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 y 4 ion, the SD is 0.0004, and as such the error bar is practically invisible; the reference y 3 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.