1
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Armentrout PB. Energetics and mechanisms for decomposition of cationized amino acids and peptides explored using guided ion beam tandem mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:928-953. [PMID: 34392555 DOI: 10.1002/mas.21723] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Fragmentation studies of cationized amino acids and small peptides as studied using guided ion beam tandem mass spectrometry (GIBMS) are reviewed. After a brief examination of the key attributes of the GIBMS approach, results for a variety of systems are examined, compared, and contrasted. Cationization of amino acids, diglycine, and triglycine with alkali cations generally leads to dissociations in which the intact biomolecule is lost. Exceptions include most lithiated species as well as a few examples for sodiated and one example for potassiated species. Like the lithiated species, cationization by protons leads to numerous dissociation channels. Results for protonated glycine, cysteine, asparagine, diglycine, and a series of tripeptides are reviewed, along with the thermodynamic consequences that can be gleaned. Finally, the important physiological process of the deamidation of asparagine (Asn) residues is explored by the comparison of five dipeptides in which the C-terminal partner (AsnXxx) is altered. The GIBMS thermochemistry is shown to correlate well with kinetic results from solution phase studies.
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Affiliation(s)
- P B Armentrout
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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2
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Rong C, Heidar-Zadeh F, Miranda-Quintana RA, Liu S, Ayers PW. Ranking the energy minima of the 20 natural amino acids using conceptual tools. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02929-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Logerot E, Cazals G, Memboeuf A, Enjalbal C. Revealing C-terminal peptide amidation by the use of the survival yield technique. Anal Biochem 2022; 655:114823. [DOI: 10.1016/j.ab.2022.114823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
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4
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Fernandez B, Armengaud J, Subra G, Enjalbal C. MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bernard Fernandez
- IBMM Université de Montpellier, CNRS, ENSCM 34293 Montpellier France
- Université Paris-Saclay, CEA, INRAE Département Médicaments et Technologies pour la Santé (DMTS) SPI 30200 Bagnols-sur-Cèze France
- Present address: CIRAD, UMR ASTRE 34398 Montpellier France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE Département Médicaments et Technologies pour la Santé (DMTS) SPI 30200 Bagnols-sur-Cèze France
| | - Gilles Subra
- IBMM Université de Montpellier, CNRS, ENSCM 34293 Montpellier France
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5
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Lee JU, Lee ST, Park CR, Moon B, Kim HI, Oh HB. TEMPO-Assisted Free-Radical-Initiated Peptide Sequencing Mass Spectrometry for Ubiquitin Ions: An Insight on the Gas-Phase Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:471-481. [PMID: 35099967 DOI: 10.1021/jasms.1c00313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
TEMPO ((2,2,6,6-tetramethylpiperidine-1-yl)oxyl)-assisted free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) is applied to the top-down tandem mass spectrometry of guanidinated ubiquitin (UB(Gu)) ions, i.e., p-TEMPO-Bn-Sc-guanidinated ubiquitin (UBT(Gu)), to shed a light on gas-phase ubiquitin conformations. Thermal activation of UBT(Gu) ions produced protein backbone fragments of radical character, i.e., a-/x- and c-/z-type fragments. It is in contrast to the collision-induced dissociation (CID) results for UB(Gu), which dominantly showed the specific charge-remote CID fragments of b-/y-type at the C-terminal side of glutamic acid (E) and aspartic acid (D). The transfer of a radical "through space" was mainly observed for the +5 and +6 UBT(Gu) ions. This provides the information about folding/unfolding and structural proximity between the positions of the incipient benzyl radical site and fragmented sites. The analysis of FRIPS MS results for the +5 charge state ubiquitin ions shows that the +5 charge state ubiquitin ions bear a conformational resemblance to the native ubiquitin (X-ray crystallography structure), particularly in the central sequence region, whereas some deviations were observed in the unstable second structure region (β2) close to the N-terminus. The ion mobility spectrometry results also corroborate the FRIPS MS results in terms of their conformations (or structures). The experimental results obtained in this study clearly demonstrate a potential of the TEMPO-assisted FRIPS MS as one of the methods for the elucidation of the overall gas-phase protein structures.
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Affiliation(s)
- Jae-Ung Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Sang Tak Lee
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Chae Ri Park
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Bongjin Moon
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
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6
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Goyal R, Jerath G, Chandrasekharan A, Christian Y, Kumar TRS, Ramakrishnan V. Molecular hybridization combining tumor homing and penetrating peptide domains for cellular targeting. Drug Deliv Transl Res 2021; 12:1285-1292. [PMID: 34333729 DOI: 10.1007/s13346-021-01035-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2021] [Indexed: 10/20/2022]
Abstract
A complete peptide-based drug delivery unit has been designed with a tumor homing domain chemically linked to a syndiotactic cell-penetrating domain. The designed peptides were synthesized, characterized, and tested in vitro for cellular uptake and cytotoxicity evaluation. The differential uptake, cellular internalization, negligible hemotoxicity, selective toxicity to MDA-MB-231 breast cancer cells, and the superior penetration in three-dimensional MDA-MB-231 tumorospheres confirm their utility as a promising delivery vector.
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Affiliation(s)
- Ruchika Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Gaurav Jerath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Aneesh Chandrasekharan
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program-1, Thiruvananthapuram, 695014, Kerala, India
| | - Yvonne Christian
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - T R Santhosh Kumar
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program-1, Thiruvananthapuram, 695014, Kerala, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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7
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Guan S, Bythell BJ. Size Dependent Fragmentation Chemistry of Short Doubly Protonated Tryptic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1020-1032. [PMID: 33779179 DOI: 10.1021/jasms.1c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tandem mass spectrometry of electrospray ionized multiply charged peptide ions is commonly used to identify the sequence of peptide(s) and infer the identity of source protein(s). Doubly protonated peptide ions are consistently the most efficiently sequenced ions following collision-induced dissociation of peptides generated by tryptic digestion. While the broad characteristics of longer (N ≥ 8 residue) doubly protonated peptides have been investigated, there is comparatively little data on shorter systems where charge repulsion should exhibit the greatest influence on the dissociation chemistry. To address this gap and further understand the chemistry underlying collisional-dissociation of doubly charged tryptic peptides, two series of analytes ([GxR+2H]2+ and [AxR+2H]2+, x = 2-5) were investigated experimentally and with theory. We find distinct differences in the preference of bond cleavage sites for these peptides as a function of size and to a lesser extent composition. Density functional calculations at two levels of theory predict that the threshold relative energies required for bond cleavages at the same site for peptides of different size are quite similar (for example, b2-yN-2). In isolation, this finding is inconsistent with experiment. However, the predicted extent of entropy change of these reactions is size dependent. Subsequent RRKM rate constant calculations provide a far clearer picture of the kinetics of the competing bond cleavage reactions enabling rationalization of experimental findings. The M06-2X data were substantially more consistent with experiment than were the B3LYP data.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 307 Chemistry Building, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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Guan S, Rabus JM, Maître P, Bythell BJ. Gas-Phase Dissociation Chemistry of Deprotonated RGD. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:55-63. [PMID: 32267154 DOI: 10.1021/jasms.0c00074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We investigate the structure and dissociation pathways of the deprotonated amphoteric peptide arginylglycylasparic acid, [RGD-H]-. We model the pertinent gas-phase structures and fragmentation chemistry of the precursor anions and predominant sequence-informative bond cleavages (b2+H2O, c2, and z1 peaks) and compare these predictions to our tandem mass spectra and infrared spectroscopy experiments. Formation of the b2+H2O anions requires rate-limiting intramolecular back biting to cleave the second amide bond and generate an anhydride structure. Facile cleavage of the newly formed ester bond with concerted expulsion of a cyclic anhydride neutral generates the product structure. IR spectroscopy supports this b2+H2O anion having structures that are essentially identical to C-terminally deprotonated arginylglycine, [RG-H]-. Formation of the c2 anion is predicted to require concerted expulsion of CO2 from the aspartyl side chain carboxylate and cleavage of the N-Calpha bond to produce a proton-bound dimer of arginylglycinamide and acrylate. Proton transfers within the dimer then enable predominant detection of a c2 anion with the negative charge nominally on the central, glycine nitrogen (amidate structure) as the proton affinity of this structure is predicted to be lower than acrylate by ∼27 kJ mol-1. Alternate means of cleaving the same N-Calpha bond produce deprotonated cis-1,4-dibut-2-enoic acid z1 anion structures. These lowest energy processes involve C-H proton mobilization from the aspartyl side chain prior to N-Calpha bond cleavage consistent with proposals from the literature.
