1
|
Bateman RH, Carruthers R, Hoyes JB, Jones C, Langridge JI, Millar A, Vissers JPC. A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation. J Am Soc Mass Spectrom 2002; 13:792-803. [PMID: 12148804 DOI: 10.1016/s1044-0305(02)00420-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A tandem quadrupole time-of-flight (Q-TOF) mass spectrometer has been programmed such that phosphorylated peptides can automatically be discovered and identified in a way similar to that of the use of precursor ion or neutral loss scanning, but without the need to scan the quadrupole mass filter. Instead, the method capitalizes on the innate capability of the Q-TOF to record mass spectra and product ion spectra quickly, with good sensitivity and with good mass accuracy. Alternate mass spectra, with and without fragmentation, are recorded at high and low collision energy with the quadrupole operating in wideband mode. The method of analysis is both compatible with and dependant on liquid chromatography for separation of complex mixtures. The method has been demonstrated by searching for the neutral loss of 98 Da (H3PO4) from phosphoserine and phosphothreonine residues, or for the phosphorylated immonium ion at m/z 216 from phosphotyrosine. The method also incorporates acquisition of the product ion spectrum from any candidate precursor ions, thereby allowing confirmation of the neutral loss or product ion and providing additional sequence information to assist identification of the protein and assign the site of phosphorylation.
Collapse
Affiliation(s)
- R H Bateman
- Micromass Ltd., Wythenshawe, Manchester, UK.
| | | | | | | | | | | | | |
Collapse
|
2
|
Abstract
Development of cancer is a complex process involving multiple changes in gene expression. To unravel these alterations, a proteome approach aimed at the identification of qualitative and quantitative changes in protein composition, including their post-translational modifications, attracts great attention. Our study was focused on the identification of proteins whose amount is altered in the course of malignant transformation of colon mucosa. Proteins extracted from tissue specimens or cell lysates were separated by two-dimensional gel electrophoresis (2-DE). Comparative analyses of 2-DE protein patterns were done using computerized image analysis. Selected proteins exhibiting statistically significant abundance alterations comparing healthy and diseased tissues were identified by mass spectrometry. Globally, we have found 57 proteins that exhibited either a significant decrease or increase in amount in pathological tissues, and 18 of these were annotated by mass spectrometry. The alterations in the expression of nine proteins were common for both precancerous and neoplastic tissues suggesting their role in colon tumorigenesis. The epithelial origin of all identified spots was checked in two cell lines Caco-2 and DLD-1 originating from well-differentiated and poorly differentiated colon carcinoma, respectively.
Collapse
Affiliation(s)
- J Stulík
- Institute of Radiobiology and Immunology, Purkyne Military Medical Academy, Hradec Králové, Czech Republic.
| | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Ishigai M, Langridge JI, Bordoli RS. A new approach for dynamics of enzyme-catalyzed glutathione conjugation by electrospray quadrupole/time-of-flight mass spectrometry. Anal Biochem 2001; 298:83-92. [PMID: 11673899 DOI: 10.1006/abio.2001.5339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The dynamics of enzyme-catalyzed glutathione conjugation was studied by electrospray quadrupole/time-of-flight (Q-TOF) mass spectrometry with a nanospray interface. After incubation of human glutathione S-transferase A1-1 (GT) with glutathione (GSH) and an electrophilic substrate, electrospray indicated the presence of enzyme/product adducts such as [2GT + product], [2GT + GSH' + product], and [2GT + 2 products] as well as [2GT] and [2GT + GSH']. The relative abundance of GT/product adduct ions increased with incubation time. The wide m/z range of detection (m/z 300-5000) allowed the observation of product, suggested to be released from enzyme/product adducts, in the same mass spectrum. The noncovalent complexes of GT/product were completely replaced by GT/inhibitor complexes following the addition of GT inhibitor to the incubation mixture. Furthermore, a collision-activated decomposition analysis of these ion species provided us with useful information to interpret or identify ion species. The results suggest that electrospray Q-TOF mass spectrometry is a powerful approach for studying the dynamics of the enzyme reaction as well as the structure of enzyme complexes at high sensitivity.
