of the gut hormone peptide PYY3-36. The lipopeptide C16-EELNRYY shows remarkable pH-dependent self-assembly above measured critical aggregation concentrations, forming fibrils at pH 7, but micelles at pH 10. The parent peptide does not show self-assembly behaviour. The lipopeptide forms hydrogels at sufficiently high concentration at pH 7, the dynamic mechanical properties of which were measured. We also show that the tyrosine functionality at the C terminus of EELNRYY can be used to enzymatically produce the pigment melanin. The enzyme tyrosinase oxidises tyrosine into 3,4-dihydroxyphenylalanine (DOPA), DOPA-quinone and further products, eventually forming eumelanin. This is a mechanism of photo-protection in the skin, for this reason controlling tyrosinase activity is a major target for skin care applications and EELNRYY has potential to be developed for such uses.
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Affiliation(s)
- Jessica A Hutchinson
- School of Chemistry, Pharmacy and Food Biosciences. University of Reading, Whiteknights, Reading RG6 6AD, UK.
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17
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Abstract
Understanding protein structure is vital for evaluating protein interactions with drugs, proteins, and other ligands. Native mass spectrometry (MS) is proving to be invaluable for this purpose, enabling analysis of "native-like" samples that mimic physiological conditions. Native MS is usually performed by electrospray ionization (ESI) with its soft ionization processes and the generation of multiply charged ions proving favorable for conformation retention and high mass analysis, respectively. There is scope to expand the currently available toolset, specifically to other soft ionization techniques such as soft laser desorption, for applications in areas like high-throughput screening and MS imaging. In this Letter, observations made from native MS experiments using an ultraviolet (UV) laser-based ion source operating at atmospheric pressure are described. The ion source is capable of producing predominately multiply charged ions similar to ESI. Proteins and protein complexes were analyzed from a native-like sample droplet to investigate the technique. Ion mobility-mass spectrometry (IM-MS) measurements showed that folded protein conformations were detected for ions with low charge states. This observation indicates the source is suitable for native MS analysis and should be further developed for higher mass analysis in the future.
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Affiliation(s)
- Oliver J Hale
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
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18
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Hale O, Morris M, Jones B, Reynolds CK, Cramer R. Liquid Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Adds Enhanced Functionalities to MALDI MS Profiling for Disease Diagnostics. ACS Omega 2019; 4:12759-12765. [PMID: 31460399 PMCID: PMC6681994 DOI: 10.1021/acsomega.9b01476] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/15/2019] [Indexed: 05/08/2023]
Abstract
A liquid matrix-assisted laser desorption/ionization (liquid MALDI) method has been developed for high-throughput atmospheric pressure (AP) mass spectrometry (MS) analysis of the molecular content of crude bioliquids for disease diagnostics. The presented method is rapid and highly robust, enabling its application in environments where speed and low-cost high-throughput analyses are required. Importantly, because of the creation of multiply charged analyte ions, it provides additional functionalities that conventional solid MALDI MS profiling is lacking, including the use of high-performance mass analyzers with limited m/z range. The concomitant superior MS/MS performance that is achieved similar to ESI MS/MS adds greater analytical power and specificity to MALDI MS profiling while retaining the advantages of a fast laser-based analysis system and off-line large-scale sample preparation. The potential of this MALDI MS profiling method is demonstrated on the detection of dairy cow mastitis, which is a substantial economic burden on the dairy industry with losses of hundreds of dollars per diseased cow per year, equating to a total annual loss of billions of dollars, as well as leading to the use of large quantities of antibiotics, adding to the proliferation of antimicrobial resistance. Only small amounts of aliquots obtained from the daily farm milking process were prepared for liquid MALDI MS profiling using a simple one-pot/two-step analyte extraction. Automated analysis was performed using a custom-built AP-MALDI ion source, enabling the simultaneous detection of lipids, peptides, and proteins. Diagnostic, multiply charged, proteinaceous ions were easily sequenced and identified by MS/MS experiments. Samples were classified according to mastitis status using multivariate analysis, achieving 98.5% accuracy (100% specificity) determined by "leave 20% out" cross-validation. The methodology is generally applicable to AP-MALDI MS profiling on most commercial high-resolution mass spectrometers, with the potential for expansion into hospitals for rapid assessment of human and other biofluids.
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Affiliation(s)
- Oliver
J. Hale
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K.
| | - Barney Jones
- The
Centre for Dairy Research, School of Agriculture, Policy and Development, University of Reading, Reading RG2 9HX, U.K.
| | - Christopher K. Reynolds
- The
Centre for Dairy Research, School of Agriculture, Policy and Development, University of Reading, Reading RG2 9HX, U.K.
