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Watts E, Potts GK, Ready DB, George Thompson AM, Lee J, Escobar EE, Patterson MJ, Brodbelt JS. Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2021; 93:13134-13142. [PMID: 34553926 DOI: 10.1021/acs.analchem.1c01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying major histocompatibility complex (MHC) class I immunopeptide antigens represents a key step in the development of immune-based targeted therapeutics and vaccines. However, the complete characterization of these antigens by tandem mass spectrometry remains challenging due to their short sequence length, high degree of hydrophobicity, and/or lack of sufficiently basic amino acids. This study seeks to address the potential for 193 nm ultraviolet photodissociation (UVPD) to improve the analysis of MHC class I immunopeptides by offering enhanced characterization of these sequences in lower charge states and differentiation of prominent isomeric leucine and isoleucine residues in the HLA-A*02:01 motif. Although electron transfer dissociation-higher energy collisional dissociation (EThcD) offered some success in the differentiation of leucine and isoleucine, 193 nm UVPD was able to confirm the identity of nearly 60% of leucine and isoleucine residues in a synthetic peptide mixture. Furthermore, 193 nm UVPD led to significantly more peptide identifications and higher scoring metrics than EThcD for peptides obtained from immunoprecipitation of MHC class I immunopeptides from in vitro cell culture. Additionally, 193 nm UVPD represents a promising complementary technique to higher-energy collisional dissociation (HCD), in which 424 of the 2593 peptides identified by 193 nm UVPD were not identified by HCD in HLA-A*02:01-specific immunoprecipitation and 804 of the 3300 peptides identified by 193 nm UVPD were not identified by HCD for pan HLA-A, -B, and -C immunoprecipitation. These results highlight that 193 nm UVPD offers an option for the characterization of immunopeptides, including differentiation of leucine and isoleucine residues.
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Affiliation(s)
- Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | - Gregory K Potts
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Damien B Ready
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | | | - Janice Lee
- AbbVie, Inc., North Chicago 60064-1802, Illinois, United States
| | - Edwin E Escobar
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
| | | | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin 78712-1139, Texas, United States
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2
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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3
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Holden DD, Sanders JD, Weisbrod CR, Mullen C, Schwartz JC, Brodbelt JS. Implementation of Fragment Ion Protection (FIP) during Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Anal Chem 2018; 90:8583-8591. [PMID: 29927232 DOI: 10.1021/acs.analchem.8b01723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ultraviolet photodissociation (UVPD) is a nonselective activation method in which both precursor and fragment ions may absorb photons and dissociate. Photoactivation of fragment ions may result in secondary or multiple generations of dissociation, which decreases the signal-to-noise ratio (S/N) of larger fragment ions owing to the prevalent subdivision of the ion current into many smaller, often less informative, fragment ions. Here we report the use of dipolar excitation waveforms to displace fragment ions out of the laser beam path, thus alleviating the extent of secondary dissociation during 193 nm UVPD. This fragment ion protection (FIP) strategy increases S/N of larger fragment ions and improves the sequence coverage obtained for proteins via retaining information deeper into the midsection of protein sequences.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - James D Sanders
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Chad R Weisbrod
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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Herburger A, van der Linde C, Beyer MK. Photodissociation spectroscopy of protonated leucine enkephalin. Phys Chem Chem Phys 2018; 19:10786-10795. [PMID: 28233882 DOI: 10.1039/c6cp08436b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated leucine enkephalin (YGGFL) was studied by ultraviolet photodissociation (UVPD) from 225 to 300 nm utilizing an optical parametric oscillator tunable wavelength laser system (OPO). Fragments were identified by absolute mass measurement in a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Bond cleavage was preferred in the vicinity of the two aromatic residues, resulting in high ion abundances for a4, a1, b3, y2 and y1 fragments. a, b and y ions dominated the mass spectrum, and full sequence coverage was achieved for those types. Photodissociation was most effective at the short wavelength end of the studied range, which is assigned to the onset of the La π-π* transition of the tyrosine chromophore, but worked well also at the Lb π-π* chromophore absorption maxima in the 35 000-39 000 cm-1 region. Several side-chain and internal fragments were observed. H atom loss is observed only above 41 000 cm-1, consistent with the requirement of a curve crossing to a repulsive 1πσ* state. It is suggested that the photochemically generated mobile H atom plays a role in further backbone cleavages, similar to the mechanism for electron capture dissociation. The b4 fragment is most intense at the Lb chromophore absorptions, undergoing additional fragmentation at higher photon energies. The high resolution of the FT-ICR MS revealed that out of all x and z-type fragments only x3 and x4 were formed, with low intensity. Other previously reported x- and z-fragments were re-assigned to internal fragments, based on exact mass measurement.