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Affiliation(s)
- Shanshan Guan
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Jordan M Rabus
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
| | - Philippe Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, Ohio University, 391 Clippinger Laboratories, Athens, Ohio 45701, United States
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, 1 University Boulevard, St. Louis, Missouri 63121, United States
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9
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Logerot E, Enjalbal C. Dissociation Pattern of Sodiated Amide Peptides as a Tool for De Novo Sequencing. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2328-2337. [PMID: 33064467 DOI: 10.1021/jasms.0c00269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As part of the de novo sequencing issue, new approaches have to be found to sequence small natural peptides (<15-20 residues), which often present amino acid compositions, inducing merely singly charged species, that are quite difficult to thoroughly fragment under low-energy activation conditions in MS/MS experiments. Cationization by alkali metals, like Na+, followed by collision-induced dissociations (CID) or the postsource metastable decay (PSD) of such cationized molecular ions was found to improve the sequence coverage of native peptides through the formation of [bn-1 + Na + OH]+ ions issued from C-terminal residue exclusion. Concerned by the identification of peptides with a C-terminal amide, the fragmentation pattern of their sodiated molecular ions was investigated. In contrast to the peptides featuring unmodified C-termini, the C-terminal loss did not occur, with the amide function triggering different fragmentation pathways. However, several residues, such as aspartic acid (D), glutamic acid (E), and arginine (R), influenced the dissociation of fixed-charge sodiated ions similarly to protonated peptides; more surprisingly, serine (S), threonine (T), and tyrosine (Y), which exhibit a hydroxyl function on their side chains, showed a very peculiar behavior that could help de novo peptide sequencing.
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Affiliation(s)
- Elodie Logerot
- IBMM, CNRS, ENSCM, University of Montpellier, 34095 Montpellier, France
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10
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Thermal dissociation of the singly protonated Arginine: Competition between side-chain and backbone fragmentation. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Cautereels J, Van Hee N, Chatterjee S, Van Alsenoy C, Lemière F, Blockhuys F. QCMS 2 as a new method for providing insight into peptide fragmentation: The influence of the side-chain and inter-side-chain interactions. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4446. [PMID: 31652378 DOI: 10.1002/jms.4446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/12/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
The identification of peptides and proteins from tandem mass spectra is a difficult task and multiple tools have been developed to aid this identification. We present a new method called quantum chemical mass spectrometry for materials science (QCMS2 ), which is based on quantum chemical calculations of bond orders, reaction, and transition-state energies at the DFT/B3LYP/6-311+G* level of theory. The method was used to describe the fragmentation pathways of five X-His-Ser tripeptides with X = Asn, Asp, Glu, Ser, and Trp, thereby focusing on the influence of the side chain and inter-side-chain interactions on the fragmentation. The main features in the mass spectra of the five tripeptides were correctly reproduced, and a number of fragments were assigned to fragmentations involving the side chain and the influence of inter-side-chain interactions. Product ion spectra were recorded to evaluate the capabilities and limitations of QCMS2 and a number of conventional tools.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Nils Van Hee
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Sneha Chatterjee
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | - Filip Lemière
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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12
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Cautereels J, Giribaldi J, Enjalbal C, Blockhuys F. Quantum chemical mass spectrometry: Ab initio study of b 2 -ion formation mechanisms for the singly protonated Gln-His-Ser tripeptide. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8778. [PMID: 32144813 DOI: 10.1002/rcm.8778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Both amide bond protonation triggering peptide fragmentations and the controversial b2 -ion structures have been subjects of intense research. The involvement of histidine (H), with its imidazole side chain that induces specific dissociation patterns involving inter-side-chain (ISC) interactions, in b2 -ion formation was investigated, focusing on the QHS model tripeptide. METHODS To identify the effect of histidine on fragmentations issued from ISC interactions, QHS was selected for a comprehensive analysis of the pathways leading to the three possible b2 -ion structures, using quantum chemical calculations performed at the DFT/B3LYP/6-311+G* level of theory. Electrospray ionization ion trap mass spectrometry allowed the recording of MS2 and MS3 tandem mass spectra, whereas the Quantum Chemical Mass Spectrometry for Materials Science (QCMS2 ) method was used to predict fragmentation patterns. RESULTS Whereas it is very difficult to differentiate among protonated oxazolone, diketopiperazine, or lactam b2 -ions using MS2 and MS3 mass spectra, the calculations indicated that the QH b2 -ion (detected at m/z 266) is probably a mixture of the lactam and oxazolone structures formed after amide nitrogen protonation, making the formation of diketopiperazine less likely as it requires an additional step for its formation. CONCLUSIONS In contrast to glycine-histidine-containing b2 -ions, known to be issued from the backbone-imidazole cyclization, we found that interactions between the side chains were not obvious to perceive, neither from a thermodynamics nor from a fragmentation perspective, emphasizing the importance of the whole sequence on the dissociation behavior usually demonstrated from simple glycine-containing tripeptides.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | | | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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13
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Ren J, Tian Y, Hossain E, Ho JS, Mann YS, Zhang Y, Browne MD, Connolly MD, Zuckermann RN. Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids. Biopolymers 2020; 111:e23358. [DOI: 10.1002/bip.23358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Jianhua Ren
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuan Tian
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Ekram Hossain
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Joshua S. Ho
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yadwinder S. Mann
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuntao Zhang
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Browne
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Connolly
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
| | - Ronald N. Zuckermann
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
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14
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Wang Y, Nakajima E, Okamura Y, Wang D, Okumura N, Takao T. Metastable decomposition at the peptide C-terminus: Possible use in protein identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8734. [PMID: 32031718 DOI: 10.1002/rcm.8734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 12/14/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE The b n-1 ion of a peptide, as well as a [b n-1 + 18] ion, can be observed not only as normal product ions, but also as prominent metastable ions in a reflectron-embedded matrix-assisted laser desorption ionization time-of-flight spectrometer. The m/z values for the peaks are slightly shifted compared with the ordinary product ions and appear as relatively broad peaks, which permits them to be discriminated from other ions. METHODS A standard protein mixture and gel-derived proteins digested with LysN protease, which cleaves peptide linkages in proteins at the N-terminal side of Lys residues, were examined. The collected data were used for protein identification using in-house software, iD-plus (http://coco.protein.osaka-u.ac.jp/id-plus/), which was developed for searching for proteins in the peptide database, based on enzyme specificity (N-terminal Lys in this study), peptide masses and C-terminal amino acids. RESULTS The b n-1 as well as [b n-1 + 18] ions were observed as broad ion peaks for all of the peptides (86 peptides) examined in this study. In silico calculations using the database of LysN digested peptides (11 969 470), created from 553 941 protein sequences (SwissProt: 2017_03), indicate that the use of no less than four peptides permits a protein to be identified without the need of any probability-based scoring. CONCLUSIONS The preference for b n-1 ion formation is probably due to the higher propensity of the C-terminal peptide bond to be cleaved than other internal bonds. The fact that such C-terminal fragmentation takes place for most of the peptides examined suggests that the use of an N-terminal specific enzyme would allow the C-terminal amino acids to be more reliably read out than other internal sequences, information that could be efficiently used for protein identification.
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Affiliation(s)
- Yang Wang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Etsuko Nakajima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Yoshihito Okamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Danqing Wang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
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15
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Gu M, Zhang J, Hase WL, Yang L. Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine. ACS OMEGA 2020; 5:1463-1471. [PMID: 32010819 PMCID: PMC6990424 DOI: 10.1021/acsomega.9b03091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/25/2019] [Indexed: 05/31/2023]
Abstract
Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H+) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000-3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1+, a2+-x0, and b1-y1+. Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H+ unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules.
