1
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Paris J, Theisen A, Marzullo BP, Haris A, Morgan TE, Barrow MP, O’Hara J, O’Connor PB. Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1126-1133. [PMID: 35604791 PMCID: PMC9264387 DOI: 10.1021/jasms.1c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.
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Affiliation(s)
- Johanna Paris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alina Theisen
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Bryan P. Marzullo
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Anisha Haris
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tomos E. Morgan
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark P. Barrow
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - John O’Hara
- UCB, 216 Bath Road, Slough SL1 3WE, United
Kingdom
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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2
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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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3
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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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4
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Ider S, Belguesmia Y, Cazals G, Boukherroub R, Coucheney F, Kihal M, Enjalbal C, Drider D. The antimicrobial peptide oranicin P16 isolated from Trichosporon asahii ICVY021, found in camel milk's, inhibits Kocuria rhizophila. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Révész Á, Rokob TA, Jeanne Dit Fouque D, Turiák L, Memboeuf A, Vékey K, Drahos L. Selection of Collision Energies in Proteomics Mass Spectrometry Experiments for Best Peptide Identification: Study of Mascot Score Energy Dependence Reveals Double Optimum. J Proteome Res 2018; 17:1898-1906. [PMID: 29607649 DOI: 10.1021/acs.jproteome.7b00912] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Collision energy is a key parameter determining the information content of beam-type collision induced dissociation tandem mass spectrometry (MS/MS) spectra, and its optimal choice largely affects successful peptide and protein identification in MS-based proteomics. For an MS/MS spectrum, quality of peptide match based on sequence database search, often characterized in terms of a single score, is a complex function of spectrum characteristics, and its collision energy dependence has remained largely unexplored. We carried out electrospray ionization-quadrupole-time of flight (ESI-Q-TOF)-MS/MS measurements on 2807 peptides from tryptic digests of HeLa and E. coli at 21 different collision energies. Agglomerative clustering of the resulting Mascot score versus energy curves revealed that only few of them display a single, well-defined maximum; rather, they feature either a broad plateau or two clear peaks. Nonlinear least-squares fitting of one or two Gaussian functions allowed the characteristic energies to be determined. We found that the double peaks and the plateaus in Mascot score can be associated with the different energy dependence of b- and y-type fragment ion intensities. We determined that the energies for optimum Mascot scores follow separate linear trends for the unimodal and bimodal cases with rather large residual variance even after differences in proton mobility are taken into account. This leaves room for experiment optimization and points to the possible influence of further factors beyond m/ z.
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Affiliation(s)
| | | | - Dany Jeanne Dit Fouque
- UMR CNRS 6521, CEMCA , Université de Bretagne Occidentale , 6 Av. Le Gorgeu , 29238 Brest Cedex 3 , France
| | | | - Antony Memboeuf
- UMR CNRS 6521, CEMCA , Université de Bretagne Occidentale , 6 Av. Le Gorgeu , 29238 Brest Cedex 3 , France
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6
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Sayegh RSR, Batista IDFC, de Melo RL, Riske KA, Daffre S, Montich G, da Silva Junior PI. Longipin: An Amyloid Antimicrobial Peptide from the Harvestman Acutisoma longipes (Arachnida: Opiliones) with Preferential Affinity for Anionic Vesicles. PLoS One 2016; 11:e0167953. [PMID: 27997568 PMCID: PMC5172563 DOI: 10.1371/journal.pone.0167953] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
In contrast to vertebrate immune systems, invertebrates lack an adaptive response and rely solely on innate immunity in which antimicrobial peptides (AMPs) play an essential role. Most of them are membrane active molecules that are typically unstructured in solution and adopt secondary/tertiary structures upon binding to phospholipid bilayers. This work presents the first characterization of a constitutive AMP from the hemolymph of an Opiliones order animal: the harvestman Acutisoma longipes. This peptide was named longipin. It presents 18 aminoacid residues (SGYLPGKEYVYKYKGKVF) and a positive net charge at neutral pH. No similarity with other AMPs was observed. However, high sequence similarity with heme-lipoproteins from ticks suggested that longipin might be a protein fragment. The synthetic peptide showed enhanced antifungal activity against Candida guilliermondii and C. tropicalis yeasts (MIC: 3.8–7.5 μM) and did not interfered with VERO cells line viability at all concentrations tested (200–0.1 μM). This selectivity against microbial cells is related to the highest affinity of longipin for anionic charged vesicles (POPG:POPC) compared to zwitterionic ones (POPC), once microbial plasma membrane are generally more negatively charged compared to mammalian cells membrane. Dye leakage from carboxyfluorescein-loaded POPG:POPC vesicles suggested that longipin is a membrane active antimicrobial peptide and FT-IR spectroscopy showed that the peptide chain is mainly unstructured in solution or in the presence of POPC vesicles. However, upon binding to POPG:POPC vesicles, the FT-IR spectrum showed bands related to β-sheet and amyloid-like fibril conformations in agreement with thioflavin-T binding assays, indicating that longipin is an amyloid antimicrobial peptide.