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Affiliation(s)
- Andreas Herburger
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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Sanders JD, Greer SM, Brodbelt JS. Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics. Anal Chem 2017; 89:11772-11778. [DOI: 10.1021/acs.analchem.7b03396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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6
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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7
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DeGraan-Weber N, Zhang J, Reilly JP. Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2041-2053. [PMID: 27613306 PMCID: PMC5748252 DOI: 10.1007/s13361-016-1487-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 05/21/2023]
Abstract
Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. Graphical Abstract ᅟ.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Jun Zhang
- Pre-Pivotal Drug Product Technologies, Amgen Inc., Thousand Oaks, CA, 91320, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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8
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Halim MA, Girod M, MacAleese L, Lemoine J, Antoine R, Dugourd P. Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1435-42. [PMID: 27287047 PMCID: PMC5031736 DOI: 10.1007/s13361-016-1419-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 05/10/2023]
Abstract
Herein we report the successful implementation of the consecutive and simultaneous photodissociation with high (213 nm) and low (10.6 μm) energy photons (HiLoPD, high-low photodissociation) on ubiquitin in a quadrupole-Orbitrap mass spectrometer. Absorption of high-energy UV photon is dispersed over the whole protein and stimulates extensive C-Cα backbone fragmentation, whereas low-energy IR photon gradually increases the internal energy and thus preferentially dissociates the most labile amide (C-N) bonds. We noticed that simultaneous irradiation of UV and IR lasers on intact ubiquitin in a single MS/MS experiment provides a rich and well-balanced fragmentation array of a/x, b/y, and z ions. Moreover, secondary fragmentation from a/x and z ions leads to the formation of satellite side-chain ions (d, v, and w) and can help to distinguish isomeric residues in a protein. Implementation of high-low photodissociation in a high-resolution mass spectrometer may offer considerable benefits to promote a comprehensive portrait of protein characterization. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69100, Villeurbanne, France
| | - Luke MacAleese
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69100, Villeurbanne, France
| | - Rodolphe Antoine
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne, France.
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9
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Robinson MR, Taliaferro JM, Dalby KN, Brodbelt JS. 193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes. J Proteome Res 2016; 15:2739-48. [PMID: 27425180 DOI: 10.1021/acs.jproteome.6b00289] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet photodissociation (UVPD) at 193 nm is evaluated for the characterization of phosphopeptides in both positive and negative ion modes. Compared to the more standard higher energy collisional dissociation (HCD), UVPD provided more extensive fragmentation with improved phosphate retention on product ions. Negative mode UVPD showed particular merit for detecting and sequencing highly acidic phosphopeptides from alpha and beta casein, but was not as robust for larger scale analysis because of lower ionization efficiencies in the negative mode. HeLa and HCC70 cell lysates were analyzed by both UVPD and HCD. While HCD identified more phosphopeptides and proteins compared to UVPD, the unique matches from UVPD analysis could be combined with the HCD data set to improve the overall depth of coverage compared to either method alone.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
| | - Juliana M Taliaferro
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
| | - Kevin N Dalby
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
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10
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DeGraan-Weber N, Ashley DC, Keijzer K, Baik MH, Reilly JP. Factors Affecting the Production of Aromatic Immonium Ions in MALDI 157 nm Photodissociation Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:834-846. [PMID: 26926443 DOI: 10.1007/s13361-015-1329-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
Immonium ions are commonly observed in the high energy fragmentation of peptide ions. In a MALDI-TOF/TOF mass spectrometer, singly charged peptides photofragmented with 157 nm VUV light yield a copious abundance of immonium ions, especially those from aromatic residues. However, their intensities may vary from one peptide to another. In this work, the effect of varying amino acid position, peptide length, and peptide composition on immonium ion yield is investigated. Internal immonium ions are found to have the strongest intensity, whereas immonium ions arising from C-terminal residues are the weakest. Peptide length and competition among residues also strongly influence the immonium ion production. Quantum calculations provide insights about immonium ion structures and the fragment ion conformations that promote or inhibit immonium ion formation.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Daniel C Ashley
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Karlijn Keijzer
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 339-701, South Korea.
