LC-MS accurate quantification of a tryptic peptide co-eluted with an isobaric interference by using in-source collisional purification

Interferences from isobaric and isomeric compounds represent a common problem in liquid chromatography coupled to mass spectrometry (LC-MS). In this paper, in-source purification and chromatographic separation were combined with the aim of identifying isobaric contamination and quantifying accurately a compound despite the presence of an isobaric co-eluted interference. This is achieved by totally fragmenting in-source the precursor ions of the isobaric interference providing then LC-pseudo-MS2 capability, which allows an accurate quantification without the need for optimizing the chromatographic conditions to separate the co-eluted interference. To illustrate this concept, mixtures of tryptic and non-tryptic peptides were used. The ratio of peak areas of the tryptic peptide and its isotopically labelled internal standard was used not only for quantification with an internal standard calibration curve but also to know (1) if an isobaric interference co-eluted with the tryptic peptide; and (2) what is the minimum cone voltage necessary to ensure the complete removal of isobaric interference. This strategy was applied to quantify the tryptic peptide of two standards with known concentrations and, intentionally contaminated with the isobaric interference. The confidence intervals of the concentrations calculated with the internal standard calibration curve were 8.0 ± 0.5 μM (prepared at 8.0 μM) and 15.7 ± 0.5 μM (prepared at 16.1 μM) that confirm the tryptic peptide can be correctly quantified by in-source purification without the need for improving the chromatographic separation from its isobaric interference.

Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics

The metabolome is composed of a vast array of molecules, including endogenous metabolites and lipids, diet- and microbiome-derived substances, pharmaceuticals and supplements, and exposome chemicals. Correct identification of compounds from this diversity of classes is essential to derive biologically relevant insights from metabolomics data. In this chapter, we aim to provide a practical overview of compound identification strategies for mass spectrometry-based metabolomics, with a particular eye toward pharmacologically-relevant studies. First, we describe routine compound identification strategies applicable to targeted metabolomics. Next, we discuss both experimental (data acquisition-focused) and computational (software-focused) strategies used to identify unknown compounds in untargeted metabolomics data. We then discuss the importance of, and methods for, assessing and reporting the level of confidence of compound identifications. Throughout the chapter, we discuss how these steps can be implemented using today's technology, but also highlight research underway to further improve accuracy and certainty of compound identification. For readers interested in interpreting metabolomics data already collected, this chapter will supply important context regarding the origin of the metabolite names assigned to features in the data and help them assess the certainty of the identifications. For those planning new data acquisition, the chapter supplies guidance for designing experiments and selecting analysis methods to enable accurate compound identification, and it will point the reader toward best-practice data analysis and reporting strategies to allow sound biological and pharmacological interpretation.

Electrospray ionization tandem mass spectrometry analysis of isopimarane diterpenes from Velloziaceae

RATIONALE

The study of natural products by electrospray ionization tandem mass spectrometry (ESI-MS/MS) is an important strategy for the characterization of the major fragmentation reactions which can then help to determine the composition of complex mixtures. Application of ESI-MS/MS to a series of isopimarane diterpenes from Velloziaceae allowed the rationalization of their fragmentation mechanisms.

METHODS

Velloziaceae diterpenes were isolated by silica gel column chromatography and investigated by ESI-MS/MS analysis. The fragmentation studies were performed on a quadrupole-time-of-flight instrument using N2 as the collision gas. To help rationalize the fragmentation pathways observed, the geometry and sites of reactivity of the diterpenes were obtained by theoretical calculations using the B3LYP/6-31 + G(d,p) model. Fragmentation mechanisms were proposed on the basis of the calculated protonation sites and product ions energies using density functional theory (DFT) methods.

RESULTS

The presence of hydroxyl and carbonyl groups on the terpene core influences the protonation site observed. One compound showed a radical cation as the base peak. MS/MS spectra exhibit water elimination as the major fragmentation pathway (via two ways), either when protonation takes place on the oxygen atom, or through elimination after activation from hydrogen migration. After the elimination of water, the formation of an endocyclic double bond induces a sequential retro-Diels-Alder (RDA) reaction as the major fragmentation step.

CONCLUSIONS

A thorough rational analysis of the fragmentation mechanisms of protonated Velloziaceae diterpenes was used to propose the dissociation mechanisms in ESI-MS/MS. The presence of esters in the side chain also influenced the intensity or occurrence of the observed protonated or cationized molecules in ESI-MS. These results will aid the identification of analogues in sample extracts in future metabolomics studies.