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Ramesh M, Raju B, Srinivas R, Sureshbabu VV, Vishwanatha TM, Hemantha HP. Characterization of Nα-Fmoc-protected dipeptide isomers by electrospray ionization tandem mass spectrometry (ESI-MS(n)): effect of protecting group on fragmentation of dipeptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1949-1958. [PMID: 21698678 DOI: 10.1002/rcm.5076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A series of positional isomeric pairs of Fmoc-protected dipeptides, Fmoc-Gly-Xxx-OY/Fmoc-Xxx-Gly-OY (Xxx=Ala, Val, Leu, Phe) and Fmoc-Ala-Xxx-OY/Fmoc-Xxx-Ala-OY (Xxx=Leu, Phe) (Fmoc=[(9-fluorenylmethyl)oxy]carbonyl) and Y=CH(3)/H), have been characterized and differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MS(n)). In contrast to the behavior of reported unprotected dipeptide isomers which mainly produce y(1)(+) and/or a(1)(+) ions, the protonated Fmoc-Xxx-Gly-OY, Fmoc-Ala-Xxx-OY and Fmoc-Xxx-Ala-OY yield significant b(1)(+) ions. These ions are formed, presumably with stable protonated aziridinone structures. However, the peptides with Gly- at the N-terminus do not form b(1)(+) ions. The [M+H](+) ions of all the peptides undergo a McLafferty-type rearrangement followed by loss of CO(2) to form [M+H-Fmoc+H](+). The MS(3) collision-induced dissociation (CID) of these ions helps distinguish the pairs of isomeric dipeptides studied in this work. Further, negative ion MS(3) CID has also been found to be useful for differentiating these isomeric peptide acids. The MS(3) of [M-H-Fmoc+H](-) of isomeric peptide acids produce c(1)(-), z(1)(-) and y(1)(-) ions. Thus the present study of Fmoc-protected peptides provides additional information on mass spectral characterization of the dipeptides and distinguishes the positional isomers.
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Affiliation(s)
- M Ramesh
- National Centre for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad 500 607, India
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Pingitore F, Tang Y, Kruppa GH, Keasling JD. Analysis of amino acid isotopomers using FT-ICR MS. Anal Chem 2007; 79:2483-90. [PMID: 17305312 DOI: 10.1021/ac061906b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluxes through known metabolic pathways and the presence of novel metabolic reactions are often determined by feeding isotopically labeled substrate to an organism and then determining the isotopomer distribution in amino acids in proteins. However, commonly used techniques to measure the isotopomer distributions require derivatization prior to analysis (gas chromatography/mass spectrometry (GC/MS)) or large sample sizes (nuclear magnetic resonance (NMR) spectroscopy). Here, we demonstrate the use of Fourier transform-ion cyclotron resonance mass spectrometry with direct infusion via electrospray ionization to rapidly measure the amino acid isotopomer distribution in a biomass hydrolysate of the soil bacterium Desulfovibrio vulgaris Hildenborough. By applying high front-end resolution for the precursor ion selection followed by sustained off-resonance irradiation collision-induced dissociation, it was possible to determine exactly and unambiguously the specific locations of the labeled atoms in the amino acids, which usually requires a combination of 2-D 13C NMR spectroscopy and GC/MS. This method should be generally applicable to all biomass samples and will allow more accurate determination of metabolic fluxes with less work and less sample.
