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Sakai R, Ichikawa T, Kondo H, Ishikawa K, Shimizu N, Ohta T, Hiramatsu M, Hori M. Effects of Carbon Nanowalls (CNWs) Substrates on Soft Ionization of Low-Molecular-Weight Organic Compoundsin Surface-Assisted Laser Desorption/Ionization Mass Spectrometry (SALDI-MS). NANOMATERIALS 2021; 11:nano11020262. [PMID: 33498479 PMCID: PMC7909522 DOI: 10.3390/nano11020262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 01/15/2023]
Abstract
Carbon nanowalls (CNWs), which are vertically oriented multi-layer graphene sheets, were employed in surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) measurements to detect low-molecular-weight organic compounds. CNWs substrates with widely different wall-to-wall distances from 142 to 467 nm were synthesized using a radical-injection plasma-enhanced chemical vapor deposition (RI-PECVD) system with nanosecond pulse biasing to a sample stage. When survival yield (SY) values of N-benzylpyridinium chloride (N-BP-Cl) were examined, which is commonly used to evaluate desorption/ionization efficiency, a narrower wall-to-wall distance presented a higher SY value. The highest SY value of 0.97 was realized at 4 mJ/cm2 for the highest-density CNWs with a wall-to-wall distance of 142 nm. The laser desorption/ionization effect of arginine, an amino acid, was also investigated. When CNWs with a narrower wall-to-wall distance were used, the signal-to-noise (SN) ratios of the arginine signals were increased, while the intensity ratios of fragment ions to arginine signals were suppressed. Therefore, the CNWs nanostructures are a powerful tool when used as a SALDI substrate for the highly efficient desorption/ionization of low-molecular-weight biomolecules.
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Affiliation(s)
- Ryusei Sakai
- Department of Electronics, Nagoya University, Furo, Chikusa, Nagoya 464-8603, Japan;
| | - Tomonori Ichikawa
- Japan Aerospace Exploration Agency, 7-44-1, Jindaiji, Higashi-machi, Chofu-shi, Tokyo 182-8522, Japan;
| | - Hiroki Kondo
- Center for Low-temperature Plasma Sciences, Nagoya University, Furo, Chikusa, Nagoya 464-8603, Japan; (K.I.); (N.S.); (M.H.)
- Correspondence: ; Tel.: +81-52-789-3461
| | - Kenji Ishikawa
- Center for Low-temperature Plasma Sciences, Nagoya University, Furo, Chikusa, Nagoya 464-8603, Japan; (K.I.); (N.S.); (M.H.)
| | - Naohiro Shimizu
- Center for Low-temperature Plasma Sciences, Nagoya University, Furo, Chikusa, Nagoya 464-8603, Japan; (K.I.); (N.S.); (M.H.)
| | - Takayuki Ohta
- Departmet of Electrical and Electronic Engineering, Meijo University, Shiogamaguchi, Tenpaku, Nagoya 468-8502, Japan; (T.O.); (M.H.)
| | - Mineo Hiramatsu
- Departmet of Electrical and Electronic Engineering, Meijo University, Shiogamaguchi, Tenpaku, Nagoya 468-8502, Japan; (T.O.); (M.H.)
| | - Masaru Hori
- Center for Low-temperature Plasma Sciences, Nagoya University, Furo, Chikusa, Nagoya 464-8603, Japan; (K.I.); (N.S.); (M.H.)
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2
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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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3
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Atmospheric Pressure Plasma-Treated Carbon Nanowalls’ Surface-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (CNW-SALDI-MS). C — JOURNAL OF CARBON RESEARCH 2019. [DOI: 10.3390/c5030040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Carbon nanowalls (CNWs), vertically standing highly crystallizing graphene sheets, were used in the application of a surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF-MS). The CNW substrates solved the issues on interferences of matrix molecules and alkali metal addition ions in low-weight molecule detection. Before SALDI sample preparations, the hydrophobic CNW was treated by atmospheric pressure plasma for exposing hydrophilicity to the CNWs’ surface. Detection of water soluble amino acids, arginine, was demonstrated.
