Mass Spectrometry
Fazal et al., J Proteomics Bioinform 2013, 6:2 http://dx.doi.org/10.4172/jpb.1000256 Proteomics & Bioinformatics
Research Article
Research Article
Open Access
Open Access
Multifactorial Understanding of Ion Abundance in Tandem Mass
Spectrometry Experiments
Zeeshan Fazal1, Bruce R Southey1, Jonathan V. Sweedler2,3 and Sandra L. Rodriguez-Zas1,3,4*
Department of Animal Sciences, University of Illinois Urbana-Champaign, IL, USA
Department of Chemistry, University of Illinois Urbana-Champaign, IL, USA
Department of Statistics, University of Illinois Urbana-Champaign, IL, USA
4
Institute of Genomic Biology, University of Illinois Urbana-Champaign, IL, USA
1
2
3
Abstract
In a bottom-up shotgun approach, the proteins of a mixture are enzymatically digested, separated, and analyzed via tandem mass spectrometry. The mass spectra relating fragment ion intensities (abundance) to the mass-tocharge are used to deduce the amino acid sequence and identify the peptides and proteins. The variables that influence intensity were characterized using a multi-factorial mixed-effects model, a ten-fold cross-validation, and stepwise feature selection on 6,352,528 fragment ions from 61,543 peptide ions. Intensity was higher in fragment ions that did not have neutral mass loss relative to any mass loss or that had a +1 charge state. Peptide ions classified for proton mobility as non-mobile had lowest intensity of all mobility levels. Higher basic residue (arginine, lysine or histidine) counts in the peptide ion and low counts in the fragment ion were associated with lower fragment ion intensities. Higher counts of proline in peptide and fragment ions were associated with lower intensities. These results are consistent with the mobile proton theory. Opposite trends between peptide and fragment ion counts and intensity may be due to the different impact of factor under consideration at different stages of the MS/MS experiment or to the different
Research Article
Research Article
Open Access
Open Access
Multifactorial Understanding of Ion Abundance in Tandem Mass
Spectrometry Experiments
Zeeshan Fazal1, Bruce R Southey1, Jonathan V. Sweedler2,3 and Sandra L. Rodriguez-Zas1,3,4*
Department of Animal Sciences, University of Illinois Urbana-Champaign, IL, USA
Department of Chemistry, University of Illinois Urbana-Champaign, IL, USA
Department of Statistics, University of Illinois Urbana-Champaign, IL, USA
4
Institute of Genomic Biology, University of Illinois Urbana-Champaign, IL, USA
1
2
3
Abstract
In a bottom-up shotgun approach, the proteins of a mixture are enzymatically digested, separated, and analyzed via tandem mass spectrometry. The mass spectra relating fragment ion intensities (abundance) to the mass-tocharge are used to deduce the amino acid sequence and identify the peptides and proteins. The variables that influence intensity were characterized using a multi-factorial mixed-effects model, a ten-fold cross-validation, and stepwise feature selection on 6,352,528 fragment ions from 61,543 peptide ions. Intensity was higher in fragment ions that did not have neutral mass loss relative to any mass loss or that had a +1 charge state. Peptide ions classified for proton mobility as non-mobile had lowest intensity of all mobility levels. Higher basic residue (arginine, lysine or histidine) counts in the peptide ion and low counts in the fragment ion were associated with lower fragment ion intensities. Higher counts of proline in peptide and fragment ions were associated with lower intensities. These results are consistent with the mobile proton theory. Opposite trends between peptide and fragment ion counts and intensity may be due to the different impact of factor under consideration at different stages of the MS/MS experiment or to the different