While tools for the automated analysis of MS and LC-MS/MS data are continuously improving, it is still often the case that at the end of an experiment, the mass spectrometrist will spend time carefully examining individual spectra. Current software support is mostly provided only by the instrument vendors, and the available software tools are often instrument-dependent. Here we present a new generation of mMass, a cross-platform environment for the precise analysis of individual mass spectra. The software covers a wide range of processing tasks such as import from various data formats, smoothing, baseline correction, peak picking, deisotoping, charge determination, and recalibration. Functions presented in the earlier versions such as in silico digestion and fragmentation were redesigned and improved. In addition to Mascot, an interface for ProFound has been implemented. A specific tool is available for isotopic pattern modeling to enable precise data validation. The largest available lipid database (from the LIPID MAPS Consortium) has been incorporated and together with the new compound search tool lipids can be rapidly identified. In addition, the user can define custom libraries of compounds and use them analogously. The new version of mMass is based on a stand-alone Python library, which provides the basic functionality for data processing and interpretation. This library can serve as a good starting point for other developers in their projects. Binary distributions of mMass, its source code, a detailed user's guide, and video tutorials are freely available from www.mmass.org .

Species of Scedosporium and Lomentospora are considered as emerging opportunists, affecting immunosuppressed and otherwise debilitated patients, although classically they are known from causing trauma-associated infections in healthy individuals. Clinical manifestations range from local infection to pulmonary colonization and severe invasive disease, in which mortality rates may be over 80%. These unacceptably high rates are due to the clinical status of patients, diagnostic difficulties, and to intrinsic antifungal resistance of these fungi. In consequence, several consortia have been founded to increase research efforts on these orphan fungi. The current review presents recent findings and summarizes the most relevant points, including the Scedosporium/Lomentospora taxonomy, environmental distribution, epidemiology, pathology, virulence factors, immunology, diagnostic methods, and therapeutic strategies.

a b s t r a c tO-glycosylation is a ubiquitous eukaryotic post-translational modification, whereas early reports of S-linked glycopeptides have never been verified. Prokaryotes also glycosylate proteins, but there are no confirmed examples of sidechain glycosylation in ribosomal antimicrobial polypeptides collectively known as bacteriocins. Here we show that glycocin F, a bacteriocin secreted by Lactobacillus plantarum KW30, is modified by an N-acetylglucosamine b-O-linked to Ser18, and an N-acetylhexosamine S-linked to C-terminal Cys43. The O-linked N-acetylglucosamine is essential for bacteriostatic activity, and the C-terminus is required for full potency (IC 50 2 nM). Genomic context analysis identified diverse putative glycopeptide bacteriocins in Firmicutes. One of these, the reputed lantibiotic sublancin, was shown to contain a hexose S-linked to Cys22.

We reviewed the licensed antifungal drugs and summarized their mechanisms of action, pharmacological profiles, and susceptibility to specific fungi. Approved antimycotics inhibit 1,3-β-d-glucan synthase, lanosterol 14-α-demethylase, protein, and deoxyribonucleic acid biosynthesis, or sequestrate ergosterol. Their most severe side effects are hepatotoxicity, nephrotoxicity, and myelotoxicity. Whereas triazoles exhibit the most significant drug–drug interactions, echinocandins exhibit almost none. The antifungal resistance may be developed across most pathogens and includes drug target overexpression, efflux pump activation, and amino acid substitution. The experimental antifungal drugs in clinical trials are also reviewed. Siderophores in the Trojan horse approach or the application of siderophore biosynthesis enzyme inhibitors represent the most promising emerging antifungal therapies.