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Affiliation(s)
- Raphael Santa Rosa Sayegh
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- * E-mail: (RSSS); (PISJ)
| | - Isabel de Fátima Correia Batista
- Unidade de Sequenciamento de Proteínas e Peptídeos, Instituto Butantan, São Paulo, Brazil
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Robson Lopes de Melo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
| | - Karin A. Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sirlei Daffre
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Guillermo Montich
- Centro de Investigaciones en Quimica Biológica de Córdoba (CIQUIBIC, UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pedro Ismael da Silva Junior
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- * E-mail: (RSSS); (PISJ)
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7
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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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8
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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9
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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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10
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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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11
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Harrison AG. Effect of the sarcosine residue on sequence scrambling in peptide b(5) ions. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:161-167. [PMID: 24464544 DOI: 10.1002/jms.3323] [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: 09/11/2013] [Revised: 11/24/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
The effect of N-methylation on sequence scrambling in the fragmentation of b5 ions has been investigated by studying a variety of peptides containing sarcosine (N-methylglycine). The product ion mass spectra for the b5 ions derived from Sar-A-A-A-Y-A and Sar-A-A-Y-A-A show only minor signals for non-direct sequence ions the major fragmentation reactions occurring from the unrearranged structures. This is in contrast to the b5 ions where the Sar residue is replaced by Ala and sequence scrambling occurs. The b5 ion derived from Y-Sar-A-A-A-A shows a product ion mass spectrum essentially identical to the spectrum of the b5 ion derived from Sar-A-A-A-Y-A, indicating that in the former case macrocyclization has occurred but the macrocyclic form shows a strong preference to reopen to put the Sar residue in the N-terminal position. Similar results were obtained in the comparison of b5 ions derived from A-Sar-A-A-Y-A and Sar-A-A-Y-A-A. The product ion mass spectra of the MH(+) ions of Y-Sar-A-A-A-A and A-Sar-A-A-Y-A show substantial signals for non-direct sequence ions indicating that fragmentation of the MH(+) ions channels extensively through the respective b5 ions and further fragmentation of these species.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Canada
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12
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The fate of b-ions in the two worlds of collision-induced dissociation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2843-8. [DOI: 10.1016/j.bbapap.2013.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/14/2013] [Accepted: 08/16/2013] [Indexed: 11/21/2022]
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13
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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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14
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Harrison AG. Fragmentation reactions of methionine-containing protonated octapeptides and fragment ions therefrom: an energy-resolved study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1555-1564. [PMID: 23943431 DOI: 10.1007/s13361-013-0706-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 05/27/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
The fragmentation reactions of the MH(+) ions as well as the b7, a7, and a7* ions derived therefrom have been studied in detail for the octapeptides MAAAAAAA, AAMAAAAA, AAAAMAAA, and AAAAAAMA. Ionization was by electrospray using a QqToF mass spectrometer, which allowed a study of the evolution of the fragmentation channels as a function of the collision energy. Not surprisingly, the product ion mass spectra for the b7 ions are independent of the original precursor sequence, indicating macrocyclization and reopening to the same mixture of protonated oxazolones prior to fragmentation. The results show that this sequence scrambling results in a distinct preference to place the Met residue in the C-terminal position of the protonated oxazolones. The a7 and a7* ions also produce product ion mass spectra independent of the original peptide sequence. The results for the a7 ions indicate that fragmentation occurs primarily from an amide structure analogous to that observed for a4 ions (Bythell et al. in J Am Chem Soc 132:14766-14779, 2010). Clearly, the rearrangement reaction they have proposed applies equally well to an ions as large as a7. The major fragmentation modes of the MH(+) ions at low collision energies produce b7, b6, and b5 ions. As the collision energy is increased further fragmentation of these primary products produces, in part, non-direct sequence ions, which become prominent at lower m/z values, particularly for the peptides with the Met residue near the N-terminus.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada,
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15
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Nihashi Y, Miyashita M, Awane H, Miyagawa H. Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing. Mass Spectrom (Tokyo) 2013; 2:A0024. [DOI: 10.5702/massspectrometry.a0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 10/29/2013] [Indexed: 11/23/2022] Open
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16
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Banerjee S, Mazumdar S. Selective deletion of the internal lysine residue from the peptide sequence by collisional activation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1967-1980. [PMID: 22923014 DOI: 10.1007/s13361-012-0456-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/15/2012] [Accepted: 07/20/2012] [Indexed: 06/01/2023]
Abstract
The gas-phase peptide ion fragmentation chemistry is always the center of attraction in proteomics to analyze the amino acid sequence of peptides and proteins. In this work, we describe the formation of an anomalous fragment ion, which corresponds to the selective deletion of the internal lysine residue from a series of lysine containing peptides upon collisional activation in the ion trap. We detected several water-loss fragment ions and the maximum number of water molecules lost from a particular fragment ion was equal to the number of lysine residues in that fragment. As a consequence of this water-loss phenomenon, internal lysine residues were found to be deleted from the peptide ion. The N,N-dimethylation of all the amine functional groups of the peptide stopped the internal lysine deletion reaction, but selective N-terminal α-amino acetylation had no effect on this process indicating involvement of the side chains of the lysine residues. The detailed mechanism of the lysine deletion was investigated by multistage CID of the modified and unmodified peptides, by isotope labeling and by energy resolved CID studies. The results suggest that the lysine deletion might occur through a unimolecular multistep mechanism involving a seven-membered cyclic imine intermediate formed by the loss of water from a lysine residue in the protonated peptide. This intermediate subsequently undergoes degradation reaction to deplete the interior imine ring from the peptide backbone leading to the deletion of an internal lysine residue.