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4
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Tanaka W, Arita M. Physicochemical Prediction of Metabolite Fragmentation in Tandem Mass Spectrometry. ACTA ACUST UNITED AC 2018; 7:A0066. [PMID: 29922568 PMCID: PMC6002374 DOI: 10.5702/massspectrometry.a0066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/16/2018] [Indexed: 11/23/2022]
Abstract
Current bottleneck of comprehensive non-target metabolite identification is insufficient spectral library. Many research groups have tried to build a theoretical product ion spectral library independent of measurement condition or settings, but mechanisms of metabolite fragmentation are not fully clarified. To achieve the mechanistic prediction of metabolite fragmentation which covers a wide range of metabolites, we will discuss utilization of physicochemical calculation. We introduce bonding patterns, which include two bound atoms and chemical groups adjacent to the bond. Cleavage of each bonding pattern is simulated and its activation energy is precisely calculated with quantum chemistry and assigned on metabolites. By tracing low-energy bond cleavages, fragmentation of a dipeptide molecule is successfully predicted. Prediction on another metabolite requires some additional features to fully reproduce its experimentally observed product ions. Physicochemical calculation shows its promising ability to predict fragmentation pathways only from metabolite structures, while required improvements suggested by comparison between our prediction and standard spectra stored in database are also discussed. Moreover, to construct a prediction strategy which withstands the vast metabolite space, we have to build a comprehensive list of bonding patterns and their activation energy. As theoretically possible bonding patterns are huge in number, proper simplification of the patterns must be implemented. We will discuss how to achieve it in addition to the prediction results.
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Affiliation(s)
- Wataru Tanaka
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies)
| | - Masanori Arita
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies).,National Institute of Genetics
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5
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Koirala D, Mistry S, Wenthold PG. Participation of C-H Protons in the Dissociation of a Proton Deficient Dipeptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1313-1323. [PMID: 28429299 DOI: 10.1007/s13361-017-1662-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
The dissociation of anionic dipeptides Phe*Gly and GlyPhe*, where Phe* refers to sulfonated phenyl alanine, has been investigated by using ion trap mass spectrometry. The dipeptides undergo collision-induced dissociation (CID) to give the same products, indicating that they rearrange to a common structure before dissociation. The rearrangement does not occur with the dipeptide methyl esters. The structures of the b2 ions were investigated to determine the effect that having a remote, anionic site has on product formation. Comparison with the CID spectra for authentic structures shows that the b2 ion obtained from GlyPhe* has predominantly a diketopiperazine structure. The CID spectra for the Phe*Gly b2 ion and the authentic oxazolone are similar, but differences in intensity suggest a two-component mixture. Isotopic labeling studies are consistent with the formation of two products, with one resulting from loss of a non-mobile proton on the Gly α-carbon. The results are attributed to the formation of an oxazole and oxazolone enol product. Electronic structure calculations predict that the enol structure of the Phe*Gly b2 ion is lower in energy than the keto version due to intramolecular hydrogen bonding with the sulfonate group. Graphical Abstract ᅟ.
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Affiliation(s)
- Damodar Koirala
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA
| | - Sabyasachy Mistry
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA
| | - Paul G Wenthold
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906, USA.
