Tandem electrospray mass spectrometric studies of proton and sodium ion adducts of neutral peptides with modified N- and C-termini: synthetic model peptides and microheterogeneous peptaibol antibiotics

Proteome-wide profiling and mapping of post translational modifications in human hearts

Post translational modifications (PTMs) are covalent modifications of proteins that can range from small chemical modifications to addition of entire proteins. PTMs contribute to regulation of protein function and thereby greatly increase the functional diversity of the proteome. In the heart, a few well-studied PTMs, such as phosphorylation and glycosylation, are known to play essential roles for cardiac function. Yet, only a fraction of the ~ 300 known PTMs have been studied in a cardiac context. Here we investigated the proteome-wide map of PTMs present in human hearts by utilizing high-resolution mass spectrometry measurements and a suite of PTM identification algorithms. Our approach led to identification of more than 150 different PTMs across three of the chambers in human hearts. This finding underscores that decoration of cardiac proteins by PTMs is much more diverse than hitherto appreciated and provides insights in cardiac protein PTMs not yet studied. The results presented serve as a catalogue of which PTMs are present in human hearts and outlines the particular protein and the specific amino acid modified, and thereby provides a detail-rich resource for exploring protein modifications in human hearts beyond the most studied PTMs.

Dissociation Pattern of Sodiated Amide Peptides as a Tool for De Novo Sequencing

As part of the de novo sequencing issue, new approaches have to be found to sequence small natural peptides (<15-20 residues), which often present amino acid compositions, inducing merely singly charged species, that are quite difficult to thoroughly fragment under low-energy activation conditions in MS/MS experiments. Cationization by alkali metals, like Na⁺, followed by collision-induced dissociations (CID) or the postsource metastable decay (PSD) of such cationized molecular ions was found to improve the sequence coverage of native peptides through the formation of [b_n-1 + Na + OH]⁺ ions issued from C-terminal residue exclusion. Concerned by the identification of peptides with a C-terminal amide, the fragmentation pattern of their sodiated molecular ions was investigated. In contrast to the peptides featuring unmodified C-termini, the C-terminal loss did not occur, with the amide function triggering different fragmentation pathways. However, several residues, such as aspartic acid (D), glutamic acid (E), and arginine (R), influenced the dissociation of fixed-charge sodiated ions similarly to protonated peptides; more surprisingly, serine (S), threonine (T), and tyrosine (Y), which exhibit a hydroxyl function on their side chains, showed a very peculiar behavior that could help de novo peptide sequencing.

Alkali Metal Cationization of Tumor-associated Antigen Peptides for Improved Dissociation and Measurement by Differential Ion Mobility-Mass Spectrometry

Tandem mass spectrometry (MS/MS) is a highly sensitive and selective method for the detection of tumor-associated peptide antigens. These short, nontryptic sequences may lack basic residues, resulting in the formation of predominantly [peptide + H]+ ions in electrospray. These singly charged ions tend to undergo inefficient dissociation, leading to issues in sequence determination. Addition of alkali metal salts to the electrospray solvent can drive the formation of [peptide + H + metal]2+ ions that have enhanced dissociation characteristics relative to [peptide + H]+ ions. Both previously identified tumor-associated antigens and predicted neoantigen sequences were investigated. The previously reported rearrangement mechanism in MS/MS of sodium-cationized peptides is applied here to demonstrate complete C-terminal sequencing of tumor-associated peptide antigens. Differential ion mobility spectrometry (DIMS) is shown to selectively enrich [peptide + H + metal]2+ species by filtering out singly charged interferences at relatively low field strengths, offsetting the decrease in signal intensity associated with the use of alkali metal cations.

Ion-Trap Mass Spectrometric Analysis of Bisphenol A Interactions With Titanium Dioxide Nanoparticles and Milk Proteins

Quantitative analysis of endocrine-disrupting molecules such as bisphenol A (BPA) in freshwater to determine their widespread occurrence in environmental resources has been challenged by various adsorption and desorption processes. In this work, ion trap mass spectrometry (ITMS) analysis of BPA was aimed at studying its molecular interactions with titanium dioxide (TiO2) nanoparticles and milk whey proteins. Addition of sodium formate prevented TiO2 nanoparticles from sedimentation while enhancing the electrospray ionization (ESI) efficiency to produce an abundance of [BPA + Na]+ ions at m/z 251.0. More importantly, the ESI-ITMS instrument could operate properly during a direct infusion of nanoparticles up to 500 μg/mL without clogging the intake capillary. Milk protein adsorption of BPA could decrease the [BPA + Na]+ peak intensity significantly unless the proteins were partially removed by curdling to produce whey, which allowed BPA desorption during ESI for quantitative analysis by ITMS.

