High-performance liquid chromatography/mass spectrometry (HPLC/MS) analysis of anionic species such as sulphonic acid dyes and intermediates requires volatile ion-pairing mobile phase additives. Six di- and trialkylammonium acetates were compared with tetraalkylammonium salts and ammonium acetate in the concentration range 0-20 mmol l(-1) as mobile phase additives for HPLC/MS of polysulphonated compounds. The effects of the structure and concentration of the ion-pairing reagents on the electrospray response of mono-, di- and tetrasulphonic aromatic acids and acid dyes were studied in detail. Further, five different mass analysers and instrument geometries were compared. A higher signal decrease is observed with linear geometry instruments in comparison to orthogonal or even Z-spray geometry mass spectrometers. The concentration of mobile phase additives has a significant influence on the abundance ratios of multiply charged ions in the mass spectra of polysulphonated compounds. The competing ions of sulphonic acids may also cause significant signal suppression.

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Siderophores play important roles in microbial iron piracy, and are applied as infectious disease biomarkers and novel pharmaceutical drugs. Inductively coupled plasma and molecular mass spectrometry (ICP-MS) combined with high resolution separations allow characterization of siderophores in complex samples taking advantages of mass defect data filtering, tandem mass spectrometry, and iron-containing compound quantitation. The enrichment approaches used in siderophore analysis and current ICP-MS technologies are reviewed. The recent tools for fast dereplication of secondary metabolites and their databases are reported. This review on siderophores is concluded with their recent medical, biochemical, geochemical, and agricultural applications in mass spectrometry context.

Abstract. Nonribosomal peptides have a wide range of biological and medical applications. Their identification by tandem mass spectrometry remains a challenging task. A new open-source de novo peptide identification engine CycloBranch was developed and successfully applied in identification or detailed characterization of 11 linear, cyclic, branched, and branch-cyclic peptides. CycloBranch is based on annotated building block databases the size of which is defined by the user according to ribosomal or nonribosomal peptide origin. The current number of involved nonisobaric and isobaric building blocks is 287 and 521, respectively. Contrary to all other peptide sequencing tools utilizing either peptide libraries or peptide fragment libraries, CycloBranch represents a true de novo sequencing engine developed for accurate mass spectrometric data. It is a stand-alone and cross-platform application with a graphical and userfriendly interface; it supports mzML, mzXML, mgf, txt, and baf file formats and can be run in parallel on multiple threads. It can be downloaded for free from http://ms.biomed.cas.cz/cyclobranch/, where the User's manual and video tutorials can be found.

ABSTRACT:Silybin (a flavonolignan, the main component of silymarin, an extract from the seeds of Silybum marianum) has been used to date mostly as a hepatoprotectant. However, it also has other interesting activities, e.g., anticancer and hypocholesterolemic effects. It is also known that silybin can inhibit the activities of the cytochrome P450 (P450) enzymes. In this study, a weak interaction of silybin with human microsomal CYP2E1, 2A6, 2B6, 2C19, and 2D6 (IC 50 > 250 M) was found; a moderate inhibition was observed for CYP1A2 and 2C8. The most prominent inhibition effect was found with CYP3A4 and CYP2C9 (IC 50 < 50 M). Using mass spectometry detection, production of O-demethylated (the main metabolite) as well as hydroxylated derivatives of silybin formed by P450 enzymes was detected. The effect of different P450 inhibitors on the formation of O-demethylated product was also studied. In particular, a relatively specific inhibitor of CYP2C8 (quercetin) markedly inhibited the formation of this metabolite. With the help of recombinant enzymes (bactosomes), it was confirmed that the CYP2C8 enzyme is responsible for the reaction leading to O-demethylated silybin.

The development of a rapid, simple and accurate analytical method aimed at the detection and quantification of bovine milk in either ovine or caprine milk samples by means of CE-MS analyses of whey proteins with high-ionic strength and presence of acidic running buffer is described. The high-ionic strength buffer was used in order to minimize the problems with the adsorption of the proteins onto the fused-silica capillary wall. The acidic running electrolyte, pH 1.9, was used to support the production of positive ions in electrospray. Highly linear dependences of the ratio of the sum of non-bovine beta-lactoglobulins (ovine or caprine) to the total beta-lactoglobulins in milk mixture (bovine plus ovine or bovine plus caprine) vs. the volume percentage of added bovine milk in ovine (or caprine) milk were obtained. This technique allowed the fast and reliable evaluation of milk adulteration. The amount of bovine milk added into the "non-bovine" ones can be well within the concentration range of 5-95%.

Current mass spectrometry, nuclear magnetic resonance spectroscopy, and X-ray diffraction are presented as structure elucidation tools for analytical chemistry of natural products. Discovering new molecular entities combined with dereplication of known organic compounds represent prerequisites for biological assays and for respective applications as pharmaceuticals or molecular markers. Liquid chromatography is briefly addressed with respect to its use in mass spectrometry- and nuclear magnetic resonance-based metabolomics studies.