Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

Abstract

Abstract. The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D Bheat map^, indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

Correlation between the shape of the ion mobility signals and the stepwise folding process of polylactide ions

“…Such a difference would also have contributed to the limited change in relative intensities of deconvoluted ATD peaks . This leads us to the hypothesis that the observed differences in the ion populations between the two instruments originate from the electrospray processes that are energetically (slightly) different within the Waters and the Bruker ion sources . Indeed, on the Waters instrument, by modifying the source parameters, it is possible to try changing the shape of the bimodal ATD signals, in particular the relative proportions of both of the different constituents.…”

Identification of small molecules using accurate mass MS/MS search

“…If QTOF data are searched against an ion trap library, the hit scores will be different from an approach where QTOF spectra are searched in QTOF libraries . It is always best practice to search similar instrument types against their reference spectra …”

“…104,113,114 It is always best practice to search similar instrument types against their reference spectra. 115 Second, the true "experimental mass accuracy" for each run or set of experiments has to be determined with internal or external reference compounds or quality check mixtures that contain known compounds.…”

An approach to estimate the activation energies of fragmentation occurring in quadrupole collision cell of the mass spectrometer

“…Although this is not the main goal of this paper, it may be interesting to see, what the reasons are for the differences between the SY plots (namely the efficiency of fragmentation) recorded on different instruments. The SY plot of leucine enkephalin presented in Figure was compared with the one measured on a Waters QQQ instrument by Bazsó et al (Figure in ref., it was digitalized and presented as Figure S4 in the Supporting Information). The characteristic point of the SY plot belongs to 50% fragmentation efficiency (SY = 0.5), the abscissa of this point is the characteristic collision energy (CE 50 ).…”

“…These approximations, which depend on the experimental conditions, were the following: (1) the number of effective oscillators S eff = DOF / 5 was used, and this approximation can be used for ions with sufficiently large values of DOF, (2) the fraction of α = 0.32 of the laboratory frame collision energy was converted into internal energy in the collision cell, and (3) the estimate 100 μs was used as the CID reaction time. It must be emphasized that the value of α strongly depends on the instrumental parameters: α = 0.2 was used to process the data recorded with different collision cell conditions and α = 0.39 was determined for a QQQ instrument . After estimating the kinetic to internal energy conversion (the value of α), eg, using leucine enkephalin as a “calibrant”, our simplified so‐called “short cut” method is capable to estimate the internal energy and the laboratory frame collision energy intervals necessary for the MS/MS structural analysis of the precursor ion, which has both theoretical and practical importance.…”