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Affiliation(s)
- Francesco Pingitore
- Virtual Institute of Microbial Stress and Survival, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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3
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Harrison AG. Fragmentation reactions of protonated peptides containing glutamine or glutamic acid. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:174-187. [PMID: 12577284 DOI: 10.1002/jms.427] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A variety of protonated dipeptides and tripeptides containing glutamic acid or glutamine were prepared by electrospray ionization or by fast atom bombardment ionization and their fragmentation pathways elucidated using metastable ion studies, energy-resolved mass spectrometry and triple-stage mass spectrometry (MS(3)) experiments. Additional mechanistic information was obtained by exchanging the labile hydrogens for deuterium. Protonated H-Gln-Gly-OH fragments by loss of NH(3) and loss of H(2)O in metastable ion fragmentation; under collision-induced dissociation (CID) conditions loss of H-Gly-OH + CO from the [MH - NH(3)](+) ion forms the base peak C(4)H(6)NO(+) (m/z 84). Protonated dipeptides with an alpha-linkage, H-Glu-Xxx-OH, are characterized by elimination of H(2)O and by elimination of H-Xxx-OH plus CO to form the glutamic acid immonium ion of m/z 102. By contrast, protonated dipeptides with a gamma-linkage, H-Glu(Xxx-OH)-OH, do not show elimination of H(2)O or formation of m/z 102 but rather show elimination of NH(3), particularly in metastable ion fragmentation, and elimination of H-Xxx-OH to form m/z 130. Both the alpha- and gamma-dipeptides show formation of [H-Xxx-OH]H(+), with this reaction channel increasing in importance as the proton affinity (PA) of H-Xxx-OH increases. The characteristic loss of H(2)O and formation of m/z 102 are observed for the protonated alpha-tripeptide H-Glu-Gly-Phe-OH whereas the protonated gamma-tripeptide H-Glu(Gly-Gly-OH)-OH shows loss of NH(3) and formation of m/z 130 as observed for dipeptides with the gamma-linkage. Both tripeptides show abundant formation of the y(2)'' ion under CID conditions, presumably because a stable anhydride neutral structure can be formed. Under metastable ion conditions protonated dipeptides of structure H-Xxx-Glu-OH show abundant elimination of H(2)O whereas those of structure H-Xxx-Gln-OH show abundant elimination of NH(3). The importance of these reaction channels is much reduced under CID conditions, the major fragmentation mode being cleavage of the amide bond to form either the a(1) ion or the y(1)'' ion. Particularly when Xxx = Gly, under CID conditions the initial loss of NH(3) from the glutamine containing dipeptide is followed by elimination of a second NH(3) while the initial loss of H(2)O from the glutamic acid dipeptide is followed by elimination of NH(3). Isotopic labelling shows that predominantly labile hydrogens are lost in both steps. Although both [H-Gly-Glu-Gly-OH]H(+) and [H-Gly-Gln-Gly-OH]H(+) fragment mainly to form b(2) and a(2) ions, the latter also shows elimination of NH(3) plus a glycine residue and formation of protonated glycinamide. Isotopic labelling shows extensive mixing of labile and carbon-bonded hydrogens in the formation of protonated glycinamide.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
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Harrison AG. Effect of phenylalanine on the fragmentation of deprotonated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:1242-1249. [PMID: 12387331 DOI: 10.1016/s1044-0305(02)00455-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The fragmentation reactions of a variety of deprotonated dipeptides and tripeptides containing phenylalanine have been studied using energy-resolved collision-induced dissociation, isotopic labeling and MS/MS/MS experiments. The benzyl a-group has a substantial effect on the fragmentation reactions observed. When the phenylalanine is in the C-terminal position of dipeptides or tripeptides a major fragmentation reaction is elimination of neutral cinnamic acid to from a deprotonated amino acid amide (c1 ion) for dipeptides and a deprotonated dipeptide amide (c2 ion) for tripeptides. Fragmentation of the [M - H]- ions of tripeptides with phenylalanine in the central position also results in substantial formation of the deprotonated amide of the N-terminal amino acid residue. When the phenylalanine residue is in the N-terminal position elimination of C7H8 from the [M - H - CO2]- ion and formation of the benzyl anion become important fragmentation pathways. Sequence ions frequently observed are the y1 ions, "b2 ions and a3-Nt ions.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Ontario, Canada.