- Institute for Basic Science (IBS), Center for Catalytic Hydrocarbon Functionalizations, Daejeon, 339-701, South Korea.
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN, 47405, USA.
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Xiao L, Nie J, Li D, Chen K. Peptides from two sanguinovorous leeches analyzed by ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometric detector. Pharmacogn Mag 2015; 11:32-7. [PMID: 25709207 PMCID: PMC4329629 DOI: 10.4103/0973-1296.149699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/25/2014] [Accepted: 01/21/2015] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Hirudo nipponica Whitman and Poecilobdella manillensis Lesson fall into the family of Hirudinidae Whitman, both of them are sanguinovorous leeches and used a anticoagulant medicines in China. Their medicinal parts are the dried bodies. However, the peptides in the dried body of the two leeches have not been very clear up to now. OBJECTIVE To analyze the peptides from two sanguinovorous leeches, H. nipponica and P. manillensis. MATERIALS AND METHODS In this article it is reported that the peptides were obtained from anticoagulant active extracted parts of dried bodies of the two leeches and their molecular weights were analyzed by ultra-performance liquid chromatography with electrospray ionization quadrupole time-of-flight mass spectrometry mass spectrometric detector online. RESULTS Three peptide components were identified from H. nipponica with their molecular weight separately 14998, 15988, and 15956, six peptide components were identified from P. manillensis with molecular weight 9590, 13642, 14998, 17631, 15988, and 16567. Two of peptides from P. manillensis have the same molecular weight 14998 and 15988 as that in H. nipponica. CONCLUSION And the two peptides are the main peaks in the base peak ion chromatogram because they occupied a large ratio of total base peak area. Hence the composition of the extracted active part of the two leeches are very close, difference is in that the extract of P. manillensis has more small peptide peaks, but the extract of H. nipponica has not. Furthermore, the tryptic digestion hydrolysates of the extracted active part of each sample were analyzed and the results showed that there were four peaks which only exist in P. manillensis, but not in Hirudo nipponia. They may be the identified peak between the two leeches. This work support the viewpoint that P. manillensis can be used as a medicinal leech as H. nipponia and these peptide components of dried bodies of the two species leeches are a basis for their chemical identification and further investigations in active action.
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Affiliation(s)
- Ling Xiao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China ; Department of TCM, Hubei Provincial Institute for Food and Drug Control, Wuhan, China
| | - Jing Nie
- Department of TCM, Hubei Provincial Institute for Food and Drug Control, Wuhan, China
| | - Danping Li
- Department of TCM, Hubei Provincial Institute for Food and Drug Control, Wuhan, China
| | - Keli Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
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Canon F, Milosavljević AR, Nahon L, Giuliani A. Action spectroscopy of a protonated peptide in the ultraviolet range. Phys Chem Chem Phys 2015; 17:25725-33. [DOI: 10.1039/c4cp04762a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Action spectroscopy of substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV.