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
- E-mail:
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19
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Lambertucci S, Orman KM, Das Gupta S, Fisher JP, Gazal S, Williamson RJ, Cramer R, Bindschedler LV. Analysis of Barley Leaf Epidermis and Extrahaustorial Proteomes During Powdery Mildew Infection Reveals That the PR5 Thaumatin-Like Protein TLP5 Is Required for Susceptibility Towards Blumeria graminis f. sp. hordei. Front Plant Sci 2019; 10:1138. [PMID: 31736984 PMCID: PMC6831746 DOI: 10.3389/fpls.2019.01138] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/20/2019] [Indexed: 05/18/2023]
Abstract
Powdery mildews are biotrophic pathogens causing fungal diseases in many economically important crops, including cereals, which are affected by Blumeria graminis. Powdery mildews only invade the epidermal cell layer of leaf tissues, in which they form haustorial structures. Haustoria are at the center of the biotrophic interaction by taking up nutrients from the host and by delivering effectors in the invaded cells to jeopardize plant immunity. Haustoria are composed of a fungal core delimited by a haustorial plasma membrane and cell wall. Surrounding these is the extrahaustorial complex, of which the extrahaustorial membrane is of plant origin. Although haustoria transcriptomes and proteomes have been investigated for Blumeria, the proteomes of barley epidermis upon infection and the barley components of the extrahaustorial complex remains unexplored. When comparing proteomes of infected and non-infected epidermis, several classical pathogenesis-related (PR) proteins were more abundant in infected epidermis. These included peroxidases, chitinases, cysteine-rich venom secreted proteins/PR1 and two thaumatin-like PR5 protein isoforms, of which TLP5 was previously shown to interact with the Blumeria effector BEC1054 (CSEP0064). Against expectations, transient TLP5 gene silencing suggested that TLP5 does not contribute to resistance but modulates susceptibility towards B. graminis. In a second proteomics comparison, haustorial structures were enriched from infected epidermal strips to identify plant proteins closely associated with the extrahaustorial complex. In these haustoria-enriched samples, relative abundances were higher for several V-type ATP synthase/ATPase subunits, suggesting the generation of proton gradients in the extrahaustorial space. Other haustoria-associated proteins included secreted or membrane proteins such as a PIP2 aquaporin, an early nodulin-like protein 9, an aspartate protease and other proteases, a lipase, and a lipid transfer protein, all of which are potential modulators of immunity, or the targets of pathogen effectors. Moreover, the ER BIP-like HSP70, may link ER stress responses and the idea of ER-like properties previously attributed to the extrahaustorial membrane. This initial investigation exploring the barley proteomes of Blumeria-infected tissues and haustoria, associated with a transient gene silencing approach, is invaluable to gain first insight of key players of resistance and susceptibility.
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Affiliation(s)
- Sebastien Lambertucci
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Kate Mary Orman
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Shaoli Das Gupta
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - James Paul Fisher
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | - Snehi Gazal
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| | | | - Rainer Cramer
- Department of Chemistry, University of Reading, Reading, United Kingdom
| | - Laurence Véronique Bindschedler
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- *Correspondence: Laurence Véronique Bindschedler,
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20
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Ryumin P, Cramer R. The composition of liquid atmospheric pressure matrix-assisted laser desorption/ionization matrices and its effect on ionization in mass spectrometry. Anal Chim Acta 2018; 1013:43-53. [PMID: 29501091 DOI: 10.1016/j.aca.2018.01.070] [Citation(s) in RCA: 16] [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: 11/22/2017] [Revised: 01/26/2018] [Accepted: 01/31/2018] [Indexed: 01/06/2023]
Abstract
New liquid atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) matrices that produce predominantly multiply charged ions have been developed and evaluated with respect to their performance for peptide and protein analysis by mass spectrometry (MS). Both the chromophore and the viscous support liquid in these matrices were optimized for highest MS signal intensity, S/N values and maximum charge state. The best performance in both protein and peptide analysis was achieved employing light diols as matrix support liquids (e.g. ethylene glycol and propylene glycol). Investigating the influence of the chromophore, it was found that 2,5-dihydroxybenzoic acid resulted in a higher analyte ion signal intensity for the analysis of small peptides; however, larger molecules (>17 kDa) were undetectable. For larger molecules, a sample preparation based on α-cyano-4-hydroxycinnammic acid as the chromophore was developed and multiply protonated analytes with charge states of more than 50 were detected. Thus, for the first time it was possible to detect with MALDI MS proteins as large as ∼80 kDa with a high number of charge states, i.e. m/z values below 2000. Systematic investigations of various matrix support liquids have revealed a linear dependency between laser threshold energy and surface tension of the liquid MALDI sample.
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Affiliation(s)
- Pavel Ryumin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, United Kingdom
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, United Kingdom.
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21
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Scollo E, Neville D, Oruna-Concha MJ, Trotin M, Cramer R. Characterization of the Proteome of Theobroma cacao Beans by Nano-UHPLC-ESI MS/MS. Proteomics 2018; 18. [PMID: 29280563 DOI: 10.1002/pmic.201700339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 09/08/2017] [Revised: 11/29/2017] [Indexed: 11/06/2022]
Abstract
Cocoa seed storage proteins play an important role in flavour development as aroma precursors are formed from their degradation during fermentation. Major proteins in the beans of Theobroma cacao are the storage proteins belonging to the vicilin and albumin classes. Although both these classes of proteins have been extensively characterized, there is still limited information on the expression and abundance of other proteins present in cocoa beans. This work is the first attempt to characterize the whole cocoa bean proteome by nano-UHPLC-ESI MS/MS analysis using tryptic digests of cocoa bean protein extracts. The results of this analysis show that >1000 proteins could be identified using a species-specific Theobroma cacao database. The majority of the identified proteins were involved with metabolism and energy. Additionally, a significant number of the identified proteins were linked to protein synthesis and processing. Several proteins were also involved with plant response to stress conditions and defence. Albumin and vicilin storage proteins showed the highest intensity values among all detected proteins, although only seven entries were identified as storage proteins. A comparison of MS/MS data searches carried out against larger non-specific databases confirmed that using a species-specific database can increase the number of identified proteins, and at the same time reduce the number of false positives. The results of this work will be useful in developing tools that can allow the comparison of the proteomic profile of cocoa beans from different genotypes and geographic origins. Data are available via ProteomeXchange with identifier PXD005586.
