Vol 74, No 14 (2019)

Mass spectrometry-based bottom-up proteomics becomes a method of choice in a broad range of biomedical studies. However, because of the growing complexity of the mass spectrometers employed in these studies, there is an increasing need in robust and rapid quality control over the instrument performance. A variety of quality control tools targeting all aspects of LC–MS instrument operation have been developed recently. These tools are typically loaded heavily with a large number of metrics. Many of these metrics are difficult for interpretation for regular users without extensive instrumentation and/or data processing experience. In this work, we introduced a set of simple and intuitively understandable metrics for assessing the quality of proteomic analysis, including the total experimental time and the number of spectral scans, ion accumulation time and intensity in both MS and MS/MS spectra, charge state distribution for precursor peptide ions, and the number of sequential MS/MS scans, etc. These metrics are implemented as an open-source utility, viQC, freely available at hg.theorchromo.ru/viQC. The developed tool has been tested experimentally using data from three different Orbitrap instruments and demonstrated its capability for assessing the possible flaws in the instrument’s operation and subsequent improving the efficiency of proteomic analysis.

The pseudopotential approach is a useful tool for the qualitative description of ion motion in inhomogeneous high-frequency electric fields, often used in mass spectrometric devices. However, in the theoretical study of the motion of ions in high-frequency electric fields with close frequencies, mathematical ambiguity arises, caused by the nonequivalence of different mathematical approaches. The paper considers and compares the time-dependent pseudopotential model and the model of solenoidal (vortex) pseudoforces, that is, vortex drift. The vortex drift model in high-frequency electric fields with close frequencies can be replaced by the model of ion motion in a pseudopotential varying in time. The theory of almost periodic time signals with two characteristic time scales, fast and slow, eliminates the ambiguity in selecting the correct mathematical method for describing ion motion in high-frequency electric fields.

A new method is proposed for the permanent-charge generation derivatization of thiols of different structures by a reaction with haloalkanes and dibromides. It was shown that 1,4-dibromobutane and 1,2-xylylene dibromide are the most effective alkylating agents, providing the formation of a stable five-membered ring with a positively charged sulfur atom. Such cations are readily detected by electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry. Sulfonium cations were further studied by tandem mass spectrometry using collision-induced dissociation (CID). Typical and specific CID directions for cyclic cations formed from thiols of different structures are revealed. They can be used to identify and quantify thiol analytes by the selected reaction monitoring method.

Orbital ion trap high-resolution mass spectrometry with acetone doped atmospheric pressure photoionization is first used to characterize the structure of grass lignins using an example of nettle (Urtíca dióica) dioxane lignin. The obtained mass spectrum contains about 3,000 peaks of deprotonated molecules of lignin oligomers in the molecular mass range up to 1.6 kDa. The study of tandem mass spectra and of a composition of monomers formed in the collision-induced dissociation of lignin macromolecules showed the special role of p-hydroxycinnamic acids in the formation of nettle lignin. Based on the results of tandem mass spectrometry, possible structures of nettle lignin oligomers formed by the addition of guaiacyl- and syringylpropane units followed by etherification by p-coumaric, ferulic, and dihydroferulic acids are proposed.

The quantitative evaluation of the errors of the 1st and 2nd kind for mass spectral criteria is obtained. These errors have been earlier proposed for distinguishing oils generated in carbonate and other rocks for the Domanic formation of the northern and central Volga−Ural regions. It is shown that none of them work: the best criteria have the 1st and 2nd kind errors close to 50%. Consequently, for all regions where carbonate oil source rocks are possible, a work similar to this should be done primarily, and only after such study, the analysis of oils becomes meaningful. It is also necessary to obtain quantitative estimates of the quality of all the other criteria used in petroleum geochemistry, for which such assessments are technically possible. New criteria should be designed only on the basis of those composition parameters for which the value of the Mann–Whitney test is close to zero.