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Chass GA, Marai CNJ, Harrison AG, Csizmadia IG. Fragmentation Reactions of a2 Ions Derived From Deprotonated DipeptidesA Synergy Between Experiment and Theory. J Phys Chem A 2002. [DOI: 10.1021/jp0208891] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gregory A. Chass
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | | | - Alex G. Harrison
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Imre G. Csizmadia
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Harrison AG. Sequence-specific fragmentation of deprotonated peptides containing H or alkyl side chains. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:1-13. [PMID: 11142353 DOI: 10.1016/s1044-0305(00)00199-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The [M - H]- ions of a variety of di- to pentapeptides containing H or alkyl side chains have been prepared by electrospray ionization and low-energy collision-induced dissociation (CID) of the deprotonated species carried out in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. Using the nomenclature applied to the fragmentation of protonated peptides, deprotonated dipeptides fragment to give a2 ions (CO2 loss) and y1 ions, where the y1 ion has two fewer hydrogens than the y"1 ions formed from protonated peptides. Deprotonated tri- and tetrapeptides fragment to give primarily y1, c1, and "b2 ions, where the "b2 ion has two fewer hydrogens than the b2 ion observed for protonated peptides. More minor yields of y2, c2, and a2 ions also are observed. The a ion formed by loss of CO2 from the [M - H]- ion shows loss of the N-terminal residue for tripeptides and sequential loss of two amino acid residues from the N-terminus for tetrapeptides. The formation of c(n) ions and the sequential loss of N-terminus residues from the [M - H - CO2]- ion serves to sequence the peptide from the N-terminus, whereas the formation of y(n) ions serves to sequence the peptide from the C-terminus. It is concluded that low-energy CID of deprotonated peptides provides as much (or more) sequence information as does CID of protonated peptides, at least for those peptides containing H or alkyl side chains. Mechanistic aspects of the fragmentation reactions observed are discussed.
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Affiliation(s)
- A G Harrison
- Department of Chemistry, University of Toronto, Ontario, Canada.
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Harrison AG, Csizmadia IG, Tang TH, Tu YP. Reaction competition in the fragmentation of protonated dipeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:683-688. [PMID: 10862119 DOI: 10.1002/1096-9888(200006)35:6<683::aid-jms994>3.0.co;2-d] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A major low-energy fragmentation reaction of many protonated dipeptides involves cleavage of the amide bond resulting in formation of either the y(1)" ion or the a(1) ion. For a series of protonated dipeptides H-Val-Xxx-OH it is observed that log(y(1)"/a(1)) is a linear function of the proton affinity of the variable C-terminal amino acid. For the series of protonated dipeptides H-Xxx-Phe-OH log(a(1)/y(1)") gives a poor correlation with the proton affinity or gas-phase basicity of H-Xxx-OH. However, a good limited correlation of log(a(1)/y(1)") with the Taft-Topsom sigma(alpha) for the alkyl group is observed when Xxx is an aliphatic amino acid. It is proposed that fragmentation occurs by initial formation of a proton-bound complex of an aziridinone and an amino acid which may fragment to form either a protonated amino acid (y(1)") or an N-protonated aziridinone with the corresponding neutrals being an aziridinone and an amino acid. Ab initio calculations show that the N-protonated aziridinone is unstable and fragments by loss of CO to form the a(1) immonium ion. However, the proton-bound complex of an aziridinone and an amine base is a stable species which exists in a potential well. Copyright 2000 John Wiley & Sons, Ltd.