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Affiliation(s)
- Emanuele Scollo
- Department of Chemistry, University of Reading, Reading, UK.,Mondelēz International, Reading Science Centre, Reading, UK
| | - David Neville
- Mondelēz International, Reading Science Centre, Reading, UK
| | - M Jose Oruna-Concha
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Martine Trotin
- Mondelēz International, Reading Science Centre, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Reading, UK
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22
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Hale OJ, Cramer R. Collision-induced dissociation of doubly-charged barium-cationized lipids generated from liquid samples by atmospheric pressure matrix-assisted laser desorption/ionization provides structurally diagnostic product ions. Anal Bioanal Chem 2017; 410:1435-1444. [DOI: 10.1007/s00216-017-0788-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/14/2017] [Accepted: 11/24/2017] [Indexed: 01/13/2023]
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23
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Torma AF, Groves K, Biesenbruch S, Mussell C, Reid A, Ellison S, Cramer R, Quaglia M. A candidate liquid chromatography mass spectrometry reference method for the quantification of the cardiac marker 1-32 B-type natriuretic peptide. Clin Chem Lab Med 2017; 55:1397-1406. [PMID: 28426429 DOI: 10.1515/cclm-2016-1054] [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] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND B-type natriuretic peptide (BNP) is a 32 amino acid cardiac hormone routinely measured by immunoassays to diagnose heart failure. While it is reported that immunoassay results can vary up to 45%, no attempt of standardization and/or harmonization through the development of certified reference materials (CRMs) or reference measurement procedures (RMPs) has yet been carried out. METHODS B-type natriuretic peptide primary calibrator was quantified traceably to the International System of Units (SI) by both amino acid analysis and tryptic digestion. A method for the stabilization of BNP in plasma followed by protein precipitation, solid phase extraction (SPE) and liquid chromatography (LC) mass spectrometry (MS) was then developed and validated for the quantification of BNP at clinically relevant concentrations (15-150 fmol/g). RESULTS The candidate reference method was applied to the quantification of BNP in a number of samples from the UK NEQAS Cardiac Markers Scheme to demonstrate its applicability to generate reference values and to preliminary evaluate the commutability of a potential CRM. The results from the reference method were consistently lower than the immunoassay results and discrepancy between the immunoassays was observed confirming previous data. CONCLUSIONS The application of the liquid chromatography-mass spectrometry (LC-MS) method to the UK NEQAS samples and the correlation of the results with the immunoassay results shows the potential of the method to support external quality assessment schemes, to improve understanding of the bias of the assays and to establish RMPs for BNP measurements. Furthermore, the method has the potential to be multiplexed for monitoring circulating truncated forms of BNP.
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24
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Owusu-Edusei K, Cramer R, Chesson HW, Gift TL, Leichliter JS. State-level gonorrhea rates and expedited partner therapy laws: insights from time series analyses. Public Health 2017; 147:101-108. [PMID: 28404485 DOI: 10.1016/j.puhe.2017.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 06/27/2016] [Revised: 12/09/2016] [Accepted: 02/22/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVE In this study, we examined state-level monthly gonorrhea morbidity and assessed the potential impact of existing expedited partner therapy (EPT) laws in relation to the time that the laws were enacted. STUDY DESIGN Longitudinal study. METHODS We obtained state-level monthly gonorrhea morbidity (number of cases/100,000 for males, females and total) from the national surveillance data. We used visual examination (of morbidity trends) and an autoregressive time series model in a panel format with intervention (interrupted time series) analysis to assess the impact of state EPT laws based on the months in which the laws were enacted. RESULTS For over 84% of the states with EPT laws, the monthly morbidity trends did not show any noticeable decreases on or after the laws were enacted. Although we found statistically significant decreases in gonorrhea morbidity within four of the states with EPT laws (Alaska, Illinois, Minnesota, and Vermont), there were no significant decreases when the decreases in the four states were compared contemporaneously with the decreases in states that do not have the laws. CONCLUSION We found no impact (decrease in gonorrhea morbidity) attributable exclusively to the EPT law(s). However, these results do not imply that the EPT laws themselves were not effective (or failed to reduce gonorrhea morbidity), because the effectiveness of the EPT law is dependent on necessary intermediate events/outcomes, including sexually transmitted infection service providers' awareness and practice, as well as acceptance by patients and their partners.