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Affiliation(s)
- Francis Canon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- UMR1324 Centre des Sciences du Goût et de l'Alimentation
| | | | - Laurent Nahon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | - Alexandre Giuliani
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- Uar1008
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13
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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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14
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Robotham SA, Kluwe C, Cannon JR, Ellington A, Brodbelt JS. De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9832-8. [PMID: 24050806 DOI: 10.1021/ac402309h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although in silico database search methods remain more popular for shotgun proteomics methods, de novo sequencing offers the ability to identify peptides derived from proteins lacking sequenced genomes and ones with subtle splice variants or truncations. Ultraviolet photodissociation (UVPD) of peptides derivatized by selective attachment of a chromophore at the N-terminus generates a characteristic series of y ions. The UVPD spectra of the chromophore-labeled peptides are simplified and thus amenable to de novo sequencing. This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptides), 47% for β-lactoglobulin (five peptides), 25% for carbonic anhydrase (six peptides), and 51% for bovine serum albumin (33 peptides). This strategy also allowed differentiation of proteins with high sequence homology as evidenced by de novo sequencing of two variants of green fluorescent protein.
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Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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15
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Baker MR, Li QX. Guanidination of tryptic peptides without desalting for matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry analysis. Anal Chem 2013; 85:8873-80. [PMID: 23964694 DOI: 10.1021/ac402246r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Derivatizations that enhance mass spectral quality often require desalting, which presents as a bottleneck in matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)-proteomics. Guanidination, which converts lysine to homoarginine, an arginine analogue, can increase detection of those peptides 5-15-fold. Our aim was to improve guanidination by using a novel reagent, O-methylisourea-freebase. In a simple reaction, interfering salts were removed prior to guanidination. Freebase preparation took about 30 min and could be applied to samples all at once as opposed to desalting samples one-by-one for 5 min each. For freebase guanidinated BSA tryptic peptides, more than 6-times the peptides were observed relative to tryptic peptides or those guanidinated with the conventional reagent, O-methylisourea hemisulfate. Peptide signals increased more than 10-fold relative to those from guanidination with the conventional reagent and were equivalent to those from conventional guanidination with desalting. In addition, freebase guanidination allowed for a lower limit of detection when combined with another derivatization, N-terminal sulfonation, as evidenced by tandem mass spectrometry (MS/MS) fragmentation analysis of in-gel digests of cytochrome c. Freebase guanidination of rat lung proteins after 2-D gel electrophoresis allowed for identification of all tested protein spots regardless of protein characteristics (MW or pI) or abundance. Co-derivatization with N-terminal sulfonation confirmed the identity of low-abundance proteins in 2-D gel spots that contained more than one protein. The freebase guanidination reagent is simple to prepare and to implement. Desalting is not needed prior to MALDI-TOF MS. Freebase guanidination effectively increases the dynamic range of detection of lysine-containing peptides while decreasing the work needed for sample preparation.
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Affiliation(s)
- Margaret R Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa , 1955 East-West Road, Honolulu, Hawaii 96822, United States
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Canon F, Milosavljević AR, van der Rest G, Réfrégiers M, Nahon L, Sarni-Manchado P, Cheynier V, Giuliani A. Photodissociation and Dissociative Photoionization Mass Spectrometry of Proteins and Noncovalent Protein-Ligand Complexes. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Canon F, Milosavljević AR, van der Rest G, Réfrégiers M, Nahon L, Sarni-Manchado P, Cheynier V, Giuliani A. Photodissociation and Dissociative Photoionization Mass Spectrometry of Proteins and Noncovalent Protein-Ligand Complexes. Angew Chem Int Ed Engl 2013; 52:8377-81. [DOI: 10.1002/anie.201304046] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Indexed: 11/06/2022]
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Madsen JA, Cheng RR, Kaoud TS, Dalby KN, Makarov DE, Brodbelt JS. Charge-site-dependent dissociation of hydrogen-rich radical peptide cations upon vacuum UV photoexcitation. Chemistry 2012; 18:5374-83. [PMID: 22431222 DOI: 10.1002/chem.201103534] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Indexed: 11/06/2022]
Abstract
Here, 193 nm vacuum ultraviolet photodissociation (VUVPD) was used to investigate the fragmentation of hydrogen-rich radical peptide cations generated by electron transfer reactions. VUVPD offers new insight into the factors that drive radical- and photon-directed processes. The location of a basic Arg site influences photon-activated C(α)-C(O) bond cleavages of singly charged peptide radical cations, an outcome attributed to the initial conformation of the peptide as supported by molecular dynamics simulated annealing and the population of excited states upon UV excitation. This hybrid ETD/VUVPD method was employed to identify phosphorylation sites of the kinase domain of human TRPM7/ChaK1.
