Quantification of the Compositional Information Provided by Immonium Ions on a Quadrupole-Time-of-Flight Mass Spectrometer

Immonium ions have been largely overlooked during the rapid expansion of mass spectrometry-based proteomics largely due to the dominance of ion trap instruments in the field. However, immonium ions are visible in hybrid quadrupole-time-of-flight (QTOF) mass spectrometers, which are now widely availa...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2008-07, Vol.80 (14), p.5596-5606
Main Authors: Hohmann, Laura J, Eng, Jimmy K, Gemmill, Andrew, Klimek, John, Vitek, Olga, Reid, Gavin E, Martin, Daniel B
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Amino acids
Analytical chemistry
Chemistry
Computational Biology
Databases, Protein
Exact sciences and technology
General, instrumentation
Ions
Ions - chemistry
Mass spectrometry
Mass Spectrometry - methods
Molecular Sequence Data
Osmolar Concentration
Peptides
Peptides - analysis
Peptides - chemistry
Proteomics
Quaternary Ammonium Compounds - chemistry
Saccharomyces cerevisiae
Spectrometric and optical methods
Time Factors
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Summary:Immonium ions have been largely overlooked during the rapid expansion of mass spectrometry-based proteomics largely due to the dominance of ion trap instruments in the field. However, immonium ions are visible in hybrid quadrupole-time-of-flight (QTOF) mass spectrometers, which are now widely available. We have created the largest database to date of high-confidence sequence assignments to characterize the appearance of immonium ions in CID spectra using a QTOF instrument under “typical” operating conditions. With these data, we are able to demonstrate excellent correlation between immonium ion peak intensity and the likelihood of the appearance of the expected amino acid in the assigned sequence for phenylalanine, tyrosine, tryptophan, proline, histidine, valine, and the indistinguishable leucine and isoleucine residues. In addition, we have clearly demonstrated a positional effect whereby the proximity of the amino acid generating the immonium ion to the amino terminal of the peptide correlates with the strength of the immonium ion peak. This compositional information provided by the immonium ion peaks could substantially improve algorithms used for spectral assignment in mass spectrometry analysis using QTOF platforms.
ISSN:0003-2700
1520-6882
1520-6882
DOI:10.1021/ac8006076