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Affiliation(s)
- K Owusu-Edusei
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - R Cramer
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - H W Chesson
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - T L Gift
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - J S Leichliter
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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25
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Castelletto V, Ryumin P, Cramer R, Hamley IW, Taylor M, Allsop D, Reza M, Ruokolainen J, Arnold T, Hermida-Merino D, Garcia CI, Leal MC, Castaño E. Self-Assembly and Anti-Amyloid Cytotoxicity Activity of Amyloid beta Peptide Derivatives. Sci Rep 2017; 7:43637. [PMID: 28272542 PMCID: PMC5341572 DOI: 10.1038/srep43637] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 09/30/2016] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
The self-assembly of two derivatives of KLVFF, a fragment Aβ(16-20) of the amyloid beta (Aβ) peptide, is investigated and recovery of viability of neuroblastoma cells exposed to Aβ (1-42) is observed at sub-stoichiometric peptide concentrations. Fluorescence assays show that NH2-KLVFF-CONH2 undergoes hydrophobic collapse and amyloid formation at the same critical aggregation concentration (cac). In contrast, NH2-K(Boc)LVFF-CONH2 undergoes hydrophobic collapse at a low concentration, followed by amyloid formation at a higher cac. These findings are supported by the β-sheet features observed by FTIR. Electrospray ionization mass spectrometry indicates that NH2-K(Boc)LVFF-CONH2 forms a significant population of oligomeric species above the cac. Cryo-TEM, used together with SAXS to determine fibril dimensions, shows that the length and degree of twisting of peptide fibrils seem to be influenced by the net peptide charge. Grazing incidence X-ray scattering from thin peptide films shows features of β-sheet ordering for both peptides, along with evidence for lamellar ordering of NH2-KLVFF-CONH2. This work provides a comprehensive picture of the aggregation properties of these two KLVFF derivatives and shows their utility, in unaggregated form, in restoring the viability of neuroblastoma cells against Aβ-induced toxicity.
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Affiliation(s)
- V. Castelletto
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - P. Ryumin
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - R. Cramer
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - I. W. Hamley
- School of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - M. Taylor
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - D. Allsop
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - M. Reza
- Department of Applied Physics, Aalto University School of Science, Aalto FI-00076, Finland
| | - J. Ruokolainen
- Department of Applied Physics, Aalto University School of Science, Aalto FI-00076, Finland
| | - T. Arnold
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D. Hermida-Merino
- European Synchrotron Radiation Facility, ESRF, 71 avenue des Martyrs, 38000 Grenoble, France
| | - C. I. Garcia
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - M. C. Leal
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - E. Castaño
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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26
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Affiliation(s)
- Kanjana Wiangnon
- Department
of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, United Kingdom
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27
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28
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Timms JF, Hale OJ, Cramer R. Advances in mass spectrometry-based cancer research and analysis: from cancer proteomics to clinical diagnostics. Expert Rev Proteomics 2016; 13:593-607. [DOI: 10.1080/14789450.2016.1182431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Bryant L, Patole C, Cramer R. Proteomic analysis of the medicinal plant Artemisia annua: Data from leaf and trichome extracts. Data Brief 2016; 7:325-31. [PMID: 26977431 PMCID: PMC4781977 DOI: 10.1016/j.dib.2016.02.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 08/18/2015] [Revised: 02/15/2016] [Accepted: 02/15/2016] [Indexed: 01/13/2023] Open
Abstract
This article contains raw and processed data related to research published by Bryant et al.[1]. Data was obtained by MS-based proteomics, analysing trichome-enriched, trichome-depleted and whole leaf samples taken from the medicinal plant Artemisia annua and searching the acquired MS/MS data against a recently published contig database [2] and other genomic and proteomic sequence databases for comparison. The processed data shows that an order-of-magnitude more proteins have been identified from trichome-enriched Artemisia annua samples in comparison to previously published data. Proteins known to have a role in the biosynthesis of artemisinin and other highly abundant proteins were found which imply additional enzymatically driven processes occurring within the trichomes that are significant for the biosynthesis of artemisinin.
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Affiliation(s)
- Laura Bryant
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Chhaya Patole
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
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30
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Pennington HG, Gheorghe DM, Damerum A, Pliego C, Spanu PD, Cramer R, Bindschedler LV. Interactions between the Powdery Mildew Effector BEC1054 and Barley Proteins Identify Candidate Host Targets. J Proteome Res 2016; 15:826-39. [DOI: 10.1021/acs.jproteome.5b00732] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helen G. Pennington
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Dana M. Gheorghe
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Annabelle Damerum
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Clara Pliego
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Pietro D. Spanu
- Department
of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Rainer Cramer
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
| | - Laurence V. Bindschedler
- Department
of Chemistry, University of Reading, Reading RG6 6AD, United Kingdom
- School
of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, United Kingdom
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Ryumin P, Brown J, Morris M, Cramer R. Investigation and optimization of parameters affecting the multiply charged ion yield in AP-MALDI MS. Methods 2016; 104:11-20. [PMID: 26827934 DOI: 10.1016/j.ymeth.2016.01.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 11/26/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 10/22/2022] Open
Abstract
Liquid matrix-assisted laser desorption/ionization (MALDI) allows the generation of predominantly multiply charged ions in atmospheric pressure (AP) MALDI ion sources for mass spectrometry (MS) analysis. The charge state distribution of the generated ions and the efficiency of the ion source in generating such ions crucially depend on the desolvation regime of the MALDI plume after desorption in the AP-to-vacuum inlet. Both high temperature and a flow regime with increased residence time of the desorbed plume in the desolvation region promote the generation of multiply charged ions. Without such measures the application of an electric ion extraction field significantly increases the ion signal intensity of singly charged species while the detection of multiply charged species is less dependent on the extraction field. In general, optimization of high temperature application facilitates the predominant formation and detection of multiply charged compared to singly charged ion species. In this study an experimental set-up and optimization strategy is described for liquid AP-MALDI MS which improves the ionization efficiency of selected ion species up to 14 times. In combination with ion mobility separation, the method allows the detection of multiply charged peptide and protein ions for analyte solution concentrations as low as 2fmol/μL (0.5μL, i.e. 1fmol, deposited on the target) with very low sample consumption in the low nL-range.
