Lipid profiling analyses from mouse models and human infants.

This protocol outlines a translational lipidomic approach to discover lipid biomarkers that could predict morphometric body and histological organ measurements (e.g., weight and adiposity gains) during specific stages of life (e.g., early life). We describe procedures ranging from animal experimentation and histological analyses to downstream analytical steps through lipid profiling, both in mice and humans. This protocol represents a reliable and versatile approach to translate and validate candidate lipid biomarkers from animal models to a human cohort. For complete details on the use and execution of this protocol, please refer to Olga et al. (2021).

Pre-processing liquid chromatography/high-resolution mass spectrometry data: extracting pure mass spectra by deconvolution from the invariance of isotopic distribution.

RATIONALE: Mass spectra obtained by deconvolution of liquid chromatography/high-resolution mass spectrometry (LC/HRMS) data can be impaired by non-informative mass-over-charge (m/z) channels. This impairment of mass spectra can have significant negative influence on further post-processing, like quantification and identification. METHODS: A metric derived from the knowledge of errors in isotopic distribution patterns, and quality of the signal within a pre-defined mass chromatogram block, has been developed to pre-select all informative m/z channels. RESULTS: This procedure results in the clean-up of deconvoluted mass spectra by maintaining the intensity counts from m/z channels that originate from a specific compound/molecular ion, for example, molecular ion, adducts, (13) C-isotopes, multiply charged ions and removing all m/z channels that are not related to the specific peak. The methodology has been successfully demonstrated for two sets of high-resolution LC/MS data. CONCLUSIONS: The approach described is therefore thought to be a useful tool in the automatic processing of LC/HRMS data. It clearly shows the advantages compared to other approaches like peak picking and de-isotoping in the sense that all information is retained while non-informative data is removed automatically.

Instrument and process independent binning and baseline correction methods for liquid chromatography-high resolution-mass spectrometry deconvolution.

Setting appropriate bin sizes to aggregate hyphenated high-resolution mass spectrometry data, belonging to similar mass over charge (m/z) channels, is vital to metabolite quantification and further identification. In a high-resolution mass spectrometer when mass accuracy (ppm) varies as a function of molecular mass, which usually is the case while reading m/z from low to high values, it becomes a challenge to determine suitable bin sizes satisfying all m/z ranges. Similarly, the chromatographic process within a hyphenated system, like any other controlled processes, introduces some process driven systematic behavior that ultimately distorts the mass chromatogram signal. This is especially seen in liquid chromatogram-mass spectrometry (LC-MS) measurements where the gradient of the solvent and the washing step cycle-part of the chromatographic process, produce a mass chromatogram with a non-uniform baseline along the retention time axis. Hence prior to any automatic signal decomposition techniques like deconvolution, it is a equally vital to perform the baseline correction step for absolute metabolite quantification. This paper will discuss an instrument and process independent solution to the binning and the baseline correction problem discussed above, seen together, as an effective pre-processing step toward liquid chromatography-high resolution-mass spectrometry (LC-HR-MS) data deconvolution.

Analysis of reaction products of food contaminants and ingredients: bisphenol A diglycidyl ether (BADGE) in canned foods.

Bisphenol A diglycidyl ether (BADGE) is an epoxide that is used as a starting substance in the manufacture of can coatings for food-contact applications. Following migration from the can coating into food, BADGE levels decay and new reaction products are formed by reaction with food ingredients. The significant decay of BADGE was demonstrated by liquid chromatographic (LC) analysis of foodstuffs, that is, tuna, apple puree, and beer, spiked with BADGE before processing and storage. Life-science inspired analytical approaches were successfully applied to study the reactions of BADGE with food ingredients, for example, amino acids and sugars. An improved mass balance of BADGE was achieved by selective detection of reaction products of BADGE with low molecular weight food components, using a successful combination of stable isotopes of BADGE and analysis by LC coupled to fluorescence detection (FLD) and high-resolution mass spectrometric (MS) detection. Furthermore, proteomics approaches showed that BADGE also reacts with peptides (from protein digests in model systems) and with proteins in foods. The predominant reaction center for amino acids, peptides, and proteins was cysteine.

Simultaneous determination of endogenous deoxynucleotides and phosphorylated nucleoside reverse transcriptase inhibitors in peripheral blood mononuclear cells using ion-pair liquid chromatography coupled to mass spectrometry.

Nucleoside reverse transcriptase inhibitors (NRTIs) are activated intracellularly to their triphosphate (TP) form, which compete with endogenous deoxynucleotide-triphosphates (dNTP) as substrate for HIV reverse transcriptase. The activity of NRTIs is thus described by the NRTI-TP-to-dNTP ratio in relevant cell types. Therefore, we developed an ion-pair (IP) LC-MS method for the simultaneous analysis of the mono-, di-, and TP forms of NRTIs and endogenous deoxynucleosides in peripheral blood mononuclear cells (PBMC). The IP-LC method was applied on an IT mass spectrometer using the MS-mode as well as on a triple quadrupole mass spectrometer using the MS/MS mode. The MS/MS approach on the triple quadrupole mass spectrometer demonstrated the best clinical applicability due to its higher sensitivity. The LOD (minimum amount on column) were 25 fmol for the TP forms of zidovudine, lamivudine, and stavudine, as well as for their endogenous dNTP counterparts. The linearity (R(2) ) of the calibration curves were>0.99. The obtained LOD readily allow for clinical applications using just one million PBMC obtained from HIV-infected patients under therapy.