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Affiliation(s)
- Shibdas Banerjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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17
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Ronga L, Verdié P, Sanchez P, Enjabal C, Maurras A, Jullian M, Puget K, Martinez J, Subra G. Supported oligomethionine sulfoxide and Ellman’s reagent for cysteine bridges formation. Amino Acids 2012; 44:733-42. [DOI: 10.1007/s00726-012-1397-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 08/30/2012] [Indexed: 01/29/2023]
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18
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Sun S, Yang F, Yang Q, Zhang H, Wang Y, Bu D, Ma B. MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions. J Proteome Res 2012; 11:4509-16. [DOI: 10.1021/pr300235v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Shiwei Sun
- Advanced Research
Laboratory,
Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent
Information Processing, Chinese Academy of Sciences, Beijing, China
| | - Fuquan Yang
- Proteomics Platform, Institute
of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qing Yang
- Advanced Research
Laboratory,
Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- School
of Computer Science, University of Science and Technology, Beijing, China
| | - Hong Zhang
- College of Food
Science and Biological
Engineering, Zhejiang Gongshang University, Hangzhou, China
| | - Yaojun Wang
- Advanced Research
Laboratory,
Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Dongbo Bu
- Advanced Research
Laboratory,
Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent
Information Processing, Chinese Academy of Sciences, Beijing, China
| | - Bin Ma
- School
of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
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19
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Harrison AG. Fragmentation reactions of b(5) and a (5) ions containing proline--the structures of a(5) ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:594-601. [PMID: 21952775 DOI: 10.1007/s13361-011-0232-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/01/2011] [Accepted: 08/11/2011] [Indexed: 05/31/2023]
Abstract
A detailed study has been made of the b(5) and a(5) ions derived from the amides H-Ala-Ala-Ala-Ala-Pro-NH(2), H-Ala-Ala-Ala-Pro-Ala-NH(2), and H-Ala-Ala-Pro-Ala-Ala-NH(2). From quasi-MS(3) experiments it is shown that the product ion mass spectra of the three b(5) ions are essentially identical, indicating macrocyclization/reopening to produce a common mixture of intermediates prior to fragmentation. This is in agreement with numerous recent studies of sequence scrambling in b ions. By contrast, the product ion mass spectra for the a(5) ions show substantial differences, indicating significant differences in the mixture of structures undergoing fragmentation for these three species. The results are interpreted in terms of a mixture of classical substituted iminium ions as well as protonated C-terminal amides formed by cyclization/rearrangement as reported recently for a(4) ions (Bythell, Maître , Paizs, J . Am. Chem. Soc. 2010, 132, 14761-14779). Novel fragment ions observed upon fragmentation of the a(5) ions are protonated H-Pro-NH(2) and H-Pro-Ala-NH(2) which arise by fragmentation of the amides. The observation of these products provides strong experimental evidence for the cyclization/rearrangement reaction to form amides and shows that it also applies to a(5) ions.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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20
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Dupré M, Cantel S, Martinez J, Enjalbal C. Occurrence of C-terminal residue exclusion in peptide fragmentation by ESI and MALDI tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:330-346. [PMID: 22095165 DOI: 10.1007/s13361-011-0254-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/14/2011] [Accepted: 09/14/2011] [Indexed: 05/31/2023]
Abstract
By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (b(n-1) + H(2)O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H(2)O and NH(3)) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to the formation of a y(m-1) ion, i.e., to the loss of the N-terminal residue following the a(1)-y(m-1) fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra of singly charged peptides not to mix up the attribution of the N- and C-terminal amino acids. Although such peculiar fragmentation behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce arginine-containing peptides.
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Affiliation(s)
- Mathieu Dupré
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Bâtiment Chimie (17), Université Montpellier 2, Universités Montpellier 1 et 2 - CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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21
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Chawner R, Gaskell SJ, Eyers CE. Proposal for a common nomenclature for peptide fragment ions generated following sequence scrambling during collision-induced dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:205-206. [PMID: 22173809 DOI: 10.1002/rcm.5294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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22
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Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. Int J Anal Chem 2011; 2012:282574. [PMID: 22611397 PMCID: PMC3348530 DOI: 10.1155/2012/282574] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/23/2011] [Accepted: 11/09/2011] [Indexed: 01/12/2023] Open
Abstract
The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.
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23
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Zhang J, Al-Eryani R, Ball HL. Mass spectrometry analysis of 2-nitrophenylhydrazine carboxy derivatized peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1958-1967. [PMID: 21952763 DOI: 10.1007/s13361-011-0220-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/14/2011] [Accepted: 07/19/2011] [Indexed: 05/31/2023]
Abstract
Peptides with two or more basic residues, including those with post-translational modifications (PTMs), such as methylation and phosphorylation, can be highly hydrophilic and, therefore, are often difficult to be retained on a reversed-phase (RP) column. In addition, these highly hydrophilic peptides may carry two or more positive charges, which often fragment poorly upon collisionally activated dissociation (CAD), resulting in few sequence-specific ions. C-terminal rearrangement may also occur during CAD. Furthermore, some PTMs are labile and tend to be lost when subjected to CAD as is the case with phosphorylation on serine or threonine. To overcome the difficulties of separation, detection, and fragmentation of highly hydrophilic peptides, we report here the effect of carboxy group derivatization with 2-nitrophenylhydrazine (this strategy will be called NPHylation for simplicity). NPHylation significantly increases the hydrophobicity of the peptides, eliminates C-terminal rearrangement in all cases, and offers enhanced sensitivity in some cases. In addition, the CAD spectra of the resulting NPHylated peptides carry more sequence-specific ions due to significant reduction of sequence scrambling as observed for peptide EHAGVISVL. Furthermore, the different carboxy derivatives of this peptide undergo sequence scrambling to varying degrees, which clearly demonstrates that the C-terminus has a profound effect on peptide fragmentation. Finally, sequence scrambling is a charge dependent phenomenon, which affects CAD of doubly charged peptides far more than their singly charged counterparts.