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Affiliation(s)
- Pavel Ryumin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Jeffery Brown
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK; Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, UK
| | - Michael Morris
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
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Leichliter JS, Cramer R, LaPollo AB, Hexem S, Chesson HW, McFarlane MM. S07.5 Sociocultural context and sexual health information among adolescents and young adults. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bryant L, Flatley B, Patole C, Brown GD, Cramer R. Proteomic analysis of Artemisia annua--towards elucidating the biosynthetic pathways of the antimalarial pro-drug artemisinin. BMC Plant Biol 2015; 15:175. [PMID: 26156581 PMCID: PMC4496932 DOI: 10.1186/s12870-015-0565-7] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/01/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND MS-based proteomics was applied to the analysis of the medicinal plant Artemisia annua, exploiting a recently published contig sequence database (Graham et al. (2010) Science 327, 328-331) and other genomic and proteomic sequence databases for comparison. A. annua is the predominant natural source of artemisinin, the precursor for artemisinin-based combination therapies (ACTs), which are the WHO-recommended treatment for P. falciparum malaria. RESULTS The comparison of various databases containing A. annua sequences (NCBInr/viridiplantae, UniProt/viridiplantae, UniProt/A. annua, an A. annua trichome Trinity contig database, the above contig database and another A. annua EST database) revealed significant differences in respect of their suitability for proteomic analysis, showing that an organism-specific database that has undergone extensive curation, leading to longer contig sequences, can greatly increase the number of true positive protein identifications, while reducing the number of false positives. Compared to previously published data an order-of-magnitude more proteins have been identified from trichome-enriched A. annua samples, including proteins which are known to be involved in the biosynthesis of artemisinin, as well as other highly abundant proteins, which suggest additional enzymatic processes occurring within the trichomes that are important for the biosynthesis of artemisinin. CONCLUSIONS The newly gained information allows for the possibility of an enzymatic pathway, utilizing peroxidases, for the less well understood final stages of artemisinin's biosynthesis, as an alternative to the known non-enzymatic in vitro conversion of dihydroartemisinic acid to artemisinin. Data are available via ProteomeXchange with identifier PXD000703.
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Affiliation(s)
- Laura Bryant
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Brian Flatley
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Chhaya Patole
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Geoffrey D Brown
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
| | - Rainer Cramer
- Department of Chemistry, Whiteknights, Reading, RG6 6AD, United Kingdom.
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Flatley B, Quaye C, Johnson E, Freeman A, Muneer A, Minhas S, Paterson JC, Musa F, Malone P, Cramer R. Distribution analysis of the putative cancer marker S100A4 across invasive squamous cell carcinoma penile tissue. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
Evidence is presented that the performance of the rationally designed MALDI matrix 4-chloro-α-cyanocinnamic acid (ClCCA) in comparison to its well-established predecessor α-cyano-4-hydroxycinnamic acid (CHCA) is significantly dependent on the sample preparation, such as the choice of the target plate. In this context, it becomes clear that any rational designs of MALDI matrices and their successful employment have to consider a larger set of physicochemical parameters, including sample crystallization and morphology/topology, in addition to parameters of basic (solution and/or gas-phase) chemistry.
