Reducing Mass Confusion over the Microbiome.

As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.

TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats.

MOTIVATION: Advances in mass spectrometry have led to the development of mass spectrometers with ion mobility spectrometry capabilities and dual-source instrumentation; however, the current software ecosystem lacks interoperability with downstream data analysis using open-source software and pipelines. RESULTS: Here, we present TIMSCONVERT, a data conversion high-throughput workflow from timsTOF Pro/fleX mass spectrometer raw data files to mzML and imzML formats that incorporates ion mobility data while maintaining compatibility with data analysis tools. We showcase several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX MS. AVAILABILITY AND IMPLEMENTATION: TIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command-line interface tool for Windows and Linux, NextFlow workflow and online in the Global Natural Products Social (GNPS) platform. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Natural Product Phenolic Diglycosides Created from Wildfires, Defining Their Impact on California and Oregon Grapes and Wines.

Forest fires produce malodorous phenols, bioaccumulated in grapes as odorless phenol glycosides (mono- to tri-), and produce unpleasant smoke tainted wines when these complexes are transformed by glycosidases in saliva. Metabolomic analyses were used to further understand smoke taint by quantitating marker phenolic diglycosides via UHPLC separations and MS/MS multiple reaction monitoring. A collection of grapes and wines provided data to forecast wine quality of grapes subjected to wildfire smoke infestations; the analytics used a panel of reference compounds (1-6). Overall, eight different Vitis vinifera varietals were examined from 2017-2021 vintages involving >218 distinct samples (wines and/or grapes) from 21 different American Viticulture Areas. Results acquired allowed correlation of phenolic diglycoside levels as a function of grape cultivar, varietal clones, and intensity of wildfire smoke. Baseline data were tabulated for nonsmoked samples (especially, Cabernet Sauvignon having a sum 1-6 of <6 µg/L) and then compared to those exposed to six other levels of smoke. Outcomes established that (1) analyzing paired samples (bottled wines versus smoke-exposed grapes) can provide diagnostic metabolomic data, (2) phenolic diglycosides are stable in wines aged for >2.5 years, and (3) major gaps exist in our current understanding of this pool of metabolites.

Re-evaluation of the Fijianolide/Laulimalide Chemotype Suggests an Alternate Mechanism of Action for C-15/C-20 Analogs.

Herein, we report on naturally derived microtubule stabilizers with activity against triple negative breast cancer (TNBC) cell lines, including paclitaxel, fijianolide B/laulimalide (3), fijianolide B di-acetate (4), and two new semisynthetic analogs of 3, which include fijianolide J (5) and fijianolide L (6). Similar to paclitaxel, compound 3 demonstrated classic microtubule stabilizing activity with potent (GI50 = 0.7-17 nM) antiproliferative efficacy among the five molecularly distinct TNBC cell lines. Alternatively, compounds 5 or 6, generated from oxidation of C-20 or C-15 and C-20 respectively, resulted in a unique profile with reduced potency (GI50 = 4-9 µM), but improved efficacy in some lines, suggesting a distinct mechanism of action. The C-15, C-20 di-acetate, and dioxo modifications on 4 and 6 resulted in compounds devoid of classic microtubule stabilizing activity in biochemical assays. While 4 also had no detectable effect on cellular microtubules, 6 promoted a reorganization of the cytoskeleton resulting in an accumulation of microtubules at the cell periphery. Compound 5, with a single C-20 oxo substitution, displayed a mixed phenotype, sharing properties of 3 and 6. These results demonstrate the importance of the C-15/C-20 chiral centers, which appear to be required for the potent microtubule stabilizing activity of this chemotype and that oxidation of these sites promotes unanticipated cytoskeletal alterations that are distinct from classic microtubule stabilization, likely through a distinct mechanism of action.