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Affiliation(s)
- Junmei Zhang
- Protein Chemistry Technology Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
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24
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Saminathan IS, Zhao J, Siu KWM, Hopkinson AC. Doubly charged protonated a ions derived from small peptides. Phys Chem Chem Phys 2011; 13:18307-14. [PMID: 21773645 DOI: 10.1039/c1cp21522a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protonated a(2) and a(3) (therefore doubly charged) ions in which both charges lie on the peptide backbone are formed in collision-induced dissociations of [La(III)(peptide)(CH(3)CN)(m)](3+) complexes. Abundant (a(3)+H)(2+) ions are formed from triproline (PPP) and peptides with a proline residue at the N-terminus; these peptides are the most effective in producing ions of the type (a(2)+H)(2+) and (a(3)+H)(2+). A systematic study of the effect of the location of the proline residue and other residues of aliphatic amino acids on the generation of protonated a ions is reported. Density functional theory calculations at B3LYP/6-311++G(d,p) gave the proton affinity of the a(3) ion derived from PPP to be 167.6 kcal mol(-1), 2.6 kcal mol(-1) higher than that of water. The protonated a(2) ions of diglycine and diproline and a(3) ions of triglycine have lower proton affinities and are only observed in lower abundances, possibly due to proton transfer to water in ion-molecule reactions.
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Affiliation(s)
- Irine S Saminathan
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Canada M3J 1P3
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25
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Verkerk UH, Zhao J, Van Stipdonk MJ, Bythell BJ, Oomens J, Hopkinson AC, Siu KM. Structure of the [M + H – H2O]+ Ion from Tetraglycine: A Revisit by Means of Density Functional Theory and Isotope Labeling. J Phys Chem A 2011; 115:6683-7. [DOI: 10.1021/jp202820h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Udo H. Verkerk
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Junfang Zhao
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - Michael J. Van Stipdonk
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260-0051, United States
| | - Benjamin J. Bythell
- Computational Proteomics Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Jos Oomens
- FOM Institute for Plasma Physics, 3430 BE Nieuwegein, The Netherlands
- University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - K.W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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26
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Yu L, Tan Y, Tsai Y, Goodlett DR, Polfer NC. On the relevance of peptide sequence permutations in shotgun proteomics studies. J Proteome Res 2011; 10:2409-16. [PMID: 21413817 DOI: 10.1021/pr101235w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom.2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., <5 ppm) of the precursor ion and at least one fragment ion that confirms the sequence. The peptides are then grouped into higher- and lower-confidence data sets, using five fragment ions as a cutoff for higher-confidence identification. It is shown that the propensity for sequence permutation increases with the length of the tryptic peptide in both data sets. A higher charge state (i.e., 3+ vs 2+) also appears to correlate with a higher appearance of permuted masses for larger peptides. The ratio of these permuted sequence ions, compared to all tandem mass spectral peaks, reaches ∼25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum ∼8%), based on a null-hypothesis decoy data set.
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Affiliation(s)
- Long Yu
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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27
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Dupré M, Cantel S, Verdié P, Martinez J, Enjalbal C. Sequencing Lys-N proteolytic peptides by ESI and MALDI tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:265-279. [PMID: 21472586 DOI: 10.1007/s13361-010-0022-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/15/2010] [Accepted: 10/22/2010] [Indexed: 05/30/2023]
Abstract
In this study, we explored the MS/MS behavior of various synthetic peptides that possess a lysine residue at the N-terminal position. These peptides were designed to mimic peptides produced upon proteolysis by the Lys-N enzyme, a metalloendopeptidase issued from a Japanese fungus Grifola frondosa that was recently investigated in proteomic studies as an alternative to trypsin digestion, as a specific cleavage at the amide X-Lys chain is obtained that provides N-terminal lysine peptide fragments. In contrast to tryptic peptides exhibiting a lysine or arginine residue solely at the C-terminal position, and are thus devoid of such basic amino acids within the sequence, these Lys-N proteolytic peptides can contain the highly basic arginine residue anywhere within the peptide chain. The fragmentation patterns of such sequences with the ESI-QqTOF and MALDI-TOF/TOF mass spectrometers commonly used in proteomic bottom-up experiments were investigated.
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Affiliation(s)
- Mathieu Dupré
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, Bâtiment Chimie (17), Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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28
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Saminathan IS, Wang XS, Guo Y, Krakovska O, Voisin S, Hopkinson AC, Siu KWM. The extent and effects of peptide sequence scrambling via formation of macrocyclic B ions in model proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:2085-2094. [PMID: 20947370 DOI: 10.1016/j.jasms.2010.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 08/18/2010] [Accepted: 09/01/2010] [Indexed: 05/30/2023]
Abstract
The extent and effects of sequence scrambling in peptide ions during tandem mass spectrometry (MS/MS) have been examined using tryptic peptides from model proteins. Sequence-scrambled b ions appeared in about 35% of 43 tryptic peptides examined under MS/MS conditions. In general, these ions had relatively low abundances with averages of 8% and 16%, depending on the instrumentation used. A few tryptic peptides gave abundant scrambled b ions in MS/MS. However, peptide and protein identifications under proteomic conditions with Mascot were not affected, even for these peptides wherein scrambling was prominent. From the 43 tryptic peptides that have been investigated, the conclusion is that sequence scrambling is unlikely to impact negatively on the accuracy of automated peptide and protein identifications in proteomics.