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Affiliation(s)
- Kanjana Wiangnon
- Department of Chemistry, University of Reading , Whiteknights, Reading RG6 6AD, United Kingdom
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Gonzalez VH, Ball S, Cramer R, Smith A. Anatomical and Morphometric Variations in the Arterial System of the Domestic Cat. Anat Histol Embryol 2014; 44:428-32. [DOI: 10.1111/ahe.12154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/17/2014] [Indexed: 11/28/2022]
Affiliation(s)
- V. H. Gonzalez
- Biological Sciences; Southwestern Oklahoma State University; 100 Campus Drive Weatherford OK 73096 USA
| | - S. Ball
- Biological Sciences; Southwestern Oklahoma State University; 100 Campus Drive Weatherford OK 73096 USA
| | - R. Cramer
- Biological Sciences; Southwestern Oklahoma State University; 100 Campus Drive Weatherford OK 73096 USA
| | - A. Smith
- Biological Sciences; Southwestern Oklahoma State University; 100 Campus Drive Weatherford OK 73096 USA
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Flatley B, Wilmott KG, Malone P, Cramer R. MALDI MS profiling of post-DRE urine samples highlights the potential of β-microseminoprotein as a marker for prostatic diseases. Prostate 2014; 74:103-11. [PMID: 24115268 DOI: 10.1002/pros.22736] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/09/2013] [Indexed: 01/14/2023]
Abstract
BACKGROUND To use spectra acquired by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) from pre- and post-digital rectal examination (DRE) urine samples to search for discriminating peaks that can adequately distinguish between benign and malignant prostate conditions, and identify the peaks' underlying biomolecules. METHODS Twenty-five participants with prostate cancer (PCa) and 27 participants with a variety of benign prostatic conditions as confirmed by a 10-core tissue biopsy were included. Pre- and post-DRE urine samples were prepared for MALDI MS profiling using an automated clean-up procedure. Following mass spectra collection and processing, peak mass and intensity were extracted and subjected to statistical analysis to identify peaks capable of distinguishing between benign and cancer. Logistic regression was used to combine markers to create a sensitive and specific test. RESULTS A peak at m/z 10,760 was identified as β-microseminoprotein (β-MSMB) and found to be statistically lower in urine from PCa participants using the peak's average areas. By combining serum prostate-specific antigen (PSA) levels with MALDI MS-measured β-MSMB levels, optimum threshold values obtained from Receiver Operator characteristics curves gave an increased sensitivity of 96% at a specificity of 26%. CONCLUSIONS These results demonstrate that with a simple sample clean-up followed by MALDI MS profiling, significant differences of MSMB abundance were found in post-DRE urine samples. In combination with PSA serum levels, obtained from a classic clinical assay led to high classification accuracy for PCa in the studied sample set. Our results need to be validated in a larger multicenter prospective randomized clinical trial.
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Affiliation(s)
- Brian Flatley
- Department of Chemistry, University of Reading, Reading, UK; Urology Research Department, Royal Berkshire Hospital, Reading, UK
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Affiliation(s)
- Rainer Cramer
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Michael Karas
- Institute
of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular
Complexes”, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Thorsten W. Jaskolla
- Institute
of Hygiene, University of Münster, Robert-Koch-Str. 41, 48149 Münster, Germany
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Agrawal GK, Job D, Kieselbach T, Barkla BJ, Chen S, Deswal R, Lüthje S, Amalraj RS, Tanou G, Ndimba BK, Cramer R, Weckwerth W, Wienkoop S, Dunn MJ, Kim ST, Fukao Y, Yonekura M, Zolla L, Rohila JS, Waditee-Sirisattha R, Masi A, Wang T, Sarkar A, Agrawal R, Renaut J, Rakwal R. INPPO Actions and Recognition as a Driving Force for Progress in Plant Proteomics: Change of Guard, INPPO Update, and Upcoming Activities. Proteomics 2013. [DOI: 10.1002/pmic.201370174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Private Limited; Adarsh Nagar Birgunj Nepal
| | - Dominique Job
- CNRS/UCBL/INSA/Bayer CropScience Joint Laboratory; UMR 5240, Bayer CropScience Lyon France
| | | | - Bronwyn J. Barkla
- Instituto de Biotecnologia; Universidad Nacional Autonoma de Mexico; Morelos Mexico
| | - Sixue Chen
- Department of Biology; Interdisciplinary Center for Biotechnology Research (ICBR); Cancer & Genetics Research Complex, University of Florida; Gainesville FL USA
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory; Department of Botany; University of Delhi; Delhi India
| | - Sabine Lüthje
- Oxidative Stress and Plant Proteomics Group; University of Hamburg; Biocenter Klein Flottbek Hamburg Germany
| | - Ramesh Sundar Amalraj
- Plant Pathology Section, Sugarcane Breeding Institute; Indian Council of Agricultural Research; Tamil Nadu India
| | - Georgia Tanou
- Faculty of Agriculture; Aristotle University of Thessalonki; Thessaloniki Greece
| | - Bongani Kaiser Ndimba
- Proteomics Research and Services Unit; Agricultural Research Council; Infruitec-Nietvoorbij Campus; Stellenbosch South Africa
- Proteomics Research Group; Department of Biotechnology, University of the Western Cape; Bellville South Africa
| | - Rainer Cramer
- Department of Chemistry; University of Reading; Reading United Kingdom
| | | | | | - Michael J. Dunn
- UCD Conway Institute of Biomolecular and Biomedical Research; School of Medicine and Medical Science; University College Dublin; Dublin Ireland
| | - Sun Tae Kim
- Department of Plant Bioscience; Pusan National University; Miryang South Korea
| | - Yochiro Fukao
- Graduate School of Biological Sciences; Nara Institute of Science and Technology; Ikoma Japan
- Plant Global Educational Project; Nara Institute of Science and Technology; Ikoma Japan
| | - Masami Yonekura
- Laboratory of Molecular Food Functionality; College of Agriculture; Ami Ibaraki Japan