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Affiliation(s)
- Meng Gu
- MIIT
Key Laboratory of Critical Materials Technology for New Energy Conversion
and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Jiaxu Zhang
- MIIT
Key Laboratory of Critical Materials Technology for New Energy Conversion
and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79401, United States
| | - Li Yang
- MIIT
Key Laboratory of Critical Materials Technology for New Energy Conversion
and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
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16
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Abutokaikah MT, Gnawali GR, Frye JW, Stump CM, Tschampel J, Murphy MJ, Lachance ES, Guan S, Spilling CD, Bythell BJ. Leaving Group Effects in a Series of Electrosprayed C cH hN 1 Anthracene Derivatives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2306-2317. [PMID: 31399941 DOI: 10.1007/s13361-019-02298-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
We investigate the gas-phase structures and fragmentation pathways of model compounds of anthracene derivatives of the general formula CcHhN1 utilizing tandem mass spectrometry and computational methods. We vary the substituent alkyl chain length, composition, and degree of branching. We find substantial experimental and theoretical differences between the linear and branched congeners in terms of fragmentation thresholds, available pathways, and distribution of products. Our calculations predict that the linear substituents initially isomerize to form lower energy branched isomers prior to loss of the alkyl substituents as alkenes. The rate-determining chemistry underlying these related processes is dominated by the ability to stabilize the alkene loss transition structures. This task is more effectively undertaken by branched substituents. Consequently, analyte lability systematically increased with degree of branching (linear < secondary < tertiary). The resulting anthracen-9-ylmethaniminium ion generated from these alkene loss reactions undergoes rate-limiting proton transfer to enable expulsion of either hydrogen cyanide or CNH. The combination of the differences in primary fragmentation thresholds and degree of radical-based fragmentation processes provide a potential means of distinguishing compounds that contain branched alkyl chain substituents from those with linear ones.
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Affiliation(s)
- Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Giri R Gnawali
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Joseph W Frye
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Curtis M Stump
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - John Tschampel
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Matthew J Murphy
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Eli S Lachance
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Christopher D Spilling
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
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17
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Lin YF, Yousef EN, Torres E, Truong L, Zahnow JM, Donald CB, Qin Y, Angel LA. Weak Acid-Base Interactions of Histidine and Cysteine Affect the Charge States, Tertiary Structure, and Zn(II)-Binding of Heptapeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2068-2081. [PMID: 31332742 DOI: 10.1007/s13361-019-02275-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Zinc fingers are proteins that are characterized by the coordination of zinc ions by an amino acid sequence that commonly contains two histidines and two cysteines (2His-2Cys motif). Investigations of oligopeptides that contain the 2His-2Cys motif, e.g., acetyl-His1-Cys2-Gly3-Pro4-Tyr5-His6-Cys7, have discovered they exhibit pH-dependent Zn(II) chelation and have redox activities with Cu(I/II), forming a variety of metal complexes. To further understand how these 2His-2Cys oligopeptides bind these metal ions, we have undertaken a series of ion mobility-mass spectrometry and B3LYP/LanL2DZ computational studies of structurally related heptapeptides. Starting with the sequence above, we have modified the potential His, Cys, or C-terminus binding sites and report how these changes in primary structure affect the oligopeptides positive and negative charge states, conformational structure, collision-induced breakdown energies, and how effectively Zn(II) binds to these sequences. The results show evidence that the weak acid-base properties of Cys-His are intrinsically linked and can result in an intramolecular salt-bridged network that affects the oligopeptide properties.
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Affiliation(s)
- Yu-Fu Lin
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Enas N Yousef
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Efren Torres
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Linh Truong
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - James M Zahnow
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Cole B Donald
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Ying Qin
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce, 2600 S Neal St, Commerce, TX, 75428, USA.
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18
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Smith ZM, Wang X, Scheerer JR, Martens J, Berden G, Oomens J, Steinmetz V, Somogyi A, Wysocki V, Poutsma JC. Spectroscopic Evidence for Lactam Formation in Terminal Ornithine b 2+ and b 3+ Fragment Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1565-1577. [PMID: 31183839 PMCID: PMC6697629 DOI: 10.1007/s13361-019-02244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Infrared multiple photon dissociation action spectroscopy was performed on the AlaOrn b2+ and AlaAlaOrn b3+ fragment ions from ornithine-containing tetrapeptides. Infrared spectra were obtained in the fingerprint region (1000-2000 cm-1) using the infrared free electron lasers at the Centre Laser Infrarouge d'Orsay (CLIO) facility in Orsay, France, and the free electron lasers for infrared experiments (FELIX) facility in Nijmegen, the Netherlands. A novel terminal ornithine lactam AO+ b2+ structure was synthesized for experimental comparison and spectroscopy confirms that the b2+ fragment ion from AOAA forms a lactam structure. Comparison of experimental spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory shows that AO+ b2+ forms a terminal lactam protonated either on the lactam carbonyl oxygen or the N-terminal nitrogen atom. Several low-lying conformers of these isomers are likely populated following IRMPD dissociation. Similarly, a comparison of the experimental IRMPD spectrum with calculated spectra shows that AAO+ b3+-ions also adopt a lactam structure, again with multiple different protonation sites, during fragmentation. This study provides spectroscopic confirmation for the lactam cyclization proposed for the "ornithine effect" and represents an alternative bn+ structure to the oxazolone and diketopiperazine/macrocycle structures most often formed.
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Affiliation(s)
- Zachary M Smith
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Xiye Wang
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Jonathan R Scheerer
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Vincent Steinmetz
- Laboratorie de Chimie Physique, CNRS UMR 8000, Université Paris, 91405, Orsay, France
| | - Arpad Somogyi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210-1173, USA
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210-1173, USA
| | - John C Poutsma
- Department of Chemistry, The College of William & Mary, Williamsburg, VA, 23187-8795, USA.
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19
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Huo D, Qin T, Zu L. Energetic switch of the proline effect in collision-induced dissociation of singly and doubly protonated peptide Ala-Ala-Arg-Pro-Ala-Ala. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:55-65. [PMID: 30426600 DOI: 10.1002/jms.4311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 10/30/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Suppression of the selective cleavage at N-terminal of proline is observed in the peptide cleavage by proteolytic enzyme trypsin and in the fragment ion mass spectra of peptides containing Arg-Pro sequence. An insight into the fragmentation mechanism of the influence of arginine residue on the proline effect can help in prediction of mass spectra and in protein structure analysis. In this work, collision-induced dissociation spectra of singly and doubly charged peptide AARPAA were studied by ESI MS/MS and theoretical calculation methods. The proline effect was evaluated by comparing the experimental ratio of fragments originated from cleavage of different amide bonds. The results revealed that the backbone amide bond cleavage was selected by the energy barrier height of the fragmentation pathway although the strong proton affinity of the Arg side chain affected the stereostructure of the peptide and the dissociation mechanism. The thermodynamic stability of the fragment ions played a secondary role in the abundance ratio of fragments generated via different pathways. Fragmentation studies of protonated peptide AACitPAA supported the energy-dependent hypothesis. The results provide an explanation to the long-term arguments between the steric conflict and the proton mobility mechanisms of proline effect.
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Affiliation(s)
- Dayujia Huo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Tai Qin
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Lily Zu
- College of Chemistry, Beijing Normal University, Beijing, China
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20
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DeGraan-Weber N, Zhao B, Reilly JP. Unusual fragmentation of derivatized cysteine-containing peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1491-1496. [PMID: 29874404 PMCID: PMC6430700 DOI: 10.1002/rcm.8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Modification of cysteines by aminoethylation results in side chains similar to those of lysine. Trypsin cleaves at this modified residue and this labeling method can facilitate the analysis of proteins, specifically antibodies. In this work, the ability to identify peptides containing aminoethylated cysteines is investigated through digestion, covalent labeling, and low-energy ion fragmentation. METHODS A prototype antibody was reduced, aminoethylated, and digested with either Lys-N or Glu-C. The resulting peptides were amidinated with SMTA and analyzed by PSD in a MALDI-TOF/TOF mass spectrometer or by CID in an ESI ion trap/orbitrap mass spectrometer. RESULTS PSD and CID fragmentation of peptides with an amidinated aminoethylated cysteine can produce an intense characteristic loss from this modified residue. A neutral loss of 118 Da or charged loss of 119 Da is observed when peptides have low charges. This fragment can form when the cysteine is located in any position in the peptide. The rationalization for this ion is that the amidino group can be initially neutral or protonated and initiates fragmentation. CONCLUSIONS The combination of a dual-labeling technique and low-energy fragmentation produces an abundant diagnostic ion for the analysis of cysteine-containing peptides. These 118 and 119 Da losses are observed when protons are sequestered.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
| | - Bingqing Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405
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21
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Bythell BJ. Comment on: "Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine" by Julie Cautereels and Frank Blockhuys, J. Am. Soc. Mass Spectrom. 28, 1227-1235 (2017). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2728-2730. [PMID: 28952060 DOI: 10.1007/s13361-017-1804-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, 63121, USA.