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Affiliation(s)
- Irine S Saminathan
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
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29
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Bythell BJ, Maître P, Paizs B. Cyclization and Rearrangement Reactions of an Fragment Ions of Protonated Peptides. J Am Chem Soc 2010; 132:14766-79. [DOI: 10.1021/ja101556g] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benjamin J. Bythell
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany, and Laboratoire de Chimie Physique, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex, France
| | - Philippe Maître
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany, and Laboratoire de Chimie Physique, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex, France
| | - Béla Paizs
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany, and Laboratoire de Chimie Physique, Université Paris-Sud 11, UMR8000 CNRS, Faculté des Sciences, Bât. 350, 91405 Orsay Cedex, France
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30
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Bythell BJ, Knapp-Mohammady M, Paizs B, Harrison AG. Effect of the His residue on the cyclization of b ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1352-1363. [PMID: 20541953 DOI: 10.1016/j.jasms.2010.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 05/07/2010] [Accepted: 05/07/2010] [Indexed: 05/29/2023]
Abstract
The MS(n) spectra of the [M + H](+) and b(5) peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b(4) ions derived from the first four peptides. The MS(2) spectra of the [M + H](+) ions show a substantial series of b(n) ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b ions when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b(4) and b(5) ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b(n) ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b(5) structures, the b(4) ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b(4) and b(5) the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.
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Affiliation(s)
- Benjamin J Bythell
- Computational Proteomics Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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31
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Shen S, Chahal B, Majumder K, You SJ, Wu J. Identification of novel antioxidative peptides derived from a thermolytic hydrolysate of ovotransferrin by LC-MS/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:7664-7672. [PMID: 20568771 DOI: 10.1021/jf101323y] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Ovotransferrin is a glycoprotein well-known for its iron-binding property. Ovotransferrin was reported to have antioxidative properties, but the presence of antioxidant peptides within the protein has not been reported. The purpose of the study was to characterize the antioxidant peptides within ovotransferrin. Ovotransferrin was sonicated and hydrolyzed by thermolysin, and peptides from the hydrolysate were fractionated by ion-exchange fast protein liquid chromatography and reversed-phase high-performance liquid chromatography. Fourteen peptides derived from ovotransferrin were characterized using LC-MS/MS, and their oxygen radical absorbance capacity (ORAC) values were determined using synthetic peptides. Two tetrapeptides (Trp-Asn-Ile-Pro and Gly-Trp-Asn-Ile) showed the highest antioxidant activity. Interestingly, the addition of amino acid residues to either the N or C terminus of the two peptides decreased the antioxidant activity, suggesting that the motif of Trp-Asn-Ile is responsible for the high antioxidant activity.
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Affiliation(s)
- Shengwen Shen
- 4-10 Agriculture Forestry Centre, Department of Agricultural and Food Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
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32
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Na S, Paek E. Prediction of novel modifications by unrestrictive search of tandem mass spectra. J Proteome Res 2010; 8:4418-27. [PMID: 19658439 DOI: 10.1021/pr9001146] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Post-translational modifications (PTMs) greatly increase the complexity and diversity of the proteome so that a protein can carry out a wide variety of functions. PTM prediction on proteins is one of the major challenges in proteomics research. Various approaches have been developed for an unrestrictive search of PTMs in proteins using tandem mass spectrometry (MS/MS). However, most tools usually addressed frequent modifications despite the fact that critical biological modifications may be rare. Here, we present MODmap for exploring potentially important rare and unknown modifications from MS/MS spectra. Extended sequence tag-based spectral alignment is proposed. It is highly sensitive to modified regions in an MS/MS spectrum and is tolerant of multiple modifications per peptide. We have developed an unrestrictive algorithm (MOD(i)), which rapidly searches for all known types of PTMs at once, without limiting a multitude of modified sites in a peptide. After MOD(i) produces spectral alignment results using all known types of PTMs, high-quality spectral alignments are subject to MODmap and are re-estimated. New mass offsets are reported via local alignment and MODmap determines novel modification candidates. In analyses of PTM-rich lens proteins, our methodology was demonstrated to be sensitive to rare modifications and suggested several confident novel modification candidates.
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Affiliation(s)
- Seungjin Na
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea
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33
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Harrison AG. Cyclization of peptide b9 ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2248-2253. [PMID: 19781958 DOI: 10.1016/j.jasms.2009.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/12/2009] [Accepted: 08/14/2009] [Indexed: 05/28/2023]
Abstract
The product ion mass spectra obtained by CID of the b(9) ions derived by loss of neutral alanine from the MH+ ion of the peptides Tyr(Ala)9, (Ala)4Tyr(Ala)5, and (Ala)8TyrAla are essentially identical, indicative of full cyclization reaction to a common intermediate before fragmentation. This leads to abundant nondirect sequence ions in the product ion mass spectra of the b9 ions. The product ion mass spectra of the b8 ions from the first two peptides also are essentially identical. The fragmentation of the MH+ ions also leads to low intensity nondirect sequence ions in the product ion mass spectra. N-terminal acetylation blocks the cyclization and eliminates nondirect sequence fragment ions in the product ion mass spectra.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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34
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Choi S, Jeong J, Na S, Lee HS, Kim HY, Lee KJ, Paek E. New Algorithm for the Identification of Intact Disulfide Linkages Based on Fragmentation Characteristics in Tandem Mass Spectra. J Proteome Res 2009; 9:626-35. [DOI: 10.1021/pr900771r] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Seonhwa Choi
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
| | - Jaeho Jeong
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
| | - Seungjin Na
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
| | - Hyo Sun Lee
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
| | - Hwa-Young Kim
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
| | - Kong-Joo Lee
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
| | - Eunok Paek
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, Korea 130-743, The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy and Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul, Korea 120-750, and Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Korea 705-717
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35
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Shenar N, Cantel S, Martinez J, Enjalbal C. Comparison of inert supports in laser desorption/ionization mass spectrometry of peptides: pencil lead, porous silica gel, DIOS-chip and NALDI target. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2371-2379. [PMID: 19575411 DOI: 10.1002/rcm.4158] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In the search for alternative inert surfaces replacing silicon chips in Desorption/Ionization On porous Silicon (DIOS)-like mass spectrometry analyses, nanostructured silicon-based NALDI chips were evaluated in Laser Desorption/Ionization (LDI) of peptides. Comparisons were made using commercially available DIOS chips (MassPREP-DIOS-target), amorphous carbon powder from lead pencil and porous silica gel used for chromatographic purposes as reference supports. A set of synthetic model peptides presenting variable amino acid sequences of various lengths was analyzed under all conditions. The LDI responses of the four 'matrix-free' techniques were compared, especially in terms of peptide detection sensitivity and overall experiment robustness.