Collapse
Affiliation(s)
- M Ishigai
- Drug Metabolism & Pharmacokinetics Research Lab, Chugai Pharmaceutical Company, Ltd., Shizuoka, 412-8513, Japan.
| | | | | |
Collapse
|
4
|
Abstract
Development of cancer is a complex process involving multiple changes in gene expression. To unravel these alterations, a proteome approach aimed at the identification of qualitative and quantitative changes in protein composition, including their post-translational modifications, attracts great attention. Our study was focused on the identification of proteins whose amount is altered in the course of malignant transformation of colon mucosa. Proteins extracted from tissue specimens or cell lysates were separated by two-dimensional gel electrophoresis (2-DE). Comparative analyses of 2-DE protein patterns were done using computerized image analysis. Selected proteins exhibiting statistically significant abundance alterations comparing healthy and diseased tissues were identified by mass spectrometry. Globally, we have found 57 proteins that exhibited either a significant decrease or increase in amount in pathological tissues, and 18 of these were annotated by mass spectrometry. The alterations in the expression of nine proteins were common for both precancerous and neoplastic tissues suggesting their role in colon tumorigenesis. The epithelial origin of all identified spots was checked in two cell lines Caco-2 and DLD-1 originating from well-differentiated and poorly differentiated colon carcinoma, respectively.
Collapse
Affiliation(s)
- J Stulík
- Institute of Radiobiology and Immunology, Purkyne Military Medical Academy, Hradec Králové, Czech Republic.
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Dudley E, Lemiere F, Van Dongen W, Langridge JI, El-Sharkawi S, Games DE, Esmans EL, Newton RP. Analysis of urinary nucleosides. II. Comparison of mass spectrometric methods for the analysis of urinary nucleosides. Rapid Commun Mass Spectrom 2001; 15:1701-1707. [PMID: 11555869 DOI: 10.1002/rcm.428] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Qualitative and quantitative analyses of urinary nucleosides have diagnostic potential as tumour markers. We have developed separation techniques linked to mass spectrometric detection in order to overcome the problems associated with past identification and quantitation methods. The three methods of analysis utilised were: gas chromatography/mass spectrometry (GC/MS), high-performance liquid chromatography/ion-trap mass spectrometry (HPLC/ITMS) and capillary liquid chromatography/triple quadrupole mass spectrometry (CapLC/TQMS). Here we compare the relative effectiveness of each of the techniques for subsequent application in the systematic study of urinary nucleoside profiles in cancer patients. All three methods proved to be valuable techniques for such urinary nucleoside analyses, and a combination rather than one single choice is concluded as the ideal.
Collapse
Affiliation(s)
- E Dudley
- Biochemistry Group, School of Biological Sciences, Wallace Building, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Ishigai M, Langridge JI, Bordoli RS, Gaskell SJ. Noncovalent associations of glutathione S-transferase and ligands: a study using electrospray quadrupole/time-of-flight mass spectrometry. J Am Soc Mass Spectrom 2000; 11:606-614. [PMID: 10883816 DOI: 10.1016/s1044-0305(00)00127-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Human glutathione S-transferase A1-1 was observed predominantly as dimeric ions (51 kDa) during electrospray mass spectrometric analysis from aqueous solution at pH 7.4, in keeping with the known dimeric structure in solution. When analyses were performed on solutions of the enzyme containing glutathione (GSH), noncovalent adducts of protein dimer and one or two ligand molecules were observed; each mass increment, which exceeded the mass of GSH alone, was provisionally interpreted to indicate concomitant association of two water molecules per bound GSH. Noncovalent adducts of ligand and protein dimer were similarly observed for oxidized glutathione and for two glutathione inhibitors, both incorporating substituted thiol structures. In these instances, the mass increments exactly matched the ligand masses, suggesting that the apparent concomitant binding of water was associated with the presence in the ligand of a free thiol group. Collisionally activated decomposition during tandem mass spectrometry analyses of noncovalent adducts incorporating protein dimer and ligands yielded initially the denuded dimer; at higher collision energies the monomer and a protein fragment were formed.
Collapse
Affiliation(s)
- M Ishigai
- Michael Barber Centre for Mass Spectrometry, UMIST, Manchester, United Kingdom
| | | | | | | |
Collapse
|
7
|
Mo W, Sakamoto H, Nishikawa A, Kagi N, Langridge JI, Shimonishi Y, Takao T. Structural characterization of chemically derivatized oligosaccharides by nanoflow electrospray ionization mass spectrometry. Anal Chem 1999; 71:4100-6. [PMID: 10500493 DOI: 10.1021/ac990247i] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligosaccharides released from several glycoproteins were derivatized with either 4-aminobenzoic acid 2-(diethylamino)ethyl ester (ABDEAE) (Yoshino, K.; et al. Anal. Chem. 1995, 67, 4028-4031) or 2-aminopyridine. The resulting derivatives were analyzed on a nanoflow electrospray ionization (ESI) quadrupole-inlet time-of-flight mass spectrometer using the low-energy collision-induced dissociation technique. In the MS/MS spectra, the oxonium (b or internal series) and y series ions, which are derived from the multiply charged precursor ions, were predominant and were used for the structural readout. Some oxonium ions that were observed in the low-mass region, but that were not found in the PSD analyses (Mo, W.; et al. Anal. Chem. 1998, 70, 4520-4526), rendered a more detailed structural insight. The oxonium ions at m/z 512.2, which are derived from the fucosylated oligosaccharides of immunoglobulin Y and thyroglobulin, were observed, suggesting that fucosylation had occurred proximal to the outer nonreducing terminus. In addition, the data herein show that structural elucidation can be routinely achieved at a low sample concentration. For the case of ABDEAE derivatives, this can be achieved at the 50 fmol/microL level and with the actual sample consumption at the attomole level using nanoflow ESI MS/MS.
