Spatial extent of fragment-ion abundances in electron transfer dissociation and electron capture dissociation mass spectrometry of peptides
Saved in:
| Title: | Spatial extent of fragment-ion abundances in electron transfer dissociation and electron capture dissociation mass spectrometry of peptides |
|---|---|
| Authors: | Simons, Jack1 simons@chem.utah.edu, Ledvina, Aaron R.2 |
| Source: | International Journal of Mass Spectrometry. Dec2012, Vol. 330-332, p85-94. 10p. |
| Subjects: | Charge exchange, Dissociation (Chemistry), Mass spectrometry, Electron capture, Lysine, Ionic structure, Peptides |
| Abstract: | Earlier work from the first author's group has suggested that, in electron capture dissociation (ECD) or electron transfer dissociation (ETD) mass spectrometry experiments, an electron is initially attached into a Rydberg orbital centered at one of the peptide's positive sites (likely a protonated N-terminus, Lysine, Arginine, or Histidine). Moreover, this earlier work predicted that only Rydberg orbitals having principal quantum numbers n = 3–6 are populated in ECD and only n = 3 and 4 in ETD (when an anion donor having an electron binding energy of ca. 0. 6eV is used), and that the populations of these levels are very similar in the nascent charge-reduced peptide. Based upon these predictions, the present paper develops a framework for predicting the abundances of closed-shell c and open-shell z• fragment as a function of distance along the backbone from the site initially holding the attached electron in a Rydberg orbital. The framework is not aimed at differences in branching ratios caused by differences in the physical properties of side chains along the backbone but on the spatial distances between the charged site holding the electron and the backbone amide units. The predictions of this model are tested using ECD and ETD data from derived from experiments carried out using simultaneous infrared photo-activation of the parent ions. Such activated-ion (AI) experiments are thought to disrupt much of the parent ion's secondary structure, which we believe allows us to make more reliable estimates of distances between the charged sites and the various amino acids’ amide groups. The abundance patterns predicted based upon the framework described herein are found to be reasonably consistent with the experimental data. However, the data also provide evidence that internal solvation of the peptide's charged sites remains intact even under AI conditions, and that some of these solvated-ion structures (those involving a charged Lys or N-terminal amine) contribute incrementally to the abundances of fragment ions arising from cleaving nearby N—Cα bonds. As a result, we conclude that ECD and ETD fragment ion abundances are determined by a combination of factors: (i) internal solvation of charged sites, (ii) spatial distributions or Rydberg orbitals charge densities within several residues of charged sites, and (iii) variations induced by differences in physical properties of side chains. It is primarily the first two of these three that the present paper addresses. [Copyright &y& Elsevier] |
| Copyright of International Journal of Mass Spectrometry is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
|---|---|
| Header | DbId: egs DbLabel: Engineering Source An: 83934496 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Spatial extent of fragment-ion abundances in electron transfer dissociation and electron capture dissociation mass spectrometry of peptides – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Simons%2C+Jack%22">Simons, Jack</searchLink><relatesTo>1</relatesTo><i> simons@chem.utah.edu</i><br /><searchLink fieldCode="AR" term="%22Ledvina%2C+Aaron+R%2E%22">Ledvina, Aaron R.</searchLink><relatesTo>2</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22International+Journal+of+Mass+Spectrometry%22">International Journal of Mass Spectrometry</searchLink>. Dec2012, Vol. 330-332, p85-94. 10p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Charge+exchange%22">Charge exchange</searchLink><br /><searchLink fieldCode="DE" term="%22Dissociation+%28Chemistry%29%22">Dissociation (Chemistry)</searchLink><br /><searchLink fieldCode="DE" term="%22Mass+spectrometry%22">Mass spectrometry</searchLink><br /><searchLink fieldCode="DE" term="%22Electron+capture%22">Electron capture</searchLink><br /><searchLink fieldCode="DE" term="%22Lysine%22">Lysine</searchLink><br /><searchLink fieldCode="DE" term="%22Ionic+structure%22">Ionic structure</searchLink><br /><searchLink fieldCode="DE" term="%22Peptides%22">Peptides</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Earlier work from the first author's group has suggested that, in electron capture dissociation (ECD) or electron transfer dissociation (ETD) mass spectrometry experiments, an electron is initially attached into a Rydberg orbital centered at one of the peptide's positive sites (likely a protonated N-terminus, Lysine, Arginine, or Histidine). Moreover, this earlier work predicted that only Rydberg orbitals having principal quantum numbers n = 3–6 are populated in ECD and only n = 3 and 4 in ETD (when an anion donor having an electron binding energy of ca. 0. 6eV is used), and that the populations of these levels are very similar in the nascent charge-reduced peptide. Based upon these predictions, the present paper develops a framework for predicting the abundances of closed-shell c and open-shell z• fragment as a function of distance along the backbone from the site initially holding the attached electron in a Rydberg orbital. The framework is not aimed at differences in branching ratios caused by differences in the physical properties of side chains along the backbone but on the spatial distances between the charged site holding the electron and the backbone amide units. The predictions of this model are tested using ECD and ETD data from derived from experiments carried out using simultaneous infrared photo-activation of the parent ions. Such activated-ion (AI) experiments are thought to disrupt much of the parent ion's secondary structure, which we believe allows us to make more reliable estimates of distances between the charged sites and the various amino acids’ amide groups. The abundance patterns predicted based upon the framework described herein are found to be reasonably consistent with the experimental data. However, the data also provide evidence that internal solvation of the peptide's charged sites remains intact even under AI conditions, and that some of these solvated-ion structures (those involving a charged Lys or N-terminal amine) contribute incrementally to the abundances of fragment ions arising from cleaving nearby N—Cα bonds. As a result, we conclude that ECD and ETD fragment ion abundances are determined by a combination of factors: (i) internal solvation of charged sites, (ii) spatial distributions or Rydberg orbitals charge densities within several residues of charged sites, and (iii) variations induced by differences in physical properties of side chains. It is primarily the first two of these three that the present paper addresses. [Copyright &y& Elsevier] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of International Journal of Mass Spectrometry is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=83934496 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.ijms.2012.07.014 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 10 StartPage: 85 Subjects: – SubjectFull: Charge exchange Type: general – SubjectFull: Dissociation (Chemistry) Type: general – SubjectFull: Mass spectrometry Type: general – SubjectFull: Electron capture Type: general – SubjectFull: Lysine Type: general – SubjectFull: Ionic structure Type: general – SubjectFull: Peptides Type: general Titles: – TitleFull: Spatial extent of fragment-ion abundances in electron transfer dissociation and electron capture dissociation mass spectrometry of peptides Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Simons, Jack – PersonEntity: Name: NameFull: Ledvina, Aaron R. IsPartOfRelationships: – BibEntity: Dates: – D: 15 M: 12 Text: Dec2012 Type: published Y: 2012 Identifiers: – Type: issn-print Value: 13873806 Numbering: – Type: volume Value: 330-332 Titles: – TitleFull: International Journal of Mass Spectrometry Type: main |
| ResultId | 1 |
