Sequential mass spectrometry applied to the study of the formation of “internal” fragment ions of protonated peptides

1991 ◽  
Vol 111 ◽  
pp. 173-189 ◽  
Author(s):  
Kevin D. Ballard ◽  
Simon J. Gaskell
Keyword(s):  
Mass Spectrometry ◽  
Protonated Peptides ◽  
Fragment Ions ◽  
Sequential Mass Spectrometry ◽  
Internal Fragment

scholarly journals Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3728
Author(s):  
Taran Driver ◽  
Nikhil Bachhawat ◽  
Leszek J. Frasinski ◽  
Jonathan P. Marangos ◽  
Vitali Averbukh ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Peptide Sequence ◽  
Two Dimensional ◽  
Peptide Ions ◽  
Finite Mass ◽  
Protein Database ◽  
Spectra Analysis ◽  
Fragment Ions ◽  
Single Precursor ◽  
The Common

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

scholarly journals Mass spectral and theoretical investigations of the transient proton-bound dimers on the cleavage processes of the peptide GHK and its analogues

RSC Advances ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 4077-4086
Author(s):  
Jinhu Wang ◽  
Cheng Wang ◽  
Han Zhang ◽  
Yang Liu ◽  
Tiesheng Shi
Keyword(s):  
Mass Spectrometry ◽  
Theoretical Calculations ◽  
Mass Spectral ◽  
Protonated Peptides ◽  
Fragmentation Mechanisms ◽  
Theoretical Investigations

Fragmentation mechanisms of the singly protonated peptides GHK, GHKH and HGHK have been investigated by mass spectrometry and theoretical calculations.

Thermochemistry of Organic and Heteroorganic Species. Part IX. Photoionization Studies of Isomerization and Fragmentation of Polysubstituted Cyclopropenes: Phenyl-Substituted Cyclopropenes

2000 ◽  
Vol 6 (1) ◽  
pp. 53-64 ◽  
Author(s):  
V.V. Takhistov ◽  
I.N. Domnin ◽  
D.A. Ponomarev
Keyword(s):  
Mass Spectrometry ◽  
Enthalpy Of Formation ◽  
Good Alternative ◽  
Enthalpies Of Formation ◽  
Isodesmic Reactions ◽  
Ion Structure ◽  
Photoionization Mass Spectrometry ◽  
General Methodology ◽  
Fragment Ions ◽  
The Enthalpy Of Formation

Ionization and appearance energies of some fragment ions from 1,2,3-trimethy1-3-phenyl-, 3-methyl-1,2,3-triphenyl-, 1,2-diphenyl-3-methoxycarbonyl-, 1,2,3-triphenyl-3-methoxycarbonyl- and 1,3,3-triphenyl-2-methoxycarbonyl-cyclopropenes were measured by photoionization mass spectrometry. It was shown that in none of these compounds did the fragment ions possess the expected stable substituted cyclopropenium ion structure. Accordingly, possible schemes of molecular ion isomerization are given. The enthalpies of formation of nearly 50 substituted cyclopropenium ions, and ions of related structure, were estimated using series of isodesmic reactions. This publication, together with the previous works of the authors in this Journal, demonstrates the general methodology for estimation of the enthalpy of formation for even-electron ions. It is suggested that the present methodology can provide a good alternative to other estimation or computation procedures applied to the thermochemistry of ions.

scholarly journals Multistage Fragmentation of Ion Trap Mass Spectrometry System and Pseudo-MS3of Triple Quadrupole Mass Spectrometry Characterize Certain (E)-3-(Dimethylamino)-1-arylprop-2-en-1-ones: A Comparative Study

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Ali S. Abdelhameed ◽  
Adnan A. Kadi ◽  
Hatem A. Abdel-Aziz ◽  
Rihab F. Angawi ◽  
Mohamed W. Attwa ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometer ◽  
Ion Trap ◽  
Quadrupole Mass Spectrometer ◽  
Ion Trap Mass Spectrometry ◽  
Triple Quadrupole ◽  
Quadrupole Mass ◽  
Triple Quadrupole Mass Spectrometer ◽  
Fragment Ions ◽  
Mass Spectrometry System

A new approach was recently introduced to improve the structure elucidation power of tandem mass spectrometry simulating the MS3of ion trap mass spectrometry system overcoming the different drawbacks of the latter. The fact that collision induced dissociation in the triple quadrupole mass spectrometer system provides richer fragment ions compared to those achieved in the ion trap mass spectrometer system utilizing resonance excitation. Moreover, extracting comprehensive spectra in the ion trap needs multistage fragmentation, whereas similar fragment ions may be acquired from one stage product ion scan using the triple quadrupole mass spectrometer. The new strategy was proven to enhance the qualitative performance of tandem mass spectrometry for structural elucidation of different chemical entities. In the current study we are endeavoring to prove our hypothesis of the efficiency of the new pseudo-MS3technique via its comparison with the MS3mode of ion trap mass spectrometry system. Ten pharmacologically and synthetically important (E)-3-(dimethylamino)-1-arylprop-2-en-1-ones (enaminones4a–j) were chosen as model compounds for this study. This strategy permitted rigorous identification of all fragment ions using triple quadrupole mass spectrometer with sufficient specificity. It can be used to elucidate structures of different unknown components. The data presented in this paper provide clear evidence that our new pseudo-MS3may simulate the MS3of ion trap spectrometry system.

