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Bagal D, Kast E, Cao P. Rapid Distinction of Leucine and Isoleucine in Monoclonal Antibodies Using Nanoflow LCMSn. Anal Chem 2016; 89:720-727. [DOI: 10.1021/acs.analchem.6b03261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhanashri Bagal
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
| | - Eddie Kast
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
| | - Ping Cao
- Discovery Attribute Sciences, Amgen, South San
Francisco, California 94080, United States
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2
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DeGraan-Weber N, Ashley DC, Keijzer K, Baik MH, Reilly JP. Factors Affecting the Production of Aromatic Immonium Ions in MALDI 157 nm Photodissociation Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:834-846. [PMID: 26926443 DOI: 10.1007/s13361-015-1329-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
Immonium ions are commonly observed in the high energy fragmentation of peptide ions. In a MALDI-TOF/TOF mass spectrometer, singly charged peptides photofragmented with 157 nm VUV light yield a copious abundance of immonium ions, especially those from aromatic residues. However, their intensities may vary from one peptide to another. In this work, the effect of varying amino acid position, peptide length, and peptide composition on immonium ion yield is investigated. Internal immonium ions are found to have the strongest intensity, whereas immonium ions arising from C-terminal residues are the weakest. Peptide length and competition among residues also strongly influence the immonium ion production. Quantum calculations provide insights about immonium ion structures and the fragment ion conformations that promote or inhibit immonium ion formation.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Daniel C Ashley
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Karlijn Keijzer
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 339-701, South Korea.
- Institute for Basic Science (IBS), Center for Catalytic Hydrocarbon Functionalizations, Daejeon, 339-701, South Korea.
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA.
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3
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Naresh Chary V, Sudarshana Reddy B, Kumar CD, Srinivas R, Prabhakar S. Characterization of N,N-dimethyl amino acids by electrospray ionization-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:771-781. [PMID: 26259661 DOI: 10.1002/jms.3588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
Methylation is an essential metabolic process for a number of critical reactions in the body. Methyl groups are involved in the healthy function of the body life processes, by conducting methylation process involving specific enzymes. In these processes, various amino acids are methylated, and the occurrence of methylated amino acids in nature is diverse. Nowadays, mass-spectrometric-based identification of small molecules as biomarkers for diseases is a growing research. Although all dimethyl amino acids are metabolically important molecules, mass spectral data are available only for a few of them in the literature. In this study, we report synthesis and characterization of all dimethyl amino acids, by electrospray ionization-tandem mass spectrometry (MS/MS) experiments on protonated molecules. The MS/MS spectra of all the studied dimethyl amino acids showed preliminary loss of H2O + CO to form corresponding immonium ions. The other product ions in the spectra are highly characteristic of the methyl groups on the nitrogen and side chain of the amino acids. The amino acids, which are isomeric and isobaric with the studied dimethyl amino acids, gave distinctive MS/MS spectra. The study also included MS/MS analysis of immonium ions of dimethyl amino acids that provide information on side chain structure, and it is further tested to determine the N-terminal amino acid of the peptides.
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Affiliation(s)
- V Naresh Chary
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - B Sudarshana Reddy
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Ch Dinesh Kumar
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - R Srinivas
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - S Prabhakar
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
- Academy of Scientific and Innovative Research, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
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4
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WANG Y, LI SM, HE MW. Fragmentation Characteristics and Utility of Immonium Ions for Peptide Identification by MALDI-TOF/TOF-Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(14)60752-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Parthasarathi R, He Y, Reilly JP, Raghavachari K. New Insights into the Vacuum UV Photodissociation of Peptides. J Am Chem Soc 2010; 132:1606-10. [DOI: 10.1021/ja907975v] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Yi He
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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6
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Trelle MB, Jensen ON. Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry. Anal Chem 2008; 80:3422-30. [PMID: 18338905 DOI: 10.1021/ac800005n] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tandem mass spectrometry (MS/MS) is a powerful tool for characterization of post-translationally modified proteins, including epsilon-N-acetyllysine-containing species. Previous reports indicate that epsilon-N-acetyllysine immonium ions are useful marker ions for peptides containing epsilon-N-acetyllysine, but the specificity and sensitivity of these ions for assignment of lysine acetylation by MS/MS have not been studied in detail. We investigated MS/MS data sets of 172 epsilon-N-acetyllysine tryptic peptides and 268 nonacetylated tryptic peptides to establish the utility and reliability of epsilon-N-acetyllysine immonium ions for identification and validation of acetylated peptides. Our analysis shows that the immonium ion at m/z 143 lacks specificity for lysine-acetylated peptides, whereas the derivative at m/z 126 is highly specific (98.1%). We also studied the positional effect of the epsilon-N-acetyllysine on the intensity of observed acetyllysine immonium ions. We observed an increase in acetyllysine immonium ion intensities when the acetylated lysine was N-terminally positioned in the peptide as compared to internal positions. Based on these observations we propose a validation scheme for unambiguous assignment of acetyllysine-containing peptides by MS/MS. Our analysis of epsilon-N-acetyllysine immonium ions provide a framework for investigation of MS/MS marker ion specificity and sensitivity that can be applied in studies of other types of post-translational modifications.