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22
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Haeffner F, Irikura KK. N-Protonated Isomers and Coulombic Barriers to Dissociation of Doubly Protonated Ala 8Arg. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2170-2180. [PMID: 28699065 DOI: 10.1007/s13361-017-1719-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/15/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules). To make progress, shortcuts are needed. Inspired by the popular mobile proton model, we have previously proposed a simplified theoretical model in which the gas-phase fragmentation pattern of protonated peptides reflects the relative stabilities of N-protonated isomers, thus avoiding the need for transition-state information. For singly protonated Ala n (n = 3-11), the resulting predictions were in qualitative agreement with the results from low-energy MS/MS experiments. Here, the comparison is extended to a model tryptic peptide, doubly protonated Ala8Arg. This is of interest because doubly protonated tryptic peptides are the most important in proteomics. In comparison with experimental results, our model seriously overpredicts the degree of backbone fragmentation at N9. We offer an improved model that corrects this deficiency. The principal change is to include Coulombic barriers, which hinder the separation of the product cations from each other. Coulombic barriers may be equally important in MS/MS of all multiply charged peptide ions. Graphical Abstract ᅟ.
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Affiliation(s)
- Fredrik Haeffner
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8320, USA
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, 02467-3860, USA
| | - Karl K Irikura
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8320, USA.
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23
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Guan X, Wang B, Wang H, Liu J, Li Y, Guo X. Characteristic NH 3 and CO losses from sodiated peptides C-terminated by glutamine residues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:649-657. [PMID: 28158936 DOI: 10.1002/rcm.7831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Under certain conditions some amino acid (AA) residues undergo special reactions in the gas phase, generating characteristic neutral losses and product ions. Taking these special fragments into account and understanding the effect of AA residues on peptide cleavages will consummate database search algorithms and manual data interpretation in peptide sequencing by mass spectrometry (MS). In this study, the details of the characteristic NH3 and CO losses of glutamine (Gln) residues located at the C-terminus of peptides are presented. METHODS A number of selected peptides were fragmented under collision-induced dissociation (CID) in electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QTOF-MS). Density functional theory (DFT) quantum mechanical calculations at the B3LYP/6-31+G(d,p) level were carried out to optimize the geometry of peptide ions and provide energy barriers of ions in each step during fragmentations. RESULTS Two characteristic peaks appear near the precursor ions of sodiated Gln C-terminated peptides, suggesting the loss of neutral NH3 and CO via a two-step process. The proposed mechanism of their formation is as follows: after losing NH3 , a non-classical bn * ion is formed with a glutaric anhydride structure that further dissociates to lose CO. The sodiated peptides show more intensive peaks corresponding to the loss of neutral molecules than the protonated ones. This type of neutral loss can also occur at the Gln residue that is rearranged to the C-terminus of sodiated peptides. CONCLUSIONS The experiments and calculations suggest that the two-step characteristic NH3 and CO loss of sodiated peptides is energetically favored, and can be applied to identify C-terminated Gln residues. This study provides a mechanistic insight into the role of sodium ion during peptide fragmentation. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xinshu Guan
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Bing Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Huixin Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Jinrong Liu
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Ying Li
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Xinhua Guo
- College of Chemistry, Jilin University, Changchun, 130012, China
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24
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Abutokaikah MT, Guan S, Bythell BJ. Stereochemical Sequence Ion Selectivity: Proline versus Pipecolic-acid-containing Protonated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:182-189. [PMID: 27730525 DOI: 10.1007/s13361-016-1510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Substitution of proline by pipecolic acid, the six-membered ring congener of proline, results in vastly different tandem mass spectra. The well-known proline effect is eliminated and amide bond cleavage C-terminal to pipecolic acid dominates instead. Why do these two ostensibly similar residues produce dramatically differing spectra? Recent evidence indicates that the proton affinities of these residues are similar, so are unlikely to explain the result [Raulfs et al., J. Am. Soc. Mass Spectrom. 25, 1705-1715 (2014)]. An additional hypothesis based on increased flexibility was also advocated. Here, we provide a computational investigation of the "pipecolic acid effect," to test this and other hypotheses to determine if theory can shed additional light on this fascinating result. Our calculations provide evidence for both the increased flexibility of pipecolic-acid-containing peptides, and structural changes in the transition structures necessary to produce the sequence ions. The most striking computational finding is inversion of the stereochemistry of the transition structures leading to "proline effect"-type amide bond fragmentation between the proline/pipecolic acid-congeners: R (proline) to S (pipecolic acid). Additionally, our calculations predict substantial stabilization of the amide bond cleavage barriers for the pipecolic acid congeners by reduction in deleterious steric interactions and provide evidence for the importance of experimental energy regime in rationalizing the spectra. Graphical Abstract ᅟ.
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Affiliation(s)
- Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
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25
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Wang B, Liu J, Cao J, Wang H, Guan X, Wei Z, Guo X. Investigation of c ions formed by N-terminally charged peptides upon collision-induced dissociation. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:989-997. [PMID: 27537939 DOI: 10.1002/jms.3841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Peptide fragments such as b and y sequence ions generated upon low-energy collision-induced dissociation have been routinely used for tandem mass spectrometry (MS/MS)-based peptide/protein identification. The underlying formation mechanisms have been studied extensively and described within the literature. As a result, the 'mobile proton model' and 'pathways in competition model' have been built to interpret a majority of peptide fragmentation behavior. However, unusual peptide fragments which involve unfamiliar fragmentation pathways or various rearrangement reactions occasionally appear in MS/MS spectra, resulting in confused MS/MS interpretations. In this work, a series of unfamiliar c ions are detected in MS/MS spectra of the model peptides having an N-terminal Arg or deuterohemin group upon low-energy collision-induced dissociation process. Both the protonated Arg and deuterohemin group play an important role in retention of a positive charge at the N-terminus that is remote from the cleavage sites. According to previous reports and our studies involving amino acid substitutions and hydrogen-deuterium exchange, we propose a McLafferty-type rearrangement via charge-remote fragmentation as the potential mechanism to explain the formation of c ions from precursor peptide ions or unconventional b ions. Density functional theory calculations are also employed in order to elucidate the proposed fragmentation mechanisms. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Bing Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Jinrong Liu
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Jungang Cao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Huixin Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xinshu Guan
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Zhonglin Wei
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xinhua Guo
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
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26
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Jarnuczak AF, Lee DCH, Lawless C, Holman SW, Eyers CE, Hubbard SJ. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics. J Proteome Res 2016; 15:2945-59. [PMID: 27454336 DOI: 10.1021/acs.jproteome.6b00048] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governing principles of peptide ionization and exploitation of the inherent ionization and detection parameters of individual peptides is thus of great value. Here, using the yeast proteome as a model system, we establish the concept of peptide F-factor as a measure of detectability, closely related to ionization efficiency. F-factor is calculated by normalizing peptide precursor ion intensity by absolute abundance of the parent protein. We investigated F-factor characteristics in different shotgun proteomics experiments, including across multiple ESI-based LC-MS platforms. We show that F-factors mirror previously observed physicochemical predictors as peptide detectability but demonstrate a nonlinear relationship between hydrophobicity and peptide detectability. Similarly, we use F-factors to show how peptide ion coelution adversely affects detectability and ionization. We suggest that F-factors have great utility for understanding peptide detectability and gas-phase ion chemistry in complex peptide mixtures, selection of surrogate peptides in targeted MS studies, and for calibration of peptide ion signal in label-free workflows. Data are available via ProteomeXchange with identifier PXD003472.
