Journal of Proteomics & Bioinformatics
Open Access

Jonathan V. Sweedler

Publications

• Research Article
  Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments
  Author(s): Zeeshan Fazal, Bruce R Southey, Jonathan V. Sweedler and L. Rodriguez-Zas Zeeshan Fazal, Bruce R Southey, Jonathan V. Sweedler and L. Rodriguez-Zas
  
  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 ass.. View More»
  DOI: 10.4172/jpb.1000256

  Abstract PDF

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