Journal:

Article Title: Correlation between y-Type Ions Observed in Ion Trap and Triple Quadrupole Mass Spectrometers

doi: 10.1021/pr900298b

Figure Lengend Snippet: General workflow of the presented analysis: (1) generation of consensus spectral libraries from ion trap MS/MS data for the two sample types of interest; in this case, a yeast spectral library created by NIST was downloaded from PeptideAtlas.org and an 18 mix spectral library was generated in-house using SpectraST, based on our previously published and publicly available shotgun MS data; (2) creation of an MRM transition list for each of the three samples in the analysis, a low-pI yeast fraction, a high-pI yeast fraction, and 18 mix, from an organism-appropriate spectral library using the software tool MaRiMba; each yeast MRM list was restricted to peptides observed in discovery MS runs conducted prior to this analysis; (3) triple quadrupole-enabled MRM-MS targeting of the top six y-ion transitions of each peptide in the three samples; (4) quantification of the MRM data using MRMer to calculate the area under the curve (AUC) of each transition elution peak; and (5) comparison of the triple quadrupole-generated transition AUC values to their corresponding ion trap-derived spectral library peak intensities in order to assess the similarity of the spectra from the two instruments.

Article Snippet: For each of the yeast fractions, MaRiMba was instructed to build a list of MRM targets from a yeast spectral library provided by the National Institute of Standards and Technology (NIST) [NIST_ yeast_IT_v2.0_2008-07-11.splib from http://www.peptideatlas.org/speclib/ ] and to restrict each list to transitions corresponding only to peptides that had been observed previously in the LTQ shotgun analysis of the given fraction.

Techniques: Tandem Mass Spectroscopy, Generated, Software, Targeted Proteomics, Comparison, Derivative Assay