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Affiliation(s)
- Nawar Shenar
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, Bâtiment Chimie (17), Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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36
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Armirotti A, Damonte G, Pozzolini M, Mussino F, Cerrano C, Salis A, Benatti U, Giovine M. Primary Structure and Post-Translational Modifications of Silicatein Beta from the Marine Sponge Petrosia ficiformis (Poiret, 1789). J Proteome Res 2009; 8:3995-4004. [DOI: 10.1021/pr900342y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Armirotti
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Gianluca Damonte
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Marina Pozzolini
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Francesca Mussino
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Carlo Cerrano
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Annalisa Salis
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Umberto Benatti
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
| | - Marco Giovine
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi, 10, 16132 Genova, Italy, Center of Excellence for Biomedical Research, Viale Benedetto XV, 7 16132 Genova, Italy, Dipartimento per lo Studio del Territorio e delle sue Risorse, Corso Europa 26, 16132 Genova, Italy, Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Viale Benedetto XV, 1 16132 Genova, Italy, and Dipartimento di Biologia, Università degli Studi di Genova, Via Pastore 3, 16132 Genova, Italy
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37
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Harrison AG. To b or not to b: the ongoing saga of peptide b ions. MASS SPECTROMETRY REVIEWS 2009; 28:640-654. [PMID: 19338048 DOI: 10.1002/mas.20228] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Modern soft ionization techniques readily produce protonated or multiply protonated peptides. Collision-induced dissociation (CID) of these protonated species is often used as a method to obtain sequence information. In many cases fragmentation occurs at amide bonds. When the charge resides on the C-terminal fragment so-called y ions are produced which are known to be protonated amino acids or truncated peptides. When the charge resides on the N-terminal fragment so-called b ions are produced. Often the sequence of y and b ions are essential for peptide sequencing. The b ions have many possible structures, a knowledge of which is useful in this sequencing. The structures of b ions are reviewed in the following with particular emphasis on the variation of structure with the number of amino acid residues in the b ion and the effect of peptide side chain on b ion structure. The recent discovery of full cyclization of larger b ions results in challenges in peptide sequencing. This aspect is discussed in detail.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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38
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Harrison AG. Fragmentation reactions of some peptide b3 ions: an energy-resolved study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1298-1302. [PMID: 19306282 DOI: 10.1002/rcm.4003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The fragmentation reactions of b3 ions of nominal structure AAAoxa, YAAoxa, AYAoxa and AAYoxa have been studied as a function of collision energy, allowing the construction of breakdown graphs expressing in a qualitative way the energy dependence of the fragmentation reactions. The primary fragmentation reactions of the AAAoxa b3 ion involve formation of the a3* (a3-NH3) ion and the b2 ion, with the latter becoming the dominant product at higher internal energies. For both YAAoxa and AYAoxa b3 ions the pathway to a3* is relatively minor with formation of b2 the dominant primary fragmentation reaction. For the AAYoxa b3 ion, in addition to a3*, abundant formation of the tyrosine (Y) iminium ion is observed with only minor formation of the b2 ion. The results support and expand upon the detailed mechanism of fragmentation of b3 ions proposed by Cooper et al. (J. Am. Soc. Mass Spectrom. 2006; 17: 1654).
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Canada.
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Shenar N, Sommerer N, Martinez J, Enjalbal C. Comparison of LID versus CID activation modes in tandem mass spectrometry of peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:621-632. [PMID: 19097045 DOI: 10.1002/jms.1535] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report our contribution to the systematic investigation of peptide fragmentations performed on high-performance Tof equipment, operating in MS and MS/MS modes, such as ESI-QqTof and MALDI-Tof/Tof instruments that are commonly available today in proteomic laboratories. Whereas the former analyzer's configuration provides low-energy collision-induced dissociations (CID), the latter allows tunable activation methods of the selected parent ion to induce either metastable laser-induced dissociations (LID) or high-energy CID ('gas on spectra LID'). Fragmentation of the monoprotonated ion of 53 peptides (FW 807-2853 g/mol) was undertaken upon low-energy CID on an ESI-QTof mass spectrometer (Waters) as well as high-energy CID and LID conditions on a MALDI Ultraflex mass spectrometer (Bruker). Systematic comparison of MS/MS spectra provided useful information on the performance of each piece of equipment for efficient peptide sequencing and also insights into the observed fragmentation behaviors.
