Figure 2.

Y-ions intensities. Relative intensities of the y series ions of the GAVLK doubly charged peptide, as measured by LCQ Deca XP Plus and LTQ-Orbitrap Velos (THERMO) mass spectrometers. Peak intensities were quantified by QualBrowser 1.4 (THERMO), and the intensity of the y-3 ion was chosen to have a reference value of 1.0 for all measurements. IT-ion trap, LIT-linear ion trap, CID-Collision Induced Decay, PQD-Pulsed-Q Dissociation. The error bars represent the standard deviation (SD). Only the average values show SD (for average CID y4 ion, the SD is 0.0004, and as such the error bar is practically invisible; the reference y3 ions have SD = 0). The ion intensities from particular measurements were accumulated for five minutes and saved as one combination of m/z and relative intensity values (see additional file 1), so no SD is given.

Pechan and Gwaltney BMC Bioinformatics 2012 13(Suppl 15):S13   doi:10.1186/1471-2105-13-S15-S13