| | - Lello Zolla
- Department of Ecology and Biology; University Tuscia; Piazzale Universita; Viterbo Italy
| | - Jai Singh Rohila
- Department of Biology and Microbiology; South Dakota State University; Brookings SD USA
| | | | | | - Tai Wang
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Xiangshan Haidianqu Beijing China
| | - Abhijit Sarkar
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Private Limited; Adarsh Nagar Birgunj Nepal
- International Plant Proteomics Organization (INPPO www.inppo.com)
- Institute of Genetic Medicine and Genomic Science (IGMGS); Badu Kolkata West Bengal India
| | - Raj Agrawal
- International Plant Proteomics Organization (INPPO www.inppo.com)
| | - Jenny Renaut
- Centre de Recherche Public-Gabriel Lippman; Department of Environment and Agrobiotechnologies (EVA); Belvaux GD Luxembourg
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu Nepal
- GRADE Academy Private Limited; Adarsh Nagar Birgunj Nepal
- Department of Anatomy I; School of Medicine; Showa University; Shinagawa Tokyo Japan
- Organization for Educational Initiatives; University of Tsukuba; Tsukuba Japan
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. Mass Spectrom Rev 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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Flatley B, Malone P, Cramer R. MALDI mass spectrometry in prostate cancer biomarker discovery. Biochim Biophys Acta 2013; 1844:940-9. [PMID: 23831156 DOI: 10.1016/j.bbapap.2013.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/23/2013] [Accepted: 06/20/2013] [Indexed: 01/14/2023]
Abstract
Matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry (MS) is a highly versatile and sensitive analytical technique, which is known for its soft ionisation of biomolecules such as peptides and proteins. Generally, MALDI MS analysis requires little sample preparation, and in some cases like MS profiling it can be automated through the use of robotic liquid-handling systems. For more than a decade now, MALDI MS has been extensively utilised in the search for biomarkers that could aid clinicians in diagnosis, prognosis, and treatment decision making. This review examines the various MALDI-based MS techniques like MS imaging, MS profiling and proteomics in-depth analysis where MALDI MS follows fractionation and separation methods such as gel electrophoresis, and how these have contributed to prostate cancer biomarker research. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Brian Flatley
- Department of Chemistry, University of Reading, Reading, UK; Urology Research Department, Royal Berkshire Hospital, Reading, UK
| | - Peter Malone
- Urology Research Department, Royal Berkshire Hospital, Reading, UK
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Reading, UK.
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Cramer R, Haderxhanaj LT, Chesson HW, Leichliter JS. P4.119 State Characteristics Associated with the Presence of Laws Authorizing Expedited Partner Therapy in the United States. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kovaleva V, Cramer R, Krynytskyy H, Gout I, Gout R. Analysis of tyrosine phosphorylation and phosphotyrosine-binding proteins in germinating seeds from Scots pine. Plant Physiol Biochem 2013; 67:33-40. [PMID: 23542181 DOI: 10.1016/j.plaphy.2013.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 02/05/2013] [Indexed: 06/02/2023]
Abstract
Protein tyrosine phosphorylation in angiosperms has been implicated in various physiological processes, including seed development and germination. In conifers, the role of tyrosine phosphorylation and the mechanisms of its regulation are yet to be investigated. In this study, we examined the profile of protein tyrosine phosphorylation in Scots pine seeds at different stages of germination. We detected extensive protein tyrosine phosphorylation in extracts from Scots pine (Pinus sylvestris L.) dormant seeds. In addition, the pattern of tyrosine phosphorylation was found to change significantly during seed germination, especially at earlier stages of post-imbibition which coincides with the initiation of cell division, and during the period of intensive elongation of hypocotyls. To better understand the molecular mechanisms of phosphotyrosine signaling, we employed affinity purification and mass spectrometry for the identification of pTyr-binding proteins from the extracts of Scots pine seedlings. Using this approach, we purified two proteins of 10 and 43 kDa, which interacted specifically with pTyr-Sepharose and were identified by mass spectrometry as P. sylvestris defensin 1 (PsDef1) and aldose 1-epimerase (EC:5.1.3.3), respectively. Additionally, we demonstrated that both endogenous and recombinant PsDef1 specifically interact with pTyr-Sepharose, but not Tyr-beads. As the affinity purification approach did not reveal the presence of proteins with known pTyr binding domains (SH2, PTB and C2), we suggest that plants may have evolved a different mode of pTyr recognition, which yet remains to be uncovered.
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Affiliation(s)
- Valentina Kovaleva
- Ukrainian National Forestry University, Chuprynka St., 103, Lviv, Ukraine
| | - Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | | | - Ivan Gout
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Roman Gout
- Ukrainian National Forestry University, Chuprynka St., 103, Lviv, Ukraine.
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Cramer R, Pirkl A, Hillenkamp F, Dreisewerd K. AP-UV-MALDI mit flüssigen Matrizes: stabile Ionenausbeuten von mehrfach geladenen Peptid- und Proteinionen für die empfindliche Massenspektrometrie. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Cramer R, Pirkl A, Hillenkamp F, Dreisewerd K. Liquid AP-UV-MALDI enables stable ion yields of multiply charged peptide and protein ions for sensitive analysis by mass spectrometry. Angew Chem Int Ed Engl 2013; 52:2364-7. [PMID: 23341077 PMCID: PMC3592991 DOI: 10.1002/anie.201208628] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Indexed: 01/05/2023]
Affiliation(s)
- Rainer Cramer
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.