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Affiliation(s)
- Andrew F Jarnuczak
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Dave C H Lee
- Faculty of Biology, Medicine and Health, University of Manchester , Second Floor, Wolfson Molecular Imaging Centre, 27 Palatine Road, Withington, Manchester, M20 3JL, United Kingdom
| | - Craig Lawless
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Stephen W Holman
- Centre for Proteome Research, University of Liverpool , Department of Biochemistry, Institute of Integrative Biology, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Claire E Eyers
- Centre for Proteome Research, University of Liverpool , Department of Biochemistry, Institute of Integrative Biology, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Simon J Hubbard
- Faculty of Biology, Medicine and Health, University of Manchester , Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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27
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Nelson CR, Abutokaikah MT, Harrison AG, Bythell BJ. Proton Mobility in b₂ Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:487-497. [PMID: 26602904 DOI: 10.1007/s13361-015-1298-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/13/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.
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Affiliation(s)
- Carissa R Nelson
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
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28
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Miladi M, Olaitan AD, Zekavat B, Solouki T. Competing noncovalent host-guest interactions and H/D exchange: reactions of benzyloxycarbonyl-proline glycine dipeptide variants with ND3. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1938-1949. [PMID: 26289383 DOI: 10.1007/s13361-015-1218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/26/2015] [Accepted: 06/17/2015] [Indexed: 06/04/2023]
Abstract
A combination of density functional theory calculations, hydrogen/deuterium exchange (HDX) reactions, ion mobility-mass spectrometry, and isotope labeling tandem mass spectrometry was used to study gas-phase "host-guest" type interactions of a benzyloxycarbonyl (Z)-capped proline (P) glycine (G) model dipeptide (i.e., Z-PG) and its various structural analogues with ND3. It is shown that in a solvent-free environment, structural differences between protonated and alkali metal ion (Na(+), K(+), or Cs(+))-complexed species of Z-PG affect ND3 adduct formation. Specifically, [Z-PG + H](+) and [Z-PG-OCH3 + H](+) formed gas-phase ND3 adducts ([Z-PG (or Z-PG-OCH3) + H + ND3](+)) but no ND3 adducts were observed for [Z-PG + alkali metal](+) or [Z-PG + H - CO2](+). Experimentally measured and theoretically calculated collision cross sections (CCSs) of protonated and alkali metal ion-complexed Z-PG species showed similar trends that agreed with the observed structural differences from molecular modeling results. Moreover, results from theoretical ND3 affinity calculations were consistent with experimental HDX observations, indicating a more stable ND3 adduct for [Z-PG + H](+) compared to [Z-PG + alkali metal](+) species. Molecular modeling and experimental MS results for [Z-PG + H](+) and [Z-PG + alkali metal](+) suggest that optimized cation-π and hydrogen bonding interactions of carbonyl groups in final products are important for ND3 adduct formation. Graphical Abstract ᅟ.
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Affiliation(s)
- Mahsan Miladi
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Abayomi D Olaitan
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Behrooz Zekavat
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA.
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Aseev O, Perez MAS, Rothlisberger U, Rizzo TR. Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling. J Phys Chem Lett 2015; 6:2524-2529. [PMID: 26266729 DOI: 10.1021/acs.jpclett.5b01088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) sequence. Some of these fragments may experience a "head-to-tail" cyclization, which after proton migration, can lead to the cyclic structure opening in a different place than the initially formed bond. This process leads to AA sequence scrambling that may hinder sequencing of the initial peptide. Here we combine cryogenic ion spectroscopy and ab initio molecular dynamics simulations to isolate and characterize the precise structures of key intermediates in the scrambling process. The most stable peptide fragments show intriguing symmetric cyclic structures in which the proton is situated on a C2 symmetry axis and forms exceptionally short H-bonds (1.20 Å) with two backbone oxygens. Other nonsymmetric cyclic structures also exist, one of which is protonated on the amide nitrogen, where ring opening is likely to occur.
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Affiliation(s)
- Oleg Aseev
- †Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- ‡Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCBC, Station 6, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- ‡Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCBC, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R Rizzo
- †Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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Bythell BJ, Harrison AG. Formation of a(1) ions directly from oxazolone b(2) ions: an energy-resolved and computational study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:774-781. [PMID: 25810075 DOI: 10.1007/s13361-015-1080-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
It is well-known that oxazolone b2 ions fragment extensively by elimination of CO to form a2 ions, which often fragment further to form a1 ions. Less well-known is that some oxazolone b2 ions may fragment directly to form a1 ions. The present study uses energy-resolved collision-induced dissociation experiments to explore the occurrence of the direct b2→a1 fragmentation reaction. The experimental results show that the direct b2→a1 reaction is generally observed when Gly is the C-terminal residue of the oxazolone. When the C-terminal residue is more complex, it is able to provide increased stability of the a2 product in the b2→a2 fragmentation pathway. Our computational studies of the relative critical reaction energies for the b2→a2 reaction compared with those for the b2→a1 reaction provide support that the critical reaction energies are similar for the two pathways when the C-terminal residue of the oxazolone is Gly. By contrast, when the nitrogen of the oxazolone ring in the b2 ion does not bear a hydrogen, as in the Ala-Sar and Tyr-Sar (Sar = N-methylglycine) oxazolone b2 ions, a1 ions are not formed but rather neutral imine elimination from the N-terminus of the b2 ion becomes a dominant fragmentation reaction. The M06-2X/6-31+G(d,p) density functional theory calculations are in general agreement with the experimental data for both types of reaction. In contrast, the B3LYP/6-31+G(d,p) model systematically underestimates the barriers of these SN2-like b2→a1 reaction. The difference between the two methods of barrier calculation are highly significant (P < 0.001) for the b2→a1 reaction, but only marginally significant (P = 0.05) for the b2→a2 reaction. The computations provide further evidence of the limitations of the B3LYP functional when describing SN2-like reactions.
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Affiliation(s)
- Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, 63131, USA,
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Schmidt R, Böhme D, Singer D, Frolov A. Specific tandem mass spectrometric detection of AGE-modified arginine residues in peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:613-624. [PMID: 25800199 DOI: 10.1002/jms.3569] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/30/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Glycation is a non-enzymatic reaction of protein amino and guanidino groups with reducing sugars or dicarbonyl products of their oxidative degradation. Modification of arginine residues by dicarbonyls such as glyoxal and methylglyoxal results in formation of advanced glycation end-products (AGEs). In mammals, these modifications impact in diabetes mellitus, uremia, atherosclerosis and ageing. However, due to the low abundance of individual AGE-peptides in enzymatic digests, these species cannot be efficiently detected by LC-ESI-MS-based data-dependent acquisition (DDA) experiments. Here we report an analytical workflow that overcomes this limitation. We describe fragmentation patterns of synthetic AGE-peptides and assignment of modification-specific signals required for unambiguous structure retrieval. Most intense signals were those corresponding to unique fragment ions with m/z 152.1 and 166.1, observed in the tandem mass spectra of peptides, containing glyoxal- and methylglyoxal-derived hydroimidazolone AGEs, respectively. To detect such peptides, specific and sensitive precursor ion scanning methods were established for these signals. Further, these precursor ion scans were incorporated in conventional bottom-up proteomic approach based on data-dependent acquisition (DDA) LC-MS/MS experiments. The method was successfully applied for the analysis of human serum albumin (HSA) and human plasma protein tryptic digest with subsequent structure confirmation by targeted LC-MS/MS (DDA). Altogether 44 hydroimidazolone- and dihydroxyimidazolidine-derived peptides representing 42 AGE-modified proteins were identified in plasma digests obtained from type 2 diabetes mellitus (T2DM) patients.
