title: Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments.
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 "heat 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. Graphical Abstract ᅟ.
authors.affiliation: MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, H-1117, Magyar tudósok krt. 2, Budapest, Hungary.
authors.forename: Fanni Laura
authors.initials: FL
authors.lastname: Bazsó
authors.affiliation: MTA-TTK NAP B MS Neuroproteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, H-1117, Magyar tudósok krt. 2, Budapest, Hungary.
authors.forename: Oliver
authors.initials: O
authors.lastname: Ozohanics
authors.affiliation: MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, 1117, Budapest, Hungary.
authors.forename: Gitta
authors.initials: G
authors.lastname: Schlosser
authors.affiliation: Department of Pharmaceutics, Semmelweis University, Hőgyes E. Street 7-9, H-1092, Budapest, Hungary.
authors.forename: Krisztina
authors.initials: K
authors.lastname: Ludányi
authors.affiliation: MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, H-1117, Magyar tudósok krt. 2, Budapest, Hungary.|Core Technologies Center, Research Center for Natural Sciences, Hungarian Academy of Sciences, H-1117, Magyar tudosok krt. 2, Budapest, Hungary.
authors.forename: Károly
authors.initials: K
authors.lastname: Vékey
authors.affiliation: MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, H-1117, Magyar tudósok krt. 2, Budapest, Hungary. drahos.laszlo@ttk.mta.hu.|MTA-TTK NAP B MS Neuroproteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, H-1117, Magyar tudósok krt. 2, Budapest, Hungary. drahos.laszlo@ttk.mta.hu.
authors.forename: László
authors.identifier: 0000-0001-9589-6652
authors.initials: L
authors.lastname: Drahos
keywords: Instrument comparison; Similarity; Tandem mass spectrometry