Whole protein characterization and identification via gas-phase ion/ion and dissociation reactions in a quadrupole ion trap

2005 2005

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Abstract (summary)

‘Top down’ protein analysis has been extended to ion trap mass spectrometry via the use of ion/ion proton transfer chemistry. Charge manipulation by ion/ion reactions is used in several ways to aid in protein ion analysis. Electrospray ionization of biomolecules produces multiple charge states that can complicate mixture analysis. Ion/ion proton transfer reactions can partially reduce the protein ion charge states, simplifying the analysis of complex mixtures. The use of “ion parking” allows protein ion signal from multiple charge states to be concentrated into a single protein charge state. After fragmentation of whole protein ions via collision-induced dissociation, ion/ion proton transfer reactions are used to reduce the charge states of the fragment ions to singly charged, simplifying spectral interpretation. Ion/ion proton transfer reactions also allow the formation of protein ion charge states not directly accessible by electrospray ionization. This can assist in the study of whole protein ion fragmentation as a function of precursor ion charge state.

‘Top down'’ protein analysis has been used in the identification of unknown proteins via database searching. Uninterpreted product ion mass spectra, obtained from whole protein ion fragmentation, were compared against the in silico fragmentation of the proteins contained in either a protein database or a translated genome database. A scoring algorithm has been developed in-house to aid in identifying unknown proteins by incorporating fragment ion abundances into the protein score for each candidate protein. Post-translational modifications in unknown proteins were identified, and potentially localized, by looking for mass shifts in the fragment ion mass values along with changes in the overall protein mass.

Indexing (details)

Analytical chemistry;
0486: Analytical chemistry
0487: Biochemistry
Identifier / keyword
Pure sciences; Dissociation; Ion/ion reactions; Protein characterization; Quadrupole ion trap
Whole protein characterization and identification via gas-phase ion/ion and dissociation reactions in a quadrupole ion trap
Hogan, Jason Michael
Number of pages
Publication year
Degree date
School code
DAI-B 66/08, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
9780542276538, 0542276534
McLuckey, Scott A.
Purdue University
University location
United States -- Indiana
Source type
Dissertations & Theses
Document type
Dissertation/thesis number
ProQuest document ID
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
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