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6
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Chiu JZS, Tucker IG, McDowell A. Quantification of Cell-Penetrating Peptide Associated with Polymeric Nanoparticles Using Isobaric-Tagging and MALDI-TOF MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1891-1894. [PMID: 27629919 DOI: 10.1007/s13361-016-1486-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
High sensitivity quantification of the putative cell-penetrating peptide di-arginine-histidine (RRH) associated with poly (ethyl-cyanoacrylate) (PECA) nanoparticles was achieved without analyte separation, using a novel application of isobaric-tagging and high matrix-assisted laser desorption/ionization coupled to time-of-flight (MALDI-TOF) mass spectrometry. Isobaric-tagging reaction equilibrium was reached after 5 min, with 90% or greater RRH peptide successfully isobaric-tagged after 60 min. The accuracy was greater than 90%, which indicates good reliability of using isobaric-tagged RRH as an internal standard for RRH quantification. The sample intra- and inter-spot coefficients of variations were less than 11%, which indicate good repeatability. The majority of RRH peptides in the nanoparticle formulation were physically associated with the nanoparticles (46.6%), whereas only a small fraction remained unassociated (13.7%). The unrecovered RRH peptide (~40%) was assumed to be covalently associated with PECA nanoparticles. Graphical Abstract ᅟ.
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Affiliation(s)
- Jasper Z S Chiu
- School of Pharmacy, University of Otago, 18 Frederick Street, Dunedin, 9016, New Zealand
| | - Ian G Tucker
- School of Pharmacy, University of Otago, 18 Frederick Street, Dunedin, 9016, New Zealand
| | - Arlene McDowell
- School of Pharmacy, University of Otago, 18 Frederick Street, Dunedin, 9016, New Zealand.
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7
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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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8
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Moghaddam MB, Fridgen TD. IRMPD Spectroscopic Study of Microsolvated [Na(GlyAla)]+ and [Ca(GlyAla–H)]+ and the Blue Shifting of the Hydrogen-Bonded Amide Stretch with Each Water Addition. J Phys Chem B 2013; 117:6157-64. [DOI: 10.1021/jp402217g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maryam B. Moghaddam
- Department
of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7 Canada
| | - Travis D. Fridgen
- Department
of Chemistry, Memorial University, St. John’s, Newfoundland
and Labrador, Canada A1B 3X7 Canada
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9
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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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10
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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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11
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Zhao J, Song T, Xu M, Quan Q, Siu KWM, Hopkinson AC, Chu IK. Intramolecular hydrogen atom migration along the backbone of cationic and neutral radical tripeptides and subsequent radical-induced dissociations. Phys Chem Chem Phys 2012; 14:8723-31. [DOI: 10.1039/c2cp40708f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Ramesh M, Raju B, Srinivas R, Sureshbabu VV, Vishwanatha TM, Hemantha HP. Characterization of Nα-Fmoc-protected dipeptide isomers by electrospray ionization tandem mass spectrometry (ESI-MS(n)): effect of protecting group on fragmentation of dipeptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1949-1958. [PMID: 21698678 DOI: 10.1002/rcm.5076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A series of positional isomeric pairs of Fmoc-protected dipeptides, Fmoc-Gly-Xxx-OY/Fmoc-Xxx-Gly-OY (Xxx=Ala, Val, Leu, Phe) and Fmoc-Ala-Xxx-OY/Fmoc-Xxx-Ala-OY (Xxx=Leu, Phe) (Fmoc=[(9-fluorenylmethyl)oxy]carbonyl) and Y=CH(3)/H), have been characterized and differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MS(n)). In contrast to the behavior of reported unprotected dipeptide isomers which mainly produce y(1)(+) and/or a(1)(+) ions, the protonated Fmoc-Xxx-Gly-OY, Fmoc-Ala-Xxx-OY and Fmoc-Xxx-Ala-OY yield significant b(1)(+) ions. These ions are formed, presumably with stable protonated aziridinone structures. However, the peptides with Gly- at the N-terminus do not form b(1)(+) ions. The [M+H](+) ions of all the peptides undergo a McLafferty-type rearrangement followed by loss of CO(2) to form [M+H-Fmoc+H](+). The MS(3) collision-induced dissociation (CID) of these ions helps distinguish the pairs of isomeric dipeptides studied in this work. Further, negative ion MS(3) CID has also been found to be useful for differentiating these isomeric peptide acids. The MS(3) of [M-H-Fmoc+H](-) of isomeric peptide acids produce c(1)(-), z(1)(-) and y(1)(-) ions. Thus the present study of Fmoc-protected peptides provides additional information on mass spectral characterization of the dipeptides and distinguishes the positional isomers.