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Affiliation(s)
- AG Harrison
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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Gur EH, de Koning L, Nibbering N. The bimolecular gas-phase reaction of protonated alkyldipeptides with acetonylacetone. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0168-1176(97)00039-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Gatlin CL, Rao RD, Turecek F, Vaisar T. Carboxylate and amine terminus directed fragmentations in gaseous dipeptide complexes with copper (II) and diimine ligands formed by electrospray. Anal Chem 1996; 68:263-70. [PMID: 9027236 DOI: 10.1021/ac950884i] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Singly and doubly charged peptide complexes with copper(II) and 2,2'-bipyridyl (bpy) are formed in the gas phase by electrospraying water-methanol solutions containing the components. Collisionally activated dissociations at low kinetic energies of singly charged complexes of the [CuII(peptide-H)(bpy)].+ type provide information about the amino acid sequence for L-Phe-Leu, L-Leu-Phe, L-Phe-Pro, L-Pro-Phe, L-Phe-Met, L-Met-Phe, L-Ser-Phe, L-Asp-Phe, and L-His-Phe. Dissociations of doubly charged complexes of the [CuII(peptide)(bpy).2+ type also allow identification of the N- and C-terminal amino acid residues. Leucine and isoleucine residues are readily distinguished in L-Ala-Leu and L-Ala-Ile through dissociations of their Cu complexes. Ion dissociation mechanisms, as elucidated by deuterium labeling, are discussed.
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Affiliation(s)
- C L Gatlin
- Deartment of Chemistry, University of Washington, Seattle, 98195-1700, USA
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Kemp TJ, Read PA. Fast atom bombardment studies of amino acid and peptide complexes of the uranyl ion: ligand attachment, dissociation and fragmentation. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(95)04716-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bouchonnet S, Gonnord MF, Hoppilliard Y, Mauriac C. Fragmentations of dipeptides in plasma desorption mass spectrometry: new rules for the sequence elucidation of oligopeptides. BIOLOGICAL MASS SPECTROMETRY 1992; 21:576-84. [PMID: 1457471 DOI: 10.1002/bms.1200211109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
252Cf plasma desorption mass spectrometry is well suited for determining both composition and sequence of unknown small oligopeptides. A systematic study of a large number of dipeptides first leads to establishing common rules of fragmentation from positive ion mass spectra. These rules are then applied to the sequence elucidation of larger peptides.
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Affiliation(s)
- S Bouchonnet
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, Palaiseau, France
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12
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Kulik W, Heerma W. A reliable method for the amino acid sequence determination in tetrapeptides: A study on the positive and negative ion tandem mass spectra of tetrapeptides. ACTA ACUST UNITED AC 1991. [DOI: 10.1002/bms.1200200908] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Seidl R, Schaefer W. Preparative purification of dipeptidyl peptidase IV. PREPARATIVE BIOCHEMISTRY 1991; 21:141-50. [PMID: 1686804 DOI: 10.1080/10826069108018009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dipeptidyl-Peptidase IV was purified from pig kidney by ammonium sulfate fractionation, gel filtration, QAE-cellulose chromatography and affinity columns with Gly-Pro- and Concanavalin A-Sepharose. The specific activity of the purified enzyme is 41.8 units/mg. Polyacrylamide gel electrophoresis and silver staining show a single band. The enzyme preparation is free of aminopeptidase and dipeptidase activity, proved fluorimetrically and by gas chromatography/mass spectrometry. The most important procedure for removal of contaminating enzyme activities is a stepwise NaCl-gradient on a QAE-ZetaPrep ion exchange disk.
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Affiliation(s)
- R Seidl
- Max-Planck-Institute for Biochemistry, Martinsried
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Van Setten D, Kulik W, Heerma W. Isomeric tripeptides: A study on structure-spectrum relationship. ACTA ACUST UNITED AC 1990. [DOI: 10.1002/bms.1200190805] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Kulik W, Heerma W. Fast atom bombardment tandem mass spectrometry for amino acid sequence determination in tripeptides. BIOMEDICAL & ENVIRONMENTAL MASS SPECTROMETRY 1989; 18:910-7. [PMID: 2804437 DOI: 10.1002/bms.1200181011] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mass spectral information obtained from the spectra of 26 tripeptides was carefully studied. The data were obtained from their mass, metastable ion and collisional activation spectra. On the basis of the positive ion tandem mass spectra a simple and unambiguous method for the sequence determination of amino acids in tripeptides and Y3" ions is proposed. The use of negative ion spectra for sequence determination in tripeptides is evaluated.
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Affiliation(s)
- W Kulik
- Laboratory for Analytical Chemistry, University of Utrecht, The Netherlands
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