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The Bordetella pertussis RTX (repeat in toxin family protein) adenylate cyclase toxin-hemolysin (ACT) acquires biological activity upon a single amide-linked palmitoylation of the ⑀-amino group of lysine 983 (Lys 983 ) by the accessory fatty-acyltransferase CyaC. However, an additional conserved RTX acylation site can be identified in ACT at lysine 860 (Lys 860 ), and this residue becomes palmitoylated when recombinant ACT (r-Ec-ACT) is produced together with CyaC in Escherichia coli K12. We have eliminated this additional acylation site by replacing Lys 860 of ACT with arginine, leucine, and cysteine residues. Two-dimensional gel electrophoresis and microcapillary high performance liquid chromatography/tandem mass spectrometric analyses of mutant proteins confirmed that the two sites are acylated independently in vivo and that mutations of The adenylate cyclase toxin-hemolysin (ACT, 1 AC-Hly, or CyaA) is a key virulence factor of the whooping cough agent Bordetella pertussis and a promising protective antigen candidate for acellular pertussis vaccines (1-5). ACT belongs to the RTX (repeats in toxin) protein family (6) and has the capacity to form small cation-selective membrane channels, which account for its weak hemolytic activity (8 -11). The major cytotoxic activity of the 1706-residue-long protein, however, consists in its capacity to invade a variety of eukaryotic cells directly across their cytoplasmic membrane (12-14) and to deliver into cells a catalytic adenylate cyclase (AC) domain. This intoxicates cells by unregulated conversion of ATP to cAMP (15-18) and causes impairment of microbicidal functions of immune effector cells and apoptosis of lung macrophages (19).The capacity of ACT to penetrate into target cell membranes and to intoxicate cells depends on a posttranslational activation by the accessory protein, CyaC (20, 21). It was first established for the Escherichia coli ␣-hemolysin (HlyA) that the activation of RTX toxins consists in amide linked fatty-acylation (22), and Hackett et al. (23) have demonstrated by mass spectrometric analysis that native ACT produced by Bordetella (Bp-ACT) is mono-acylated by a palmitoyl residue at the ⑀-amino group of lysine 983. In contrast, the HlyA from E. coli was found to be acylated at two lysines, both in vitro and in vivo (24,25). Moreover, two highly conserved RTX acylation sites (25), corresponding to lysine 983 (Lys 983 ) and lysine 860 (Lys 860 ) are also found in ACT, and for an unknown reason, the CyaCactivated recombinant ACT produced in E. coli (r-Ec-ACT) is palmitoylated also at Lys 860 , in addition to acylation of Lys 983 (26). When compared with the native mono-acylated Bp-ACT, the doubly acylated r-Ec-ACT exhibits about four times lower specific hemolytic activity on sheep erythrocytes (20) and about 10 times lower specific channel-forming activity in artificial planar lipid bilayers (10). At the same time, however, the characteristics of the channels formed by both proteins are identical, and both proteins have identical capacity to insert ...

Mass spectrometry imaging of tissue-lipid transfers without MALDI matrix is demonstrated. Commercially available nanostructured surfaces (nano-assisted laser desorption-ionization or NALDI) are used as substrates for imprinting of tissue sections. The lithographic transfers are then washed and the two-dimensional distribution of the lipids is imaged by laser desorption-ionization mass spectrometry. The NALDI imaging of lipid transfers is compared with standard MALDI imaging of matrix-coated tissue sections. The obtained images are of the same quality, and no spatial information is lost due to the imprinting process. NALDI imaging is faster due to the absence of the time-consuming matrix deposition step, and the NALDI mass spectra are less complex and easier to interpret than standard MALDI. In this particular application example, NALDI mass spectrometry is able to identify the same lipid species as MALDI mass spectrometry and provides better distinction between kidney and adrenal gland tissues based on the lipid analysis.

Detergents are frequently used for protein isolation and solubilization. Their presence is crucial in membrane protein protocols or in lipid raft proteomics. However, they are usually poorly compatible with mass spectrometry. Several different sample preparation protocols are routinely used, but they are either laborious or suffer from sample losses. Here, we describe our alternative method for nonionic detergent removal. It is based on selective detergent extraction after capture of the sample on a reversed phase cartridge. The extraction is performed by chlorinated solvents and works well for polyoxyethylene based nonionic detergents, but also for polymers like polyethylene and propylene glycol. Detergent removal can be also carried out on the protein level but a special care must be taken with hydrophobic proteins. In such cases, it is preferable to perform detergent removal after proteolysis which digests the protein to peptides and reduces the hydrophobicity. The method can easily be automated and is compatible with hydrogen/deuterium exchange coupled to mass spectrometry.