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Affiliation(s)
- Rico Schmidt
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig, Leipzig, Germany
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32
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Wang H, Wang B, Wei Z, Cao Y, Guan X, Guo X. Characteristic neutral loss of CH3CHO from Thr-containing sodium-associated peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:488-494. [PMID: 25800185 DOI: 10.1002/jms.3555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/15/2014] [Accepted: 11/23/2014] [Indexed: 06/04/2023]
Abstract
A characteristic neutral loss of 44 Da is observed in the MS/MS spectra of Thr-containing sodiated peptides. A combination of tandem mass spectrometry and quantum chemical calculations calculated at the B3LYP/6-311G (d, p) level of ab initio theory is used to elucidate this fragmentation pathway. The high resolution mass spectrometry data indicate this neutral loss is acetaldehyde lost from the side chain of Thr rather than CO2. The intensity of this neutral loss can be enhanced when Thr residue is far from the C-terminus and when the C-terminus is esterified as well. The mechanism of the acetaldehyde loss is proposed to adopt a McLafferty-type rearrangement reaction, which involves a proton transfer from the hydroxyl of Thr side chain to its C-terminal neighboring carbonyl oxygen inducing the cleavage of the Ca-Cβ bond. This mechanism is further supported by examining the fragmentation of a [GT(tBu)G + Na](+) peptide derivative and by comparing the product ion spectra of [M + Na-44](+) of [GTGA + Na](+) with [M + Na](+) of [GGGA + Na](+). A similar neutral loss of HCHO can also be detected in Ser-containing peptides. Our computational results reveal that the most stable [GTG + Na](+) ion is present as a tridentate charge-solvated structure and the dissociation leading to the 44 loss is dynamically and energetically favorable.
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Affiliation(s)
- Huixin Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
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33
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Qian JQ, Correra TC, Li J, Maître P, Song DQ, Hu CQ. Differentiation of cefaclor and its delta-3 isomer by electrospray mass spectrometry, infrared multiple photon dissociation spectroscopy and theoretical calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:265-269. [PMID: 25601701 DOI: 10.1002/jms.3510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/08/2014] [Accepted: 09/12/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Jian-Qin Qian
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China; National Institutes for Food and Drug Control, Beijing, 100050, China
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Wang B, Yu J, Wang H, Wei Z, Guo X, Xiao Z, Zeng Z, Kong W. Investigation of bn-44 peptide fragments using high resolution mass spectrometry and isotope labeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2116-2124. [PMID: 25280401 DOI: 10.1007/s13361-014-0994-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 06/03/2023]
Abstract
An N-terminal deuterohemin-containing hexapeptide (DhHP-6) was designed as a short peptide cytochrome c (Cyt c) mimetic to study the effect of N-terminal charge on peptide fragmentation pathways. This peptide gave different dissociation patterns than normal tryptic peptides. Upon collision-induced dissociation (CID) with an ion trap mass spectrometer, the singly charged peptide ion containing no added proton generated abundant and characteristic bn-44 ions instead of bn-28 (an) ions. Studies by high resolution mass spectrometry (HRMS) and isotope labeling indicate that elimination of 44 Da fragments from b ions occurs via two different pathways: (1) loss of CH3CHO (44.0262) from a Thr side chain; (2) loss of CO2 (43.9898) from the oxazolone structure in the C-terminus. A series of analogues were designed and analyzed. The experimental results combined with Density Functional Theory (DFT) calculations on the proton affinity of the deuteroporphyrin demonstrate that the production of these novel bn-44 ions is related to the N-terminal charge via a charge-remote rather than radical-directed fragmentation pathway.
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Affiliation(s)
- Bing Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
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35
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Harper B, Miladi M, Solouki T. Loss of internal backbone carbonyls: additional evidence for sequence-scrambling in collision-induced dissociation of y-type ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1716-1729. [PMID: 25070583 DOI: 10.1007/s13361-014-0955-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/14/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MS(n)), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.
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Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA
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36
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Guo M, Guo C, Pan Y. Competitive formation of b2 and c2-H2O ions from b3 ions containing Asp residue during tandem mass spectrometry: the influence of neighboring Arg. Amino Acids 2014; 46:1939-46. [DOI: 10.1007/s00726-014-1743-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/04/2014] [Indexed: 11/28/2022]
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Frolov A, Schmidt R, Spiller S, Greifenhagen U, Hoffmann R. Arginine-derived advanced glycation end products generated in peptide-glucose mixtures during boiling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:3626-3635. [PMID: 24725187 DOI: 10.1021/jf4050183] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Glycation refers to the reaction of amino groups, for example in proteins, with reducing sugars. Intermediately formed Amadori products can be degraded by oxidation (Maillard reactions) leading to a heterogeneous class of advanced glycation end-products (AGEs), especially during exposure to heat. AGEs are considered to be toxic in vivo due to their pronounced local and systemic inflammatory effects. At high temperatures, these reactions have been mostly investigated at the amino acid level. Here, we studied the formation of arginine-related AGEs in peptides under conditions simulating household cooking at physiological d-glucose concentrations. High quantities of AGE-modified peptides were produced within 15 min, especially glyoxal-derived products. The intermediately formed dihydroxy-imidazolidine yielded glyoxal- (Glarg) and methylglyoxal-derived hydro-imidazolinones (MG-H), with Glarg being further degraded to carboxymethyl-l-arginine (CMA). Carboxyethyl-l-arginine was not detected. The formation rates and yields were strongly increased in the presence of physiologically relevant concentrations of Fe(II)-ions and ascorbate. A nearby histidine residue increased the content of AGEs, whereas glutamic acid significantly reduced the CMA levels.
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Affiliation(s)
- Andrej Frolov
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy and Center for Biotechnology and Biomedicine, Universität Leipzig , Deutscher Platz 5, 04103 Leipzig, Germany
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Ma C, Li C, Luan X, Zhang J, Qiao R, Zhao Y. Electrospray ionization mass spectrometric studies on the characteristic fragmentation of Asp/cyclen conjugates. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:645-652. [PMID: 24519827 DOI: 10.1002/rcm.6822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 12/25/2013] [Accepted: 12/31/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Differentiation and structural characterization of Asp/cyclen conjugates by electrospray ionization tandem mass spectrometry (ESI-MS(n)) are significantly important for their biomedical application. Hence, the present study is conducted. METHODS The fragmentations of Asp/cyclen conjugates generated by positive ion mode electrospray ionization were examined here by low-energy collision-induced dissociation (CID). ESI-MS(n) spectra of cyclen were acquired to confirm cyclen contraction products derived from the studied compounds. The fragments derived from the Asp/cyclen conjugates were proved by deuterium-exchange experiments. RESULTS Asp/cyclen conjugates displayed characteristic dissociation pathways, including cleavages of amide bonds, loss of NH3 and cyclen contraction pathways. It was observed that cleavages of C-terminal amide bonds generated b2 and b2 + H2O ions from the protonated CyclenAspAspAsp and a b1 + H2O ion from the protonated CyclenAspAsp. In addition, various cyclen contraction products were also observed. CONCLUSIONS In ESI-MS(n) spectra of studied compounds, fragments of bn-1 + H2O or cyclic anhydride were generated due to facile mobilization of C-terminal or side-chain COOH protons. In addition, the cyclen contraction products were detected. These results might provide sufficient information for the identification of Asp/cyclen conjugates by mass spectrometry.
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Affiliation(s)
- Chunying Ma
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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Darii E, Saravanamuthu G, Gut IG, Tabet JC. Structural studies of the sBBI/trypsin non-covalent complex using covalent modification and mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:413-429. [PMID: 24497279 DOI: 10.1002/rcm.6797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 11/21/2013] [Accepted: 12/01/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE The study of protein recognition sites is crucial for understanding the mechanisms of protein interaction. Mass spectrometry can be a method of choice for the investigation of the contact surface within the protein non-covalent complexes. METHODS Probing the reactivity of essential amino acid residues of soybean Bowman-Birk inhibitor (sBBI) within the non-covalent sBBI/bovine trypsin complex was performed using covalent labeling by the BS3 cross-linker and charge tag with a quaternary ammonium group in combination with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analysis. RESULTS Significant modulation of the reactivity of essential K16 and S17 residues in the sBBI molecule upon binding to trypsin was established. The studies of sBBI proteolytic peptides with the same structure but carrying different labels using metastable dissociation in LIFT mode demonstrated that fragmentation pathways were oriented by used modification (BS3 cross-linker or charge tag). CONCLUSIONS The effectiveness of the mass spectrometric approach including covalent modification for exploring protein-protein interaction sites has been demonstrated. The alteration of the reactivity of functionally important amino acid residues in the sBBI molecule is most likely related to changes in their microenvironment. It has been suggested that in the presence of charge tags fragmentation in LIFT mode proceeds through the formation of salt bridges between quaternary ammonium groups and acidic residues due to the occurrence of zwitterions (including basic and acidic residues). Despite the presence of one or several charge tags, fragmentation takes place yielding modulated bi /yj ion series depending on the positions of the tags.