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Affiliation(s)
- Morten B Trelle
- Department of Biochemistry and Molecular Biology and Centre for Epigenetics, University of Southern Denmark, DK-5230 Odense M, Denmark
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7
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Herrmann KA, Somogyi A, Wysocki VH, Drahos L, Vekey K. Combination of sustained off-resonance irradiation and on-resonance excitation in FT-ICR. Anal Chem 2005; 77:7626-38. [PMID: 16316170 PMCID: PMC4543312 DOI: 10.1021/ac050828+] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry is becoming more widely used among the mass spectrometric techniques and has excellent figures of merit. Ion activation and fragmentation via sustained off-resonance irradiation (SORI) collision-induced dissociation (CID) is commonly used in FT-ICR. However, one of the limitations of SORI-CID is that only low-energy processes are typically observed in the product ion spectra. Here we present another option for performing CID in FT-ICR, a combination of SORI and on-resonance excitation (RE), termed SORI-RE. In comparison to SORI, this method produces more abundant ions resulting from higher energy fragmentation pathways. The result is the observation of a significant abundance of both higher and lower energy fragmentation pathways in the same mass spectrum. The comparison of SORI, RE, and SORI-RE spectra may lead to mechanistic insights as the relative abundances of certain fragment ions change as a function of internal energy deposition. This technique is simple to incorporate in existing instruments, does not require hardware or software modification, and requires only an additional 20-40 ms acquisition time. The technique is illustrated for a peptide (YGGFL), two disaccharides differing in the position of the glycosidic linkage (2alpha-mannobiose, 3alpha-mannobiose), an oligosaccharide (Alditol XT), a small protein (ubiquitin), and an inorganic cation (UO2+). Examples of higher energy fragmentation pathways enhanced by SORI-RE include the formation of immonium ions and oligosaccharide cross-ring cleavages.
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Affiliation(s)
| | - Arpad Somogyi
- University of Arizona, Department of Chemistry, Tucson, Arizona, USA
| | - Vicki H. Wysocki
- University of Arizona, Department of Chemistry, Tucson, Arizona, USA
| | - Laszlo Drahos
- Institute of Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, H-1025, Pusztaszeri u. 59-67, Budapest, Hungary
| | - Karoly Vekey
- Institute of Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, H-1025, Pusztaszeri u. 59-67, Budapest, Hungary
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8
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Wieghaus A, Schmidt L, Popova AM, Komarov VV, Jungclas H. Grazing incidence surface-induced dissociation of protonated peptides generated by matrix-assisted laser desorption/ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:1654-1661. [PMID: 10962486 DOI: 10.1002/1097-0231(20000930)14:18<1654::aid-rcm76>3.0.co;2-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The grazing incidence surface-induced dissociation (GI-SID) of various protonated peptides with typical kinetic energies of 350 eV was investigated. Peptide ions were generated by matrix-assisted laser desorption/ionization (MALDI) using delayed extraction. The collision target surfaces used were aluminum and a liquid film of perfluorinated hydrocarbons. All peptides studied in these experiments showed enhanced fragment ion yields at grazing incidence (GI-SID effect) as observed in our former experiments with other precursor ion types. In general the GI-SID spectra exhibit N-terminal a(1)-type fragment ions, immonium ions and side-chain fragment ions in the low mass-to-charge region. Fragment ion series of the peptide backbone were not observed, which are typical and abundant in the spectra of established fragmentation techniques like collision-induced dissociation, MALDI post-source decay or surface-induced dissociation at steeper angles. The potential of the GI-SID process to yield useful information for primary structure determination of peptides is indicated by the observed differences in the GI-SID spectra of the isomeric dipeptides LR and IR.
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Affiliation(s)
- A Wieghaus
- Department of Chemistry, Philipps-University Marburg, D-35032 Marburg, Germany
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Vachet RW, Ray KL, Glish GL. Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1998; 9:341-344. [PMID: 9879364 DOI: 10.1016/s1044-0305(98)00008-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Stored waveform inverse Fourier transform and double resonance techniques have been used in conjunction with a quadrupole ion trap to study the dissociation patterns of peptide ions. These experiments provide insight into the origin of individual product ions in an MS/MS spectrum. Results show for a series of leucine enkephalin analogues with five amino acid residues that the b4 ion is the main product ion through which many other product ions arise. It was also observed that the percentage of the a4 product ions that are formed directly from the protonated molecule (M + H)+ depends on the nature of the fourth amino acid residue. In addition, it was determined that in the peptides studies here lower series b ions (e.g., b3) arise from direct dissociation of higher series b ions (e.g., b4) only about 50% of the time.
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Affiliation(s)
- R W Vachet
- Department of Chemistry, University of North Carolina, Chapel Hill 27599, USA
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10
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Morgan DG, Bursey MM. A linear free-energy correlation in the low-energy tandem mass spectra of protonated tripeptides Gly-Gly-Xxx. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/oms.1210290705] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Falick AM, Hines WM, Medzihradszky KF, Baldwin MA, Gibson BW. Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1993; 4:882-893. [PMID: 24227532 DOI: 10.1016/1044-0305(93)87006-x] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/1993] [Revised: 07/06/1993] [Accepted: 07/07/1993] [Indexed: 06/02/2023]
Abstract
High-energy collision-induced dissociation (CID) mass spectrometry provides a rapid and sensitive means for determining the primary sequence of peptides. The low-mass region (below mass 300) of a large number of tandem CID spectra of peptides has been analyzed. This mass region contains several types of informative fragment ions, including dipeptide ions, immonium ions, and other related ions. Useful low-mass ions are also present in negative-ion CID spectra. Immonium ions (general structure [H2N=CH-R](+), where R is the amino acid side chain) and related ions characteristic of specific amino acid residues give information as to the presence or absence of these residues in the peptide being analyzed. Tables of observed immonium and reiated ions for the 20 standard amino acids and for a number of modified amino acids are presented. A database consisting of 228 high-energy CID spectra of peptides has been established, and the frequency of occurrence of various ions indicative of specific ammo acid residues has been determined. Two model computer-aided schemes for analysis of the ammo-acid content of unknown peptides have been developed and tested against the database.
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Affiliation(s)
- A M Falick
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, 91143-0446, San Francisco, California
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