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Graphical abstract Abstract A host of vanadyl petroporphyrins containing multiple sulfur and oxygen atoms and their combinations (C c H 2c+Z N 4 VO o S s , s = 0–3, o = 1–4, Z = −28 to −70) in a vacuum residue were observed by a combination of extensive enrichment of petroporphyrins and detailed analysis using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Many of the petroporphyrin species are being observed for the very first time. The patterns of the porphyrin type distribution revealed dramatic differences in the sulfur and oxygen atom incorporations and their impact on Z number. For each sulfur atom addition, the average Z-number was reduced by ∼4–7, implying that sulfur may be incorporated by the additions of thiophene or cyclic thiophene moieties. In contrast, oxygen addition had little to no impact on the average Z number, implying that oxygen may be incorporated as carbonyl or hydroxyl groups. The porphyrin-based structures were found to contain as many as 8 aromatic rings in addition to the porphyrin macrocycle. Petroporphyrins in longer wavelength absorption fractions were found to contain more heteroatoms and more condensed aromatic rings. [ABSTRACT FROM AUTHOR]

Tandem mass spectrometry (MS/MS) provides detailed information for structural characterization of biomolecules. The combination of electron capture dissociation (ECD) techniques with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) often provides unique ion-electron reactions and fragmentation channels in MS/MS. ECD is often a complimentary, sometimes even a superior tool to conventional MS/MS techniques. This article is aimed at providing a short overview of ECD-based fragmentation techniques (ExD) and optimization of ECD experiments for FTICR mass analyzers. Most importantly, it is meant to pique the interest of potential users for this exciting research field. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:4-15, 2017. [ABSTRACT FROM AUTHOR]

Lignin is the second most abundant natural biopolymer, and lignin wastes are therefore potentially significant sources for renewable chemicals such as fuel compounds, as alternatives to fossil fuels. Waste valorisation of lignin is currently limited to a few applications such as in the pulp industry, however, because of the lack of effective extraction and characterisation methods for the chemically highly complex mixtures after decomposition. Here, we have implemented high resolution mass spectrometry and developed two-dimensional mass defect matrix plots as a data visualisation tool, similar to the Kendrick mass defect plots implemented in fields such as petroleomics. These 2D matrix plots greatly simplified the highly convoluted lignin mass spectral data acquired from Fourier transform ion cyclotron resonance (FTICR)-mass spectrometry, and the derived metrics provided confident peak assignments and strongly improved structural mapping of lignin decomposition product series from the various linkages within the lignin polymer after electrochemical decomposition. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Fourier transform mass spectrometry (FTMS) is the method of choice for measurements that require ultra-high resolution. The establishment of Fourier transform ion cyclotron resonance (FTICR) MS, the availability of biomolecular ionization techniques and the introduction of the OrbitrapΓ mass spectrometer have widened the number of FTMS-applications enormously. One recent example involves clinical proteomics using FTICR-MS to discover and validate protein biomarker signatures in body fluids such as serum or plasma. These biological samples are highly complex in terms of the type and number of components, their concentration range, and the structural identity of each species, and thus require extensive sample cleanup and chromatographic separation procedures. Clearly, such an elaborate and multi-step sample preparation process hampers high-throughput analysis of large clinical cohorts. A final MS read-out at ultra-high resolution enables the analysis of a more complex sample and can thus simplify upfront fractionations. To this end, FTICR-MS offers superior ultra-high resolving power with accurate and precise mass-to-charge ratio (m/z) measurement of a high number of peptides and small proteins (up to 20 kDa) at isotopic resolution over a wide mass range, and furthermore includes a wide variety of fragmentation strategies to characterize protein sequence and structure, including post-translational modifications (PTMs). In our laboratory, we have successfully applied FTICR "next-generation" peptide profiles with the purpose of cancer disease classifications. Here we will review a number of developments and innovations in FTICR-MS that have resulted in robust and routine procedures aiming for ultra-high resolution signatures of clinical samples, exemplified with state-of-the-art examples for serum and saliva. [ABSTRACT FROM AUTHOR]

Highlights: [•] Wines from distinct vineyards managed by a same producer were analysed by FTICR–MS. [•] Thousands of metabolites specific to skin/must extracts and wines could be revealed. [•] Vintages are initially the most discriminant factors. [•] Terroir-related complex chemical fingerprints could be revealed after bottle ageing. [Copyright &y& Elsevier]