Collapse
Affiliation(s)
- W Mo
- Institute for Protein Research, Osaka University, Japan
| | | | | | | | | | | | | |
Collapse
|
8
|
Vinh J, Langridge JI, Bré MH, Levilliers N, Redeker V, Loyaux D, Rossier J. Structural characterization by tandem mass spectrometry of the posttranslational polyglycylation of tubulin. Biochemistry 1999; 38:3133-9. [PMID: 10074368 DOI: 10.1021/bi982304s] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Polyglycylation is a posttranslational modification specific to tubulin. This modification was originally identified in highly stable microtubules from Paramecium cilia. As many as 34 posttranslationally added glycine residues have been located in the C-terminal domains of Paramecium alpha- and beta-tubulin. In this study, post source decay matrix-assisted laser desorption/ionization mass spectrometry (PSD MALDI MS) and electrospray ionization on a hybrid quadrupole orthogonal time-of-flight tandem mass spectrometer (ESI Q-TOF MS/MS) were both used to demonstrate that a single molecule of beta-tubulin, from either dynamic cytoplasmic microtubules or stable axonemal microtubules, can be glycylated on each of the last four C-terminal glutamate residues Glu437, Glu438, Glu439, and Glu441 in the sequence 427DATAEEEGEFEEEGEQ442. In both dynamic and stable microtubules the most abundant beta-tubulin isoform contains six posttranslationally added glycine residues: two glycine residues on both Glu437 and Glu438 and one glycine residue on both Glu439 and Glu441. The number and relative abundance of glycylated isoforms of beta-tubulin in both cytoplasmic and axonemal microtubules were compared by MALDI MS.1 The abundance of the major glycylated isoforms in axonemal tubulin decreases regularly with glycylation levels from 6 to 19 whereas it drops abruptly in cytoplasmic tubulin with glycylation levels from 6 to 9. However, the polyglycine chains are similarly distributed on the four C-terminal glutamate residues of cytoplasmic and axonemal tubulin. The polyglycylation results in bulky C-terminal domains with negatively charged surfaces, all surrounding the microtubular structure.
Collapse
Affiliation(s)
- J Vinh
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Laboratoire de Neurobiologie, CNRS UMR 7637, Paris, France.
| | | | | | | | | | | | | |
Collapse
|
9
|
Rademaker GJ, Pergantis SA, Blok-Tip L, Langridge JI, Kleen A, Thomas-Oates JE. Mass spectrometric determination of the sites of O-glycan attachment with low picomolar sensitivity. Anal Biochem 1998; 257:149-60. [PMID: 9514784 DOI: 10.1006/abio.1997.2548] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A sensitive protocol for unambiguously and positively identifying O-glycosylation sites in glycopeptides is described, based on beta-elimination of the glycan chain(s) using NH4OH. On glycan elimination, NH3 is incorporated into the amino acid residue(s) to which the glycan(s) had been attached, to yield a modified amino acid residue having a distinct mass. Electrospray ionization collision-induced dissociation tandem mass spectrometry allows the released, modified peptide to be sequenced and the site(s) of the modified amino acid residue(s) to be identified. The protocol has been optimized using a series of structurally related O-glycopeptides, and standard conditions are recommended for handling unknowns. We demonstrate that site determination can be achieved using as little as 1 pmol of starting material.