Acremotins A-D, peptaibiotics produced by the soil-derived fungus Acremonium persicinum SC0105

Four new peptaibiotics, acremotins A-D (1-4) featuring three α,α-dialkylated amino acid-imino acid motifs and an unreduced C-terminal residue, along with the known peptaibiotic XR586 (5) were isolated from the solid cultures of the soil-derived fungus Acremonium persicinum SC0105. Their primary structures were characterized by detailed analysis of the HRESIMS/MS fragmentation pattern combined with comprehensive interpretation of the 1D and 2D NMR spectroscopic data. The absolute configurations of amino acid residues were determined by the advanced Marfey's method. Sequence alignment result shows that 1-4 are closely related to zervamicin IIB and emerimicin IIA, thus belong to peptaibiotic subfamily-3 (SF3). The three-dimensional (3D) structure of 4 was established by theoretical conformational analysis using the ab initio density functional theory (DFT) method, which, together with the CD spectrum, indicated an amphiphilic and helical structure for 4. 1-5 actively inhibited the growth of gram-positive bacterial pathogens, and amongst them 4 was the most potent compound showing MIC of 12.5 and 6.25 µg/ml against S. aureu and MRSA strains, respectively. 1-5 were also cytotoxic against three human cancer cell lines with IC₅₀ ranging from 1.2 to 21.6 μM.

Multifarious allelochemicals exhibiting antifungal activity from Bacillus subtilis MBCU5

A potential antagonist, designated strain Bacillus subtilis MBCU5 was previously isolated from vermicompost-amended soils of Gandhinagar, Gujarat, India. Crude allelochemicals from strain MBCU5 displayed strong antifungal activity against Macrophomina phaseolina as well as Rhizoctonia solani. These crude allelochemicals were tentatively identified as iturin, fengycin and surfactin through TLC and HPTLC analysis. Lipopeptides produced by MBCU5 were identified by MALDI-TOF-MS and LC-ESI-MS/MS analysis showed that iturin homologues (m/z 1020-1120), surfactin (m/z 1008.7 and m/z 1022.7), fengycin A and fengycin B (m/z 1400-1550) types of allelochemicals which are responsible for antifungal activity against pathogens. PCR analysis showed presence of genes (i.e. Iturin A synthetase KJ531680 and Surfactin synthetase KJ601726) involved in the biosynthesis of allelochemicals. Many reports showed lipopeptides from Bacillus species; this is the first report executed of multifarious allelochemicals from vermicompost-amended soil due to the presence of predominant Bacillus species.

Gas-phase fragmentations of N-methylimidazolidin-4-one organocatalysts

N-methylimidazolidin-4-one organocatalysts were studied in the gas phase. Protonated and sodium-cationized (sodiated) molecules are conveniently accessible by electrospray mass spectrometry. Protonation enables three different closed-shell paths of ring cleavage leading to iminium ions. The fragmentation pattern is largely unaffected by exocyclic substituents and thus is valuable to characterize the substance type as N-methylimidazolidin-4-ones. Sodiated species show a distinctly different fragmentation that is less useful for characterization purposes: apart from signal loss due to dissociation of Na⁺ , the observation of benzyl radical loss is by far predominant. Only in absence of a benzyl substituent, an analogue of the third ring cleavage (loss of [C₂ H₅ NO]) is observed. Copyright © 2017 John Wiley & Sons, Ltd.

Neutral losses of sodium benzoate and benzoic acid in the fragmentation of the [M + Na]+ ions of methoxyfenozide and tebufenozide via intramolecular rearrangement in electrospray ionization tandem mass spectrometry

RATIONALE

Electrospray ionization (ESI) tandem mass spectrometry can be applied to determine structural information about organic compounds. The [M + Na]⁺ ion is one of the major precursor ions in ESI mass spectrometry, but its fragmentation mechanism study is still insufficient. This study reveals the interesting fragmentation reactions of the [M + Na]⁺ ions of methoxyfenozide and tebufenozide.

METHODS

The fragmentations of the [M + Na]⁺ , [M + Li]⁺ , and [M + H]⁺ ions of methoxyfenozide and tebufenozide were studied using a hybrid quadrupole-orbitrap mass spectrometer and an ion trap mass spectrometer. A hydrogen/deuterium (H/D)-exchange experiment in the amide group of methoxyfenozide allowed for the confirmation of the fragmentation mechanism. Density functional theory (DFT) calculations were performed for a further understanding of the fragmentation mechanism of the [M + Na]⁺ ion of methoxyfenozide.

RESULTS

Neutral losses of sodium benzoate and benzoic acid in the fragmentation of the [M + Na]⁺ ions of methoxyfenozide and tebufenozide were observed as the major fragmentation pathways. In contrast, similar fragmentations were not observed or minor pathways in the fragmentation of the [M + Li]⁺ and [M + H]⁺ ions of methoxyfenozide and tebufenozide. In addition, a minor product ion resulting from loss of NaOH was identified, which was the first reported example in the fragmentation of sodiated compounds in mass spectrometry.

CONCLUSIONS

Losses of sodium benzoate and benzoic acid in the fragmentation of the [M + Na]⁺ ions of methoxyfenozide and tebufenozide are proposed to be formed through an intramolecular rearrangement reaction, which is supported by DFT calculations. An H/D-exchange experiment confirms that the carboxyl hydrogen of benzoic acid and the hydrogen of NaOH exclusively derive from the amide hydrogen of the precursor ion. This study enriches our knowledge on the Na⁺ -induced fragmentation reactions. Copyright © 2016 John Wiley & Sons, Ltd.

Structure and further fragmentation of significant [a3 + Na - H]+ ions from sodium-cationized peptides

A good understanding