scholarly journals Novel Cyclic Peptides from Lethal Amanita Mushrooms through a Genome-Guided Approach

2021 ◽  
Vol 7 (3) ◽  
pp. 204
Author(s):  
Shengwen Zhou ◽  
Xincan Li ◽  
Yunjiao Lüli ◽  
Xuan Li ◽  
Zuo H. Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Amino Acid Residues ◽  
Fragment Ions ◽  
Peptide Pair ◽  
A Genome ◽  
Peptide Toxins ◽  
Poisonous Mushrooms ◽  
Large Peptide

Most species in the genus Amanita are ectomycorrhizal fungi comprising both edible and poisonous mushrooms. Some species produce potent cyclic peptide toxins, such as α-amanitin, which places them among the deadliest organisms known to mankind. These toxins and related cyclic peptides are encoded by genes of the “MSDIN” family (named after the first five amino acid residues of the precursor peptides), and it is largely unknown to what extent these genes are expressed in the basidiocarps. In the present study, Amanita rimosa and Amanita exitialis were sequenced through the PacBio and Illumina techniques. Together with our two previously sequenced genomes, Amanita subjunquillea and Amanita pallidorosea, in total, 46 previously unknown MSDIN genes were discovered. The expression of over 80% of the MSDIN genes was demonstrated in A. subjunquillea. Through a combination of genomics and mass spectrometry, 12 MSDIN genes were shown to produce novel cyclic peptides. To further confirm the results, three of the cyclic peptides were chemically synthesized. The tandem mass spectrometry (MS/MS) spectra of the natural and the synthetic peptides shared a majority of the fragment ions, demonstrating an identical structure between each peptide pair. Collectively, the results suggested that the genome-guided approach is reliable for identifying novel cyclic peptides in Amanita species and that there is a large peptide reservoir in these mushrooms.

Differentiation of the Isomeric o-(m- and p-) Nitro-(Chloro- and Bromo-)Benzyl-2,4-(and 2,1-) Disubstituted 2-Thiocytosinium Halides by Electron Impact Ionisation and Fast Atom Bombardment Mass Spectrometry

2009 ◽  
Vol 15 (4) ◽  
pp. 497-506 ◽  
Author(s):  
Tomasz Pospieszny ◽  
Elżbieta Wyrzykiewicz
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Fast Atom Bombardment ◽  
Collision Induced Dissociation ◽  
Mass Measurements ◽  
Fragmentation Pathways ◽  
Mass Spectral ◽  
Fragment Ions ◽  
Accurate Mass Measurements ◽  
Impact Ionisation

Electron ionisation (EI) and fast atom bombardment (FAB) mass spectral fragmentations of nine 2,4-(and 2,1-) disubstituted o-( m- and p-)nitro-(chloro- and bromo-)-2-thiocytosinium halides are investigated. Fragmentation pathways, whose elucidation is assisted by accurate mass measurements and metastable transitions [EI-mass spectrometry (MS)], as well as FAB/collision-induced dissociation (CID) mass spectra measurements are discussed. The correlations between the abundances of the (C11H10N4SO2)+1–3; (C11H10N3SCl)+4–6 and (C11H10N3SBr)+7–9 ions and the selected fragment ions (EI-MS), as well as (C18H16N5SO4)+1–3; (C18H16N3SCl2)+4–6 and (C18H16N3SBr2) + 7–9 ions and the selected ions (C7H6NO2)+1–3; (C7H6Cl)+ 4–6; (C7H6Br)+ 7–9 (FAB-MS) are discussed. The data obtained can be used for distinguishing isomers.

Continuous flow fast atom bombardment mass spectrometry of mononucleotides and their metal complexes

1989 ◽  
Vol 67 (5) ◽  
pp. 910-920 ◽  
Author(s):  
M. J. Bertrand ◽  
V. Benham ◽  
R. St-Louis ◽  
M. J. Evans
Keyword(s):  
Mass Spectrometry ◽  
Continuous Flow ◽  
Fast Atom Bombardment ◽  
Aqueous Media ◽  
Molecular Ions ◽  
Fragment Ions ◽  
Low Concentrations ◽  
Metal Adducts ◽  
Matrix Concentration

The mass spectra of mononucleotides and their metal adducts Na, K, Mg, Ca, Ni, Co, Cu, and Zn of guanosine 5′-monophosphate (5′-GMP) as well as H, Na, and Mg of adenosine 5′-monophosphate (5′-AMP) and H and Ni of inosine 5′-monophosphate (5′-IMP) have been obtained in low concentrations of matrix in water using continuous-flow fast atom bombardment. The results indicate that this technique is suitable for the analysis of these complexes in aqueous media and yields spectra that are highly characteristic of the compounds analyzed. Parent-molecular ions and structurally significant fragment ions are observed for all compounds studied and the different binding sites for the metal on the nucleotides can be isolated from the fragment ions. Experimental parameters influencing the quality of the spectra such as flow rate, matrix concentration, matrix nature, and analyte concentration have been studied and optimized. For the thirteen compounds studied, it appears that continuous-flow FAB is superior to conventional FAB and that good quality spectra can be obtained with as little as 0.5% of added matrix thus minimizing spectral interferences. Keywords: continuous flow FAB, FAB MS, mass spectrometry, nucleotides, metal-nucleotides.

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