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Affiliation(s)
- Ekaterina Darii
- CEA/Institut de Génomique/Centre National de Génotypage, Evry, France; CEA/Institut de Génomique/Centre National de Séquençage, Evry, France
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40
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Leeming MG, White JM, O'Hair RAJ, Donald WA. Mobile proton triggered radical fragmentation of nitroarginine containing peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:427-438. [PMID: 24435794 DOI: 10.1007/s13361-013-0794-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/25/2013] [Accepted: 11/26/2013] [Indexed: 06/03/2023]
Abstract
Protonated nitroarginine, [R(NO2) + H](+), which contains the nitroguanidine 'explosophore,' undergoes homolytic N - N nitro-imine bond cleavage to expel NO2(•) and form a radical cation of arginine in high yield (100% relative abundance) upon low-energy collision-induced dissociation (CID). Other ionization states of nitroarginine, including [R(NO2) - H](-), and a fixed-charge derivative of nitroarginine do not expel NO2(•) (<1%), but instead dissociate via heterolytic bond cleavage with abundant losses of small molecules (N2O and H2N2O2) from the nitroguanidine group. The effects of proton mobility on the CID reactions of nitroarginine containing peptides was investigated for peptide derivatives of leucine enkephalin, including XYGGFLR(NO2), X = D, G, K, and R, by examining the different protonation states: [M - H](-); [M + H](+); and [M + 2H](2+). For [M + H](+) containing the less basic N-terminal residues (X = D, G) and all [M + 2H](2+), mobile proton fragmentation reactions that result in peptide sequence ions dominate. In contrast, for peptides containing the basic N-terminal residues (R and K), the CID spectra of both the [M - H](-) and [M + H](+) are dominated by the losses of small even-electron neutrals from the nitroarginine side-chain. The fraction of nitroguanidine directed fragmentation of the nitroarginine side chain that results in bond homolysis to form [XYGGFLR](+•) by expulsion of NO2(•) increases by more than 10 times as the protonation state changes from [M - H](-) (<10%) to [M + 2H](2+) (ca. 90%) and by about four times as the acidity of the [M + H](+) N-terminal residue increases from R (19.0%) to D (76.5%). These results indicate that protonated peptides containing nitroarginine can undergo non-canonical mobile proton triggered radical fragmentation.
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Affiliation(s)
- Michael G Leeming
- School of Chemistry, Bio21 Institute of Molecular Science and Biotechnology, & Australian Research Council Centre of Excellence for Free Radical Chemistry and Biotechnology, The University of Melbourne, Melbourne, Victoria, Australia
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Wang J, Song W, Hu X, Yu Z, Liu Y, Liu R. Comparative studies on the discrepant fragmentation mechanisms of the GLy-Asp-Gly-Arg and Arg-Gly-Asp-Gly: evidence for the mobile proton model. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:317-325. [PMID: 25420344 DOI: 10.1255/ejms.1287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The fragmentation mechanisms of singly protonated Gly-Asp-Gly-Arg (GDGRI and Arg-Gly-Asp-Gly (RGDGJ were investigated by mass spectrometry and theoretical methods. Both protonated molecules are fragmented mainly at the Asp-Gly amide bond C-terminal to Asp, as supported by quantum chemical calculations. Charge distributions of C and N atoms (Qc + QN) on the amide bonds were collected when the ionizing proton was fixed at different nitrogen atoms along the backbone for each peptide. Compared with the neutral molecules, the total charges of C and N atoms (Qc + QN] for the singly charged peptides tended to be negative when the proton was located at the backbone nitrogen atoms. A relatively larger value of QC + QN corresponds to a higher trend of fragmentation, which is consistent with the experimental relative abundances data that the predominant ions are y2 for [GDGR + H]+ and b3 for [RGDG + H]+. Also, the anhydride mechanism driven by the C-terminal COOH for [RGDG + H]+ was explored by a quantum-mechanical/molecular-mechanical method. Calculations indicate that the protonated peptide can be cleaved through an unusual charge-directed pathway by forming a salt bridge at the C-termini. The formation of the anhydride linkage is much more feasible since this process needs very little energy and is exother- mic, though the subsequent nucleophilic attack on the Asp carbonyl carbon is more difficult. The combined experimental and theoretical methods substantiate the mobile proton model, which opens a way to analyze quantitatively the discrepant fragmentation of dissociated peptides in peptide/protein identification.
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Affiliation(s)
- Jinhu Wang
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
- College of Chemistry Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Wei Song
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Xinxin Hu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Zehua Yu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Yongjun Liu
- Key Lab of Theoretical and Computational Chemistry in University of Shandong, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
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Zhao J, Lau JKC, Grzetic J, Verkerk UH, Oomens J, Siu KWM, Hopkinson AC. Structures of a(n)* ions derived from protonated pentaglycine and pentaalanine: results from IRMPD spectroscopy and DFT calculations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1957-1968. [PMID: 24026976 DOI: 10.1007/s13361-013-0728-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 06/02/2023]
Abstract
Infrared multiple-photon dissociation (IRMPD) spectroscopy and DFT calculations have been used to probe the most stable structures of a3(*) and a4(*) ions derived from both protonated pentaglycine (denoted G5) and pentaalanine (A5). The a3(*) and a4(*) ions derived from protonated A5 feature a CHR=N-CHR'- group at the N-terminus and an oxazolone ring at the C-terminus, as proposed previously [J. Am. Soc. Mass Spectrom. 19, 1788-1798 (2008)]. The isomeric a4(*) ion derived from A5 with a 3,5-dihydro-4H-imidazol-4-one ring structure was calculated to have a slightly better energy than the oxazolone, but the barrier to its formation is higher and there was no evidence of this ion in the IRMPD spectrum. By contrast, the a4(*) and [a4 - H2O](+) (denoted a4(0)) ions from G5 gave strikingly similar IRMPD spectra and both have the 3,5-dihydro-4H-imidazol-4-one ring structure similar to that recently reported for the [GGGG + H - H2O](+) ion [Int. J. Mass Spectrom. 316-318, 268-272 (2012)]. In the absence of a solvent molecule, the pathway to the oxazolone is calculated to be lower than those to thermodynamically more stable products, the a4(0) and the a4(*) with the 3,5-dihydro-4H-imidazol-4-one ring structure. Incorporation of one water molecule is sufficient to reduce the barrier to formation of the a4(0) of G5 to below that for formation of the oxazolone. On the equivalent potential energy surface for protonated A5 the barrier to formation of the a4(0) ion is 12.3 kcal mol(-1) higher than that for oxazolone formation and the a4(0) ion is not observed experimentally.
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Affiliation(s)
- Junfang Zhao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, ON, M3J 1P3, Canada
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McGee WM, McLuckey SA. Gas Phase Dissociation Behavior of Acyl-Arginine Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 354-356:181-187. [PMID: 24465154 PMCID: PMC3899352 DOI: 10.1016/j.ijms.2013.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The gas phase dissociation behavior of peptides containing acyl-arginine residues is investigated. These acylations are generated via a combination of ion/ion reactions between arginine-containing peptides and N-hydroxysuccinimide (NHS) esters and subsequent tandem mass spectrometry (MS/MS). Three main dissociation pathways of acylated arginine, labeled Paths 1-3, have been identified and are dependent on the acyl groups. Path 1 involves the acyl-arginine undergoing deguanidination, resulting in the loss of the acyl group and dissociation of the guanidine to generate an ornithine residue. This pathway generates selective cleavage sites based on the recently discussed "ornithine effect". Path 2 involves the coordinated losses of H2O and NH3 from the acyl-arginine side chain while maintaining the acylation. We propose that Path 2 is initiated via cyclization of the δ-nitrogen of arginine and the C-terminal carbonyl carbon, resulting in rapid rearrangement from the acyl-arginine side chain and the neutral losses. Path 3 occurs when the acyl group contains α-hydrogens and is observed as a rearrangement to regenerate unmodified arginine while the acylation is lost as a ketene.