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Affiliation(s)
- James A Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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Liu X, Li YF, Bohrer BC, Arnold RJ, Radivojac P, Tang H, Reilly JP. Investigation of VUV Photodissociation Propensities Using Peptide Libraries. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 308:142-154. [PMID: 22125417 PMCID: PMC3224043 DOI: 10.1016/j.ijms.2011.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PSD does not usually generate a complete series of y-type ions, particularly at high mass, and this is a limitation for de novo sequencing algorithms. It is demonstrated that b(2) and b(3) ions can be used to help assign high mass x(N-2) and x(N-3) fragments that are found in vacuum ultraviolet (VUV) photofragmentation experiments. In addition, v(N)-type ion fragments with side chain loss from the N-terminal residue often enable confirmation of N-terminal amino acids. Libraries containing several thousand peptides were examined using photodissociation in a MALDI-TOF/TOF instrument. 1345 photodissociation spectra with a high S/N ratio were interpreted.
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Brodbelt JS. Shedding light on the frontier of photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:197-206. [PMID: 21472579 DOI: 10.1007/s13361-010-0023-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 05/30/2023]
Abstract
The development of new ion activation/dissociation methods is motivated by the need for more versatile ways to characterize structures of ions, especially in the growing arena of biological mass spectrometry in which better tools for determining sequences, modifications, interactions, and conformations of biopolymers are essential. Although most agree that collision-induced dissociation (CID) remains the gold standard for ion activation/dissociation, recent inroads in electron- and photon-based activation methods have cemented their role as outstanding alternatives. This article will focus on the impact of photodissociation, including its strengths and drawbacks as an analytical tool, and its potential for further development in the next decade. Moreover, the discussion will emphasize photodissociation in quadrupole ion traps, because that platform has been used for one of the greatest arrays of new applications over the past decade.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.
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Madsen JA, Boutz DR, Brodbelt JS. Ultrafast ultraviolet photodissociation at 193 nm and its applicability to proteomic workflows. J Proteome Res 2010; 9:4205-14. [PMID: 20578723 DOI: 10.1021/pr100515x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet photodissociation (UVPD) at 193 nm was implemented on a linear ion trap mass spectrometer for high-throughput proteomic workflows. Upon irradiation by a single 5 ns laser pulse, efficient photodissociation of tryptic peptides was achieved with production of a, b, c, x, y, and z sequence ions, in addition to immonium ions and v and w side-chain loss ions. The factors that influence the UVPD mass spectra and subsequent in silico database searching via SEQUEST were evaluated. Peptide sequence aromaticity and the precursor charge state were found to influence photodissociation efficiency more so than the number of amide chromophores, and the ion trap q-value and number of laser pulses significantly affected the number and abundances of diagnostic product ions (e.g., sequence and immonium ions). Also, photoionization background subtraction was shown to dramatically improve SEQUEST results, especially when peptide signals were low. A liquid chromatography-mass spectrometry (LC-MS)/UVPD strategy was implemented and yielded comparable or better results relative to LC-MS/collision induced dissociation (CID) for analysis of proteolyzed bovine serum albumin and lysed human HT-1080 cytosolic fibrosarcoma cells.
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Affiliation(s)
- James A Madsen
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, USA
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