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Affiliation(s)
- M Ramesh
- National Centre for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad 500 607, India
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13
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Kwon SH, Shin HJ, Park JM, Lee KR, Kim YJ, Lee SH. Electrospray ionization tandem mass fragmentation pattern of camostat and its degradation product, 4-(4-guanidinobenzoyloxy)phenylacetic acid. ANALYTICAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5806/ast.2011.24.2.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Gao X, Hu X, Zhu J, Zeng Z, Han D, Tang G, Huang X, Xu P, Zhao Y. An isotope (18O, 15N, and 2H) technique to investigate the metal ion interactions between the phosphoryl group and amino acid side chains by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:689-702. [PMID: 21472608 DOI: 10.1007/s13361-010-0069-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Revised: 12/24/2010] [Accepted: 12/28/2010] [Indexed: 05/30/2023]
Abstract
Cationic metal ion-coordinated N-diisopropyloxyphosphoryl dipeptides (DIPP-dipeptides) were analyzed by electrospray ionization multistage tandem mass spectrometry (ESI-MS(n)). Two novel rearrangement reactions with hydroxyl oxygen or carbonyl oxygen migrations were observed in ESI-MS/MS of the metallic adducts of DIPP-dipeptides, but not for the corresponding protonated DIPP-dipeptides. The possible oxygen migration mechanisms were elucidated through a combination of MS/MS experiments, isotope ((18)O, (15)N, and (2)H) labeling, accurate mass measurements, and density functional theory (DFT) calculations at the B3LYP/6-31 G(d) level. It was found that lithium and sodium cations catalyze the carbonyl oxygen migration more efficiently than does potassium and participation through a cyclic phosphoryl intermediate. In addition, dipeptides having a C-terminal hydroxyl or aromatic amino acid residue show a more favorable rearrangement through carbonyl oxygen migration, which may be due to metal cation stabilization by the donation of lone pair of the hydroxyl oxygen or aromatic π-electrons of the C-terminal amino acid residue, respectively. It was further shown that the metal ions, namely lithium, sodium, and potassium cations, could play a novel directing role for the migration of hydroxyl or carbonyl oxygen in the gas phase. This discovery suggests that interactions between phosphorylated biomolecules and proteins might involve the assistance of metal ions to coordinate the phosphoryl oxygen and protein side chains to achieve molecular recognition.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry and The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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15
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Bythell BJ, Csonka IP, Suhai S, Barofsky DF, Paizs B. Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine. J Phys Chem B 2010; 114:15092-105. [PMID: 20973555 PMCID: PMC3664278 DOI: 10.1021/jp108452y] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.
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Affiliation(s)
- Benjamin J. Bythell
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Chemistry, Oregon State University, Corvallis, Oregon, USA
| | - István P. Csonka
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Sándor Suhai
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | | | - Béla Paizs
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
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16
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Laskin J, Yang Z, Song T, Lam C, Chu IK. Effect of the Basic Residue on the Energetics, Dynamics, and Mechanisms of Gas-Phase Fragmentation of Protonated Peptides. J Am Chem Soc 2010; 132:16006-16. [DOI: 10.1021/ja104438z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Julia Laskin
- Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States, and Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Zhibo Yang
- Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States, and Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Tao Song
- Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States, and Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Corey Lam
- Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States, and Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Ivan K. Chu
- Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States, and Department of Chemistry, The University of Hong Kong, Hong Kong, China
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17
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Parthasarathi R, He Y, Reilly JP, Raghavachari K. New Insights into the Vacuum UV Photodissociation of Peptides. J Am Chem Soc 2010; 132:1606-10. [DOI: 10.1021/ja907975v] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Yi He
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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Prell JS, Demireva M, Oomens J, Williams ER. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J Am Chem Soc 2008; 131:1232-42. [DOI: 10.1021/ja808177z] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Maria Demireva
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, and FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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