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Affiliation(s)
- Nawar Shenar
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-Universités Montpellier 1 et 2, Bâtiment Chimie (17), Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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40
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Armirotti A, Benatti U, Damonte G. Top-down proteomics with a quadrupole time-of-flight mass spectrometer and collision-induced dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:661-666. [PMID: 19184982 DOI: 10.1002/rcm.3925] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
With slight modifications of the instrumental parameters, we demonstrate that satisfactory top-down data can be obtained with collision-induced dissociation (CID) tandem mass spectrometry on a quadrupole time-of-flight (qTOF) instrument not originally designed for this purpose. Protein identification is achieved with both N- and C-terminal sequence tags and BLAST database searches. The accurate mass measurement of multiply charged fragment ions (mostly y and b-type) supplements the limited set of cleavage sites and provides a high degree of sequence coverage (90-100%). Post-translational modification issues can be addressed too. This approach might help those mass spectrometry (MS) core facilities that are not able to afford very high-resolution instruments, thus expanding the benefits of top-down protein analysis over the worldwide MS community.
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Affiliation(s)
- Andrea Armirotti
- Centro Biotecnologie Avanzate, Largo Rosanna Benzi 10, 16132 Genova, Italy.
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41
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Deepalakshmi PD. Characterization of recombinant protein mutants by top-down sequencing using quadrupole time-of-flight mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009; 15:641-649. [PMID: 19679944 DOI: 10.1255/ejms.1012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Top-down sequencing using quadrupole time-of-flight mass spectrometry is used as a direct way of locating the mutated sites of recombinant proteins and posttranslational modification in a protein. Several mutants of barstar, expressed in E.coli, were confirmed by analyzing the fragmentation pattern of mutants. A contaminant protein, that appeared while purifying mutants of barstar, was identified as acyl carrier protein from E.coli with a posttranslational modification on serine residue, indicating that the protein was biologically active. A mutant of ribosomal protein S6 has been characterized with neutral loss of ammonia at the N-terminal region of the protein. The power of the "top-down" approach in characterizing the mutants of recombinant proteins has been demonstrated.
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42
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Riba Garcia I, Giles K, Bateman RH, Gaskell SJ. Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1781-1787. [PMID: 18930410 DOI: 10.1016/j.jasms.2008.09.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 09/15/2008] [Accepted: 09/22/2008] [Indexed: 05/26/2023]
Abstract
The structures of peptide a- and b-type fragment ions were studied using synthetic peptides including a set of isomeric peptides, differing in the sequence location of an alanine residue labeled with (15)N and uniformly with (13)C. The pattern of isotope labeling of second-generation fragment ions derived via a(n) and b(n) ions (where n = 4 or 5) suggested that these intermediates existed in part as macrocyclic structures, where alternative sites of ring opening gave rise to different linear forms whose simple cleavage might give rise to the observed final products. Similar conclusions were derived from combined ion mobility/tandem MS analyses where different fragmentation patterns were observed for isomeric a- or b-type ions that display different ion mobilities. These analyses were facilitated by a new approach to the processing of ion mobility/tandem MS data, from which distinct and separate product ion spectra are derived from ions that are incompletely separated by ion mobility. Finally, an example is provided of evidence for a macrocyclic structure for b(n) ions where n = 8 or 9.
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Affiliation(s)
- Isabel Riba Garcia
- Michael Barber Centre for Mass Spectrometry, School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
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43
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Harrison AG. Peptide sequence scrambling through cyclization of b(5) ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:1776-1780. [PMID: 18639467 DOI: 10.1016/j.jasms.2008.06.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 05/29/2008] [Accepted: 06/25/2008] [Indexed: 05/26/2023]
Abstract
The CID mass spectra of the MH(+) ions and the b(5) ions derived therefrom have been determined for the hexapeptides YAAAAA, AYAAAA, AAYAAA, AAAYAA, and AAAAYA. The CID mass spectra for the b(5) ions derived from the five isomers are essentially identical and show abundant ion signals for nonsequence b ions. This result is consistent with cyclization of the b(5) ions to a cyclic pentapeptide before fragmentation; this cyclic peptide can open at various positions, leading to losses of amino acid residues that are not characteristic of the original amino acid sequence. These nonsequence b ions are also observed in the fragmentation of the MH(+) ions and increase substantially in importance with increasing collision energy. A comparison of the fragmentation of AAAYAA and Ac-AAAYAA indicates that N-acetylation eliminates the cyclization of b(5) ions and, thus, eliminates the nonsequence ions in the CID mass spectra of both b(5) and MH(+) ions.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Canada.
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44
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Palumbo AM, Reid GE. Evaluation of Gas-Phase Rearrangement and Competing Fragmentation Reactions on Protein Phosphorylation Site Assignment Using Collision Induced Dissociation-MS/MS and MS3. Anal Chem 2008; 80:9735-47. [DOI: 10.1021/ac801768s] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amanda M. Palumbo
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gavin E. Reid
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Na S, Jeong J, Park H, Lee KJ, Paek E. Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach. Mol Cell Proteomics 2008; 7:2452-63. [PMID: 18701446 DOI: 10.1074/mcp.m800101-mcp200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Identification of post-translational modifications (PTMs) is important to understanding the biological functions of proteins. MS/MS is a useful tool to identify PTMs. Most existing search tools are restricted to take only a few types of PTMs as input. Here we describe a new algorithm, called MOD(i) (pronounced "mod eye"), that rapidly searches for all known types of PTMs at once without limiting a multitude of modified sites in a peptide. MOD(i) introduces the notion of a tag chain, a combination structure made from multiple sequence tags, that effectively localizes modified regions within a spectrum and overcomes de novo sequencing errors common in tag-based approaches. MOD(i) showed its performance competence by identifying various types of PTMs in analysis of PTM-rich proteins such as glyceraldehyde-3-phosphate dehydrogenase and lens protein. We demonstrated that MOD(i) innovatively manages the computational complexity of identifying multiple PTMs in a peptide, which may exist in a greater variety than usually expected. In addition, it is suggested that MOD(i) has great potential to discover novel modifications.