Abstract: The optical absorption of the green fluorescent protein chromophore anion (HBDI−) in the gas phase has been addressed by a number of experimental and theoretical studies; however, there is no consensus on its spectral characteristics yet. In this report, the intrinsic absorption of HBDI− was probed by photo-induced dissociation (“action”) spectroscopy using discrete lines of a continuous-wave (CW) laser source. The observed spectral profile of dissociation efficiency revealed a pronounced dependence on the laser irradiance. Dissociation at high irradiance is governed by multiple-photon absorption processes whose efficiency peaks between 476 and 488nm. At very low irradiance (<0.4mWcm−2) dissociation of gas-phase HBDI− is mostly promoted by single-photon transitions and suggests an intrinsic absorption maximum of gas-phase HBDI− <476nm, blue-shifted compared to earlier results obtained with pulsed lasers. [Copyright &y& Elsevier]

With the discovery of Na-sulphate minerals on Mars and Europa, recent studies using these minerals have focused on their ability to assist in the detection of bio/organic signatures. This study further investigates the ability of thenardite (Na2SO4) to effectively facilitate the ionization and identification of aromatic amino acids (phenylalanine, tyrosine and tryptophan) using a technique called geomatrix-assisted laser desorption/ionization in conjunction with a Fourier transform ion cyclotron resonance mass spectrometry. This technique is based on the ability of a mineral host to facilitate desorption and ionization of bio/organic molecules for detection. Spectra obtained from each aromatic amino acid alone and in combination with thenardite show differences in ionization mechanism and fragmentation patterns. These differences are due to chemical and structural differences between the aromatic side chains of their respective amino acid. Tyrosine and tryptophan when combined with thenardite were observed to undergo cation-attachment ([M+Na]+), due to the high alkali ion affinity of their aromatic side chains. In addition, substitution of the carboxyl group hydrogen by sodium led to formation of [M-H+Na]Na+ peaks. In contrast, phenylalanine mixed with thenardite showed no evidence of Na+ attachment. Understanding how co-deposition of amino acids with thenardite can affect the observed mass spectra is important for future exploration missions that are likely to use laser desorption mass spectrometry to search for bio/organic compounds in extraterrestrial environments. [ABSTRACT FROM AUTHOR]

Geomatrix-assisted laser desorption/ionization (GALDI) in conjunction with a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) has been employed to determine how effectively bio/organic molecules associated with the mineral thenardite (Na2SO4) can be detected. GALDI is based on the ability of the mineral host to assist desorption and ionization of bio/organic molecules without additional sample preparation. When glycine was mixed with thenardite, glycine was deprotonated to produce C2H4NO2- at m/z 74.025. The combination of stearic acid with thenardite produced a complex cluster ion at m/z 390.258 in the negative mode, which was assigned a composition of C18H39O7Na-. A natural sample of thenardite from Searles Lake in California also produced a peak at m/z 390.260. The bio/organic signatures in both the laboratory-based and natural samples were heterogeneously dispersed as revealed by chemical imaging. The detection limits for the stearic acid and thenardite combination were estimated to be 3 parts per trillion or ∼7 zeptomoles (10- 21) per laser spot. Attempts to improve the signal-to-noise ratio by co-adding FTICR-MS data predetermined to contain the biosignatures of interest revealed problems due to a lack of phase coherence between data sets. [ABSTRACT FROM AUTHOR]

Size-exclusion chromatography was coupled to electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (SEC–FTICR–MS) to separate a fulvic acid isolate into three size fractions and to determine the elemental composition of fulvic acids in these fractions. Molecular formulas of about 3000 ions in the mass range of 200–700Da were derived, many of which occur in all three fractions and follow the same system of elemental composition. Product ion spectra generated by SEC coupled to quadrupol-time-of-flight-MS (Q-TOF-MS) confirmed that the ions of all three fractions are basically polycarboxylates with hardly any other functional moiety. However, SEC–FTICR–MS revealed that the ions generated from the high molecular weight (HMW) fraction are enriched in carboxyl groups and are more aromatic as compared with the low molecular weight (LMW) fraction. These findings support the idea that the HMW fulvic acids are formed from LMW fulvic acids. The shift in the relative frequency of ions from the LMW to the HMW fraction is in line with different interaction mechanisms: HMW fulvic acids may be aggregates held together by electrostatic interaction of the carboxylate groups via hydrogen bonds or with polyvalent cations or by hydrophobic interaction of their carbon backbone, or consist of LMW fulvic acids covalently bound to each other or to (aliphatic) alcohols. [Copyright &y& Elsevier]