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Affiliation(s)
| | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey, 560 Oval Drive, Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA, Phone: (765) 494-5270, Fax: (765) 494-0239,
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44
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Miladi M, Harper B, Solouki T. Evidence for sequence scrambling in collision-induced dissociation of y-type fragment ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1755-1766. [PMID: 23982935 DOI: 10.1007/s13361-013-0714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 06/19/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where "A" denotes carbon thirteen ((13)C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic "b-type" ions.
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Affiliation(s)
- Mahsan Miladi
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
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45
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Harrison AG, Tasoglu C, Yalcin T. Non-direct sequence ions in the tandem mass spectrometry of protonated peptide amides--an energy-resolved study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1565-1572. [PMID: 23918462 DOI: 10.1007/s13361-013-0707-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
The fragmentation reactions of the MH(+) ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of bn ions, including significant loss of NH3 from the MH(+) ions. Further fragmentation of these bn ions occurs following macrocyclization/ring opening leading in many cases to bn ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada,
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46
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Rudowska M, Wieczorek R, Kluczyk A, Stefanowicz P, Szewczuk Z. Gas-phase fragmentation of oligoproline peptide ions lacking easily mobilizable protons. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:846-856. [PMID: 23609183 PMCID: PMC3650240 DOI: 10.1007/s13361-013-0585-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/17/2012] [Accepted: 12/31/2012] [Indexed: 06/02/2023]
Abstract
The fragmentation of peptides containing quaternary ammonium group, but lacking easily mobilizable protons, was examined with the aid of deuterium-labeled analogs and quantum-chemical modeling. The fragmentation of oligoproline containing quaternary ammonium group involves the mobilization of hydrogens localized at α- and γ- or δ-carbon atoms in the pyrrolidine ring of proline. The study of the dissociation pattern highlights the unusual proline residue behavior during MS/MS experiments of peptides.
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Affiliation(s)
| | | | - Alicja Kluczyk
- Faculty of Chemistry, University of Wrocław, Wrocław, Poland
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47
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Šekutor M, Glasovac Z, Mlinarić-Majerski K. Neighboring effect in fragmentation pathways of cage guanylhydrazones in the gas phase. J Phys Chem A 2013; 117:2242-52. [PMID: 23413989 DOI: 10.1021/jp311049f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ESI-MS/MS investigation of the mono- and bis(guanylhydrazone) derivatives 1-5 based on adamantane and pentacycloundecane (PCU) skeleton was described. Elimination of neutral guanidine is the most abundant reaction channel in the case of 2,4-adamantyl and PCU derivatives 4 and 5, while the elimination of CH2N2 fragment is preferred for other compounds. This was attributed to the cage opening of adamantane or PCU skeletons in the former case leading to the formation of the cyclohexyl- or cyclopropylcarbinyl carbocation stabilized by the conjugation with the guanylhydrazone subunit. The main fragmentation pathways observed experimentally were analyzed by using DFT calculations. All investigated bis(guanylhydrazone)s formed dications and their abundances were found to be proportional to the interguanidine distance in the considered ions. Calculation of the first and the second proton affinities supported qualitative interpretation of the dication abundance. Close contact of two guanidine subunits is thus confirmed to be crucial in determining preferential fragmentation pathway and to suppress formation of the dication.
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Affiliation(s)
- Marina Šekutor
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, P.O. Box 180, 10 002 Zagreb, Croatia
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Barone V, Biczysko M, Bloino J, Puzzarini C. Characterization of the Elusive Conformers of Glycine from State-of-the-Art Structural, Thermodynamic, and Spectroscopic Computations: Theory Complements Experiment. J Chem Theory Comput 2013; 9:1533-47. [DOI: 10.1021/ct3010672] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Malgorzata Biczysko
- Center for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127
Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche,
Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS
di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “G.
Ciamician,” Università di Bologna, Via F. Selmi 2, 40126
Bologna, Italy
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49
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Lakowski TM, Szeitz A, Pak ML, Thomas D, Vhuiyan MI, Kotthaus J, Clement B, Frankel A. MS³ fragmentation patterns of monomethylarginine species and the quantification of all methylarginine species in yeast using MRM³. J Proteomics 2013; 80:43-54. [PMID: 23333926 DOI: 10.1016/j.jprot.2013.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 01/06/2023]
Abstract
Protein arginine methylation is one of the epigenetic modifications to proteins that is studied in yeast and is known to be involved in a number of human diseases. All eukaryotes produce Nη-monomethylarginine (ηMMA), asymmetric Nη1, Nη1-dimethylarginine (aDMA), and most produce symmetric Nη1, Nη2-dimethylarginine (sDMA) on proteins, but only yeast produce Nδ-monomethylarginine (δMMA). It has proven difficult to differentiate among all of these methylarginines using mass spectrometry. Accordingly, we demonstrated that the two forms of MMA have indistinguishable primary product ion spectra. However, the secondary product ion spectra of δMMA and ηMMA exhibited distinct patterns of ions. Using incorporation of deuterated methyl-groups in yeast, we determined which secondary product ions were methylated and their structures. Utilizing distinct secondary product ions, a triple quadrupole multiple reaction monitoring cubed (MRM(3)) assay was developed to measure δMMA, ηMMA, sDMA and aDMA derived from hydrolyzed protein. As a proof-of-concept, δMMA and ηMMA were measured using the MRM(3) method in wild type and mutant strains of Saccharomyces cerevisiae and compared to the total MMA measured using an existing assay. The MRM(3) assay represents the only method to directly quantify δMMA and the only method to simultaneously quantify all yeast methylarginines.
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Affiliation(s)
- Ted M Lakowski
- Faculty of Pharmacy, The University of Manitoba, Winnipeg, Manitoba, Canada.
| | - András Szeitz
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Magnolia L Pak
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dylan Thomas
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mynol I Vhuiyan
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Joscha Kotthaus
- Pharmaceutical Institute, Gutenbergstr. 76, 24118 Kiel, Germany
| | - Bernd Clement
- Pharmaceutical Institute, Gutenbergstr. 76, 24118 Kiel, Germany
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
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50
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Bush DR, Wysocki VH, Scaraffia PY. Study of the fragmentation of arginine isobutyl ester applied to arginine quantification in Aedes aegypti mosquito excreta. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1364-1371. [PMID: 23019169 PMCID: PMC3462363 DOI: 10.1002/jms.3063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
It has been demonstrated that argininolysis and uricolysis are involved in the synthesis and excretion of urea in Aedes aegypti female mosquitoes. To further investigate the metabolic regulation of urea in female mosquitoes, it is desirable to have a rapid and efficient method to monitor arginine (Arg) concentration in mosquito excreta. Thus, a procedure currently used for the identification of Arg in urea cycle disorders in newborn babies was adapted to analyze Arg in A. aegypti excreta. The fragmentation patterns of the isobutyl esters of Arg and (15)N(2)-Arg (labeled at the guanidino group) were explored by electrospray ionization (ESI)-tandem mass spectrometry and fragmentation pathways not described before were characterized. In addition, Arg, (18)O(2)-Arg, (15)N(2)-Arg and (15)N(2)-(18)O(2)-Arg were also analyzed to elucidate some of the minor fragments in greater detail. Mosquito excreta from individual females were collected before and at different times after feeding a blood meal, mixed with (15)N(2)-Arg, an internal standard, and then derivatized as isobutyl esters. Based on the fragmentation mechanisms of Arg standards, studied by MS(2) and MS(3), Arg in the mosquito excreta was successfully analyzed by ESI-multiple reaction monitoring in a triple-quadrupole mass spectrometer. Arg excretion was monitored over a 120 h window before and after feeding female mosquitoes with a blood meal, with the maximum level of Arg excretion observed at 36-48 h post blood feeding. This method provides an efficient and rapid tool to quantify Arg in individual blood-fed mosquitoes, and can be applied to other organisms, whose small size severally limits the use of conventional biochemical analysis.
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