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Greenland BW, Bird MB, Burattini S, Cramer R, O'Reilly RK, Patterson JP, Hayes W, Cardin CJ, Colquhoun HM. Mutual binding of polymer end-groups by complementary π–π-stacking: a molecular “Roman Handshake”. Chem Commun (Camb) 2013; 49:454-6. [DOI: 10.1039/c2cc35965k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pedersen C, Ver Loren van Themaat E, McGuffin LJ, Abbott JC, Burgis TA, Barton G, Bindschedler LV, Lu X, Maekawa T, Wessling R, Cramer R, Thordal-Christensen H, Panstruga R, Spanu PD. Structure and evolution of barley powdery mildew effector candidates. BMC Genomics 2012; 13:694. [PMID: 23231440 PMCID: PMC3582587 DOI: 10.1186/1471-2164-13-694] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [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: 07/12/2012] [Accepted: 11/28/2012] [Indexed: 11/11/2022] Open
Abstract
Background Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to suppress or avoid host immunity if it is to survive and cause disease. Results Here we characterise a superfamily predicted to be the full complement of Candidates for Secreted Effector Proteins (CSEPs) in the fungal barley powdery mildew parasite B. graminis f.sp. hordei. The 491 genes encoding these proteins constitute over 7% of this pathogen’s annotated genes and most were grouped into 72 families of up to 59 members. They were predominantly expressed in the intracellular feeding structures called haustoria, and proteins specifically associated with the haustoria were identified by large-scale mass spectrometry-based proteomics. There are two major types of effector families: one comprises shorter proteins (100–150 amino acids), with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300–400 amino acids), with lower levels of differential expression and evidence of purifying selection between paralogs. An analysis of the predicted protein structures underscores their overall similarity to known fungal effectors, but also highlights unexpected structural affinities to ribonucleases throughout the entire effector super-family. Candidate effector genes belonging to the same family are loosely clustered in the genome and are associated with repetitive DNA derived from retro-transposons. Conclusions We employed the full complement of genomic, transcriptomic and proteomic analyses as well as structural prediction methods to identify and characterize the members of the CSEPs superfamily in B. graminis f.sp. hordei. Based on relative intron position and the distribution of CSEPs with a ribonuclease-like domain in the phylogenetic tree we hypothesize that the associated genes originated from an ancestral gene, encoding a secreted ribonuclease, duplicated successively by repetitive DNA-driven processes and diversified during the evolution of the grass and cereal powdery mildew lineage.
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Affiliation(s)
- Carsten Pedersen
- Department of Agriculture & Ecology, Plant and Soil Science, University ofCopenhagen, Copenhagen, Denmark
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Nagano K, Akpan A, Warnasuriya G, Corless S, Totty N, Yang A, Stein R, Zvelebil M, Stensballe A, Burlingame A, Waterfield M, Cramer R, Timms JF, Naaby-Hansen S. Functional proteomic analysis of long-term growth factor stimulation and receptor tyrosine kinase coactivation in Swiss 3T3 fibroblasts. Mol Cell Proteomics 2012; 11:1690-708. [PMID: 22956732 DOI: 10.1074/mcp.m112.019778] [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] [Indexed: 11/06/2022] Open
Abstract
In Swiss 3T3 fibroblasts, long-term stimulation with PDGF, but not insulin-like growth factor 1 (IGF-1) or EGF, results in the establishment of an elongated migratory phenotype, characterized by the formation of retractile dendritic protrusions and absence of actin stress fibers and focal adhesion complexes. To identify receptor tyrosine kinase-specific reorganization of the Swiss 3T3 proteome during phenotypic differentiation, we compared changes in the pattern of protein synthesis and phosphorylation during long-term exposure to PDGF, IGF-1, EGF, and their combinations using 2DE-based proteomics after (35)S- and (33)P-metabolic labeling. One hundred and five differentially regulated proteins were identified by mass spectrometry and some of these extensively validated. PDGF stimulation produced the highest overall rate of protein synthesis at any given time and induced the most sustained phospho-signaling. Simultaneous activation with two or three of the growth factors revealed both synergistic and antagonistic effects on protein synthesis and expression levels with PDGF showing dominance over both IGF-1 and EGF in generating distinct proteome compositions. Using signaling pathway inhibitors, PI3K was identified as an early site for signal diversification, with sustained activity of the PI3K/AKT pathway critical for regulating late protein synthesis and phosphorylation of target proteins and required for maintaining the PDGF-dependent motile phenotype. Several proteins were identified with novel PI3K/Akt-dependent synthesis and phosphorylations including eEF2, PRS7, RACK-1, acidic calponin, NAP1L1, Hsp73, and fascin. The data also reveal induction/suppression of key F-actin and actomyosin regulators and chaperonins that enable PDGFR to direct the assembly of a motile cytoskeleton, despite simultaneous antagonistic signaling activities. Together, the study demonstrates that long-term exposure to different growth factors results in receptor tyrosine kinase-specific regulation of relatively small subproteomes, and implies that the strength and longevity of receptor tyrosine kinase-specific signals are critical in defining the composition and functional activity of the resulting proteome.
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Affiliation(s)
- Kohji Nagano
- Discovery Research Department, Chugai Pharmaceutical Co. Ltd., Japan
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