Bacterial intraspecies and interspecies communication in the rhizosphere is mediated by diffusible signal molecules. Many Gram-negative bacteria use N-acyl-homoserine lactones (AHLs) as autoinducers in the quorum sensing response. While bacterial signalling is well described, the fate of AHLs in contact with plants is much less known. Thus, adsorption, uptake and translocation of N-hexanoyl- (C6-HSL), N-octanoyl- (C8-HSL) and N-decanoyl-homoserine lactone (C10-HSL) were studied in axenic systems with barley ( Hordeum vulgare L.) and the legume yam bean ( Pachyrhizus erosus (L.) Urban) as model plants using ultra-performance liquid chromatography (UPLC), Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and tritium-labelled AHLs. Decreases in AHL concentration due to abiotic adsorption or degradation were tolerable under the experimental conditions. The presence of plants enhanced AHL decline in media depending on the compounds’ lipophilicity, whereby the legume caused stronger AHL decrease than barley. All tested AHLs were traceable in root extracts of both plants. While all AHLs except C10-HSL were detectable in barley shoots, only C6-HSL was found in shoots of yam bean. Furthermore, tritium-labelled AHLs were used to determine short-term uptake kinetics. Chiral separation by GC-MS revealed that both plants discriminated D-AHL stereoisomers to different extents. These results indicate substantial differences in uptake and degradation of different AHLs in the plants tested. [ABSTRACT FROM AUTHOR]

Abstract: The 14-3-3s are a ubiquitous class of eukaryotic proteins that participate in a second regulatory step in many phosphorylation-based signal transduction systems. The Arabidopsis family of 14-3-3 proteins represents a rather large 14-3-3 gene family. The biological motive for such diversity within a single protein family is not yet completely understood. The work presented here utilizes 14-3-3 micro-affinity chromatography in conjunction with Fourier transform ion cyclotron resonance mass spectrometry to survey the substrate sequence selectivity of two Arabidopsis 14-3-3 isoforms that represent the two major subclasses of this protein family. A method was developed to compare the relative binding of eight synthetic phosphopeptide sequences. The degree to which each phosphopeptide bound to either isoform was assigned a relative value, defined here as the binding ratio. The method provided a simple means for visualizing differences in substrate sequence selection among different 14-3-3 isoforms. A reproducible preference for specific phosphopeptide sequences was measured for both isoforms. This binding preference was consistent among the two classes of isoforms, suggesting that any pressure for isoform selectivity must reside outside the central core that interacts with the phosphopeptide sequence of the client. [Copyright &y& Elsevier]

N-Acylated homoserine lactones (AHLs) are produced by Gram-negative bacteria as communication signals and are frequently studied as mediators of the “quorum sensing” response of bacterial communities. Several reports have recently been published on the identification of AHLs from different species and attempts have been made to study their role in natural habitats, for example the surface of plant roots in the rhizosphere. In this article, different analytical methods, including bacterial biosensors and chromatographic techniques, are reviewed. A concept for assignment of the structures of AHLs is also presented. The retention behaviour of derivatives of AHLs containing β-keto or hydroxyl groups and/or double bonds has been evaluated in relation to the separation behaviour of AHLs with saturated and unsubstituted alkanoyl chains. Samples have also been analysed by high resolution mass spectrometry (Fourier-transform ion-cyclotron-resonance mass spectrometry, FTICR-MS), nano liquid chromatography–electrospray ionization ion trap mass spectrometry (nano-LC–MS) and by the aid of a biosensor. The results obtained from ultra performance liquid chromatography (UPLC), FTICR-MS, nano-LC–MS, and bioassays have been compared to attempt structural characterisation of AHL without chemical synthesis of analytical standards. The method was used to identify the major AHL compound produced by the rhizosphere bacterium Acidovorax sp. N35 as N-(3-hydroxydecanoyl)homoserine lactone. [ABSTRACT FROM AUTHOR]