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 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.
Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
Laura J
LJ
Hohmann
Jimmy K
JK
Eng
Andrew
A
Gemmill
John
J
Klimek
Olga
O
Vitek
Gavin E
GE
Reid
Daniel B
DB
Martin
D000595:Amino Acid Sequence; D019295:Computational Biology; D030562:Databases, Protein; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D009994:Osmolar Concentration; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D000644:Quaternary Ammonium Compounds / Q000737:chemistry*; D012441:Saccharomyces cerevisiae; D013997:Time Factors
D007477:Ions; D010455:Peptides; D000644:Quaternary Ammonium Compounds