Collapse
Affiliation(s)
- G J Rademaker
- Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | | | | | | | | | | |
Collapse
|
10
|
el-Shazley H, Newton RP, Harris FM, Brenton AG, Walton TJ, Restall CJ, Bayliss M, Wilkins A, Games DE, Langridge JI. Assay of adenylyl cyclase activity by quantitative mass spectrometry. Biochem Soc Trans 1996; 24:474S. [PMID: 8879018 DOI: 10.1042/bst024474s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- H el-Shazley
- School of Biological Sciences, University of Wales Swansea, U.K
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Newton RP, Evans AM, Langridge JI, Walton TJ, Harris FM, Brenton AG. Assay of adenosine 3',5'-cyclic monophosphate-dependent protein kinase activity by quantitative fast atom bombardment mass spectrometry. Anal Biochem 1995; 224:32-8. [PMID: 7710089 DOI: 10.1006/abio.1995.1005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [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] [Indexed: 01/26/2023]
Abstract
Cyclic AMP-dependent protein kinase is conventionally assayed by measuring the incorporation of radiolabeled phosphate into a histone substrate. Here the assay of the protein kinase is carried out by the positive-ion fast atom bombardment mass spectrometric analysis of the enzyme incubation mixture after the reaction has been terminated. The data obtained are in good agreement with those obtained from the conventional radiometric assay of the same kinase preparation. The inherent advantage of this mass spectrometric assay is the capacity for multiple component monitoring; in addition to the kinase activity, the ability of the enzyme to bind cyclic nucleotides, together with integral ATPase and phosphodiesterase activity, can also be estimated from the same spectra.
Collapse
Affiliation(s)
- R P Newton
- Biochemistry Group, School of Biological Sciences, University of Wales Swansea, United Kingdom
| | | | | | | | | | | |
Collapse
|
12
|
Langridge JI, McClure TD, el-Shakawi S, Fielding A, Schram KH, Newton RP. Gas chromatography/mass spectrometric analysis of urinary nucleosides in cancer patients; potential of modified nucleosides as tumour markers. Rapid Commun Mass Spectrom 1993; 7:427-434. [PMID: 8329765 DOI: 10.1002/rcm.1290070605] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Analysis of urine from cancer patients by capillary gas chromatography/mass spectrometry positively identified 14 urinary nucleosides including several modified nucleosides. Levels of the modified nucleosides 1-methyl-adenosine, 2-methylguanosine, N2,N2-dimethylguanosine and 1-methylinosine as well as the total nucleoside level were elevated in the urine when a malignant tumour was present; the levels of N2,N2-dimethylguanosine were found to correlate with the stage of the cancer.
Collapse
Affiliation(s)
- J I Langridge
- Biochemistry Research Group (SoBS), University College of Swansea, UK
| | | | | | | | | | | |
Collapse
|
13
|
Langridge JI, Brenton AG, Walton TJ, Harris FM, Newton RP. Analysis of cyclic nucleotide-related enzymes by continuous-flow fast-atom bombardment mass spectrometry. Rapid Commun Mass Spectrom 1993; 7:293-303. [PMID: 8387838 DOI: 10.1002/rcm.1290070407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Continuous-flow fast-atom bombardment mass spectrometry has been developed to directly monitor cyclic nucleotide (substrate) and its product levels from an on-going phosphodiesterase reaction. Analysis of cAMP and cCMP phosphodiesterase incubates have been performed where the temporal evolution of the enzymic reaction is monitored and the effect of enzyme concentration upon the rate of reaction determined. Quantitative data on the enzyme kinetics have been obtained, in the form of Lineweaver-Burke plots, that are shown to correlate well with well-established radiometric methods.
Collapse
Affiliation(s)
- J I Langridge
- School of Biological Sciences, University of Wales, Swansea, UK
| | | | | | | | | |
Collapse
|
14
|
Langridge JI, Walton TJ, Brenton AG, Harris FM, Ghosh D, Evans AM, Newton RP. Fast atom bombardment mass spectrometric analysis of cyclic nucleotides. Biochem Soc Trans 1992; 20:153S. [PMID: 1397544 DOI: 10.1042/bst020153s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J I Langridge
- Biochemistry Research Group, School of Biological Sciences, University College Swansea, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
15
|
Evans AM, Harris FM, Walton TJ, Brenton AG, Langridge JI, Khan JA, Newton RP. Determination of cyclic nucleotide-responsive protein kinase activity by quantitative fast atom bombardment mass spectrometry. Biochem Soc Trans 1992; 20:152S. [PMID: 1327905 DOI: 10.1042/bst020152s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- A M Evans
- Biochemistry Research Group, School of Biological Sciences, University College Swansea, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
16
|
Walton TJ, Langridge JI, Khan JA, Evans AM, Brenton AG, Ghosh D, Harris FM, Newton RP. Analysis of kinetic parameters of cyclic nucleotide phosphodiesterase systems by fast atom bombardment tandem mass spectrometry. Biochem Soc Trans 1991; 19:397S. [PMID: 1665433 DOI: 10.1042/bst019397s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- T J Walton
- School of Biological Sciences, University College of Swansea, UK
| | | | | | | | | | | | | | | |
Collapse
|