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Affiliation(s)
- Seungjin Na
- Department of Mechanical and Information Engineering, University of Seoul, Seoul, 130-743, Korea
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46
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Shenar N, Martinez J, Enjalbal C. Laser desorption/ionization mass spectrometry on porous silica and alumina for peptide mass fingerprinting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:632-644. [PMID: 18356075 DOI: 10.1016/j.jasms.2008.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 02/06/2008] [Accepted: 02/19/2008] [Indexed: 05/26/2023]
Abstract
We investigated a variant of desorption/ionization on porous silicon (DIOS) mass spectrometry utilizing an aqueous suspension of either porous silica gel or porous alumina (pore size of 60 and 90 A, respectively). Laser desorption/ionization (LDI) from samples directly deposited on a stainless steel surface without any inorganic substrates was also achieved. Synthetic peptides designed to cover large sequence diversity constituted our model compounds. Sample preparation, including material conditioning, peptide solubilization, and deposition protocol onto standard matrix-assisted laser desorption/ionization (MALDI) probe, as well as ionization source tuning were optimized to perform sensitive reproducible LDI analyses. The addition of either a cationizing agent or an alkali metal scavenger to the sample suspension allowed modification of the ionization output. Comparing hydrophilic silica gel to hydrophobic reversed-phase silica gel as well as increasing material pore size provided further insights into desorption/ionization processes. Furthermore, mixtures of peptides were analyzed to probe the spectral suppression phenomenon when no interfering organic matrix was present. The results gathered from synthetic peptide cocktails indicated that LDI mass spectrometry on silica gel or alumina constitutes a promising complementary method to MALDI in proteomics for peptide mass fingerprinting.
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Affiliation(s)
- Nawar Shenar
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-Universités Montpellier 1 et 2, Université Montpellier 2, Montpellier, France
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47
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Dodds ED, German JB, Lebrilla CB. Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation. Anal Chem 2007; 79:9547-56. [PMID: 18001128 DOI: 10.1021/ac701763t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a central tool for proteomic analysis, yet the singly protonated tryptic peptide ions produced by MALDI are significantly more difficult to dissociate for tandem mass spectrometry (MS/MS) than the corresponding multiply protonated ions. In order to overcome this limitation, current proteomic approaches using MALDI-MS/MS involve high-energy collision-induced dissociation (CID). Unfortunately, the use of high-energy CID complicates product ion spectra with a significant proportion of irrelevant fragments while also reducing mass accuracy and mass resolution. In order to address the lack of a high-resolution, high mass accuracy MALDI-MS/MS platform for proteomics, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and a recently developed MS/MS technique termed CIRCA (for combination of infrared and collisional activation) have been applied to proteomic analysis. Here, CIRCA is shown to be suitable for dissociating singly protonated tryptic peptides, providing greater sequence coverage than either CID or infrared multiphoton dissociation (IRMPD) alone. Furthermore, the CIRCA fragmentation spectra are of sufficient quality to allow protein identification based on the MS/MS spectra alone or in concert with the peptide mass fingerprint (PMF). This is accomplished without compromising mass accuracy or mass resolution. As a result, CIRCA serves to enable MALDI-FTICR-MS/MS for high-performance proteomics experiments.
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Affiliation(s)
- Eric D Dodds
- Department of Chemistry, School of Medicine, University of California Davis, One Shields Avenue, Davis, California 95616, USA
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Fälth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA. SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides. J Proteome Res 2007; 6:4063-7. [PMID: 17711326 DOI: 10.1021/pr070345h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A database of high-mass accuracy tryptic peptides has been created. The database contains 15 897 unique, annotated MS/MS spectra. It is possible to search for peptides according to their mass, number of missed cleavages, and sequence motifs. All of the data contained in the database is downloadable, and each spectrum can be visualized. An example is presented of how the database can be used for studying peptide fragmentation. Fragmentation of different types of missed cleaved peptides has been studied, and the results can be used to improve identification of these types of peptides.
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Affiliation(s)
- Maria Fälth
- Laboratory for Biological and Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden.
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Armirotti A, Scapolla C, Benatti U, Damonte G. Electrospray ionization ion trap multiple-stage mass spectrometric fragmentation pathways of leucine and isoleucine: an ab initio computational study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3180-4. [PMID: 17768698 DOI: 10.1002/rcm.3198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We recently demonstrated the possibility to distinguish between leucine and isoleucine in several tryptic peptides by means of consecutive tandem mass steps (Armirotti et al. J. Am. Soc. Mass Spectrom. 2007; 18: 57), exploiting a gas-phase rearrangement of the immonium ion of Ile. In the present paper we explore the tandem mass spectrometric behaviour of the two amino acids. We propose a plausible structure for the diagnostic m/z 69 ion of Ile, that was reported for the first time in 1996 (Hulst and Kientz J. Mass. Spectrom. 1996; 31: 1188), and we explain why its formation is favoured with respect to Leu. Our conclusions are supported by ab initio quantum chemistry calcultations and isotope-labelled standards experiments.
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Affiliation(s)
- Andrea Armirotti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genoa, Viale Benedetto XV, 7 Genova, Italy
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