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. Author manuscript; available in PMC: 2014 May 1.
Published in final edited form as: Proteomics. 2013 May;13(9):1412–1416. doi: 10.1002/pmic.201200583

Figure 2. LDA Enables Species-dependent Acquisition of MS/MS Spectra in an Orbitrap Mass Analyzer.

Figure 2

The acquisition database (left column) is set to either S. cerevisiae (top row) or E. coli (bottom row). Mixtures of tryptic peptides from each species (middle column) are analyzed by LC-MS/MS in replicate for each acquisition database. Fragment ion MS/MS spectra acquired in the linear ion trap are interrogated in real time by dot-product search against NIST spectral libraries; those peptides not assigned with high confidence are subjected to high resolution MS/MS in the Orbitrap mass analyzer. All MS/MS spectra were searched post-acquisition using Mascot. For a 1:1 mixture of S. cerevisiae and E. coli peptides, the linear ion trap faithfully reproduces the underlying species composition (right column, LTQ piechart) while the majority of MS/MS scans in the Orbitrap are devoted to the “novel” species (right column, Orbitrap piechart). The species-specific trend is well represented in the relative proportions of Orbitrap MS/MS scans acquired across a wide range of species mixtures (middle column).