The goal of this study was to qualify gas chromatography coupled to atmospheric pressure ionization tandem mass spectrometry (APGC-MS/MS) as a reliable and valid technique for analysis of halogenated dioxins and furans that could be used in place of more traditional gas chromatography coupled to high-resolution mass spectrometry (GC-HRMS) analysis. A direct comparison of the two instrumental techniques was performed. APGC-MS/MS system sensitivity was demonstrated to be on the single femtogram level. The APGC-MS/MS analysis also demonstrated method detection limits (MDLs) in both sediment and fish that were 2-18 times lower than those determined for the GC-HRMS. Inlet conditions were established to prevent issues with sample carry-over, due largely to the enhanced sensitivity of this technique. Additionally, this work utilized direct injection for sample introduction through the split/splittless inlet. Finally, quantification of both sediment and fish certified reference materials were directly compared between the APGC-MS/MS and GC-HRMS. The APGC-MS/MS performed similarly to, if not better than, the GC-HRMS instrument in the analysis of these samples. This data is intended to substantiate APGC-MS/MS as a comparable technique to GC-HRMS for the analysis of dioxins and furans.

Internodes of grass stems function in mechanical support, transport, and, in some species, are a major sink organ for carbon in the form of cell wall polymers. This study reports cell wall composition, proteomic, and metabolite analyses of the rice elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material along eight segments of the second rice internode (internode II) at booting stage, from the younger to the older internode segments, indicating active cell wall synthesis. Liquid-chromatography tandem mass spectrometry (LC-MS/MS) of trypsin-digested proteins from this internode at booting reveals 2,547 proteins with at least two unique peptides in two biological replicates. The dataset includes many glycosyltransferases, acyltransferases, glycosyl hydrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. Phospho-enrichment of internode II peptides identified 21 unique phosphopeptides belonging to 20 phosphoproteins including a leucine rich repeat-III family receptor like kinase. GO over-representation and KEGG pathway analyses highlight the abundances of proteins involved in biosynthetic processes, especially the synthesis of secondary metabolites such as phenylpropanoids and flavonoids. LC-MS/MS of hot methanol-extracted secondary metabolites from internode II at four stages (booting/elongation, early mature, mature, and post mature) indicates that internode secondary metabolites are distinct from those of roots and leaves, and differ across stem maturation. This work fills a void of in-depth proteomics and metabolomics data for grass stems, specifically for rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes characteristic of internode development, toward improving grass agronomic properties.

We developed a metabolomics workflow using ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry to determine the effect of thermal treatment on milk composition and metabolites based on multivariate data analysis. We analyzed raw, pasteurized, and UHT milk samples. The samples were first centrifuged to remove the fat layer and mixed with methanol to precipitate proteins. Subsequently, the supernatant was analyzed by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry in electrospray negative mode. Mass spectral data were acquired in MS mode, a technique whereby both precursor and fragment mass spectral are simultaneously acquired by alternating between low and high collision energy (CE) during a single analytical run, to enable metabolite identification. Based on multivariate data analysis, these markers were significantly affected by thermal treatment. Among the 8 potential markers, we identified 7 oxylipids (9-hydroxydecanoic acid, 12-hydroxydodecanoic acid, 2-hydroxymyristic acid, 3-hydroxytetradecanoic acid, 5-hydroxyeicosatetraenoic acid, 3-hydroxyhexadecanoic acid, and 10-hydroxyoctadecanoic acid) and 1 phospholipid (LysoPE, hexadecanoyl-lysophosphatidylethanolamine). The oxylipids seemed to be adequate for distinguishing UHT milk from raw and pasteurized milk. The structures of the 8 potential markers were identified and characterized using informatics software. Our metabolomics workflow provides a fast approach for the identification of various types of milk.

In plants, cellulose biosynthesis is an essential process for anisotropic growth and therefore is an ideal target for inhibition. Based on the documented utility of small-molecule inhibitors to dissect complex cellular processes we identified a cellulose biosynthesis inhibitor (CBI), named acetobixan, by bio-prospecting among compounds secreted by endophytic microorganisms. Acetobixan was identified using a drug-gene interaction screen to sift through hundreds of endophytic microbial secretions for one that caused synergistic reduction in root expansion of the leaky AtcesA6prc1-1 mutant. We then mined this microbial secretion for compounds that were differentially abundant compared with Bacilli that failed to mimic CBI action to isolate a lead pharmacophore. Analogs of this lead compound were screened for CBI activity, and the most potent analog was named acetobixan. In living Arabidopsis cells visualized by confocal microscopy, acetobixan treatment caused CESA particles localized at the plasma membrane (PM) to rapidly re-localize to cytoplasmic vesicles. Acetobixan inhibited 14C-Glc uptake into crystalline cellulose. Moreover, cortical microtubule dynamics were not disrupted by acetobixan, suggesting specific activity towards cellulose synthesis. Previous CBI resistant mutants such as ixr1-2, ixr2-1 or aegeus were not cross resistant to acetobixan indicating that acetobixan targets a different aspect of cellulose biosynthesis.

The identity of an unknown environmental pollutant is reflected by the mass and dissociation chemistry of its (quasi)­molecular ion. Gas chromatography–atmospheric pressure chemical ionization–mass spectrometry (GC-APCI-MS) increases the yield of molecular ions (compared to conventional electron ionization) by collisional cooling. Scanning quadrupole data-independent acquisition (SQDIA) permits unbiased, unattended selection of (quasi)­molecular ions and acquisition of structure-diagnostic collision-induced dissociation mass spectra, while minimizing interferences, by sequentially cycling a quadrupole isolation window through the m/z range. This study reports on the development of a suspect screening method based on industrial compounds with bioaccumulation potential. A comparison of false and correct identifications in a mixed standard containing 30 analytes suggests that SQDIA results in a markedly lower false-positive rate than standard DIA: 5 for SQDIA and 82 for DIA. Electronic waste dust was analyzed using GC and quadrupole time-of-flight MS with APCI and SQDIA acquisition. A total of 52 brominated, chlorinated, and organophosphorus compounds were identified by suspect screening; 15 unique elemental compositions were identified using nontargeted screening; 17 compounds were confirmed using standards and others identified to confidence levels 2, 3, or 4. SQDIA reduced false-positive identifications, compared to experiments without quadrupole isolation. False positives also varied by class: 20% for Br, 37% for Cl, 75% for P, and >99% for all other classes. The structure proposal of a previously reported halogenated compound was revisited. The results underline the utility of GC-SQDIA experiments that provide information on both the (quasi)­molecular ions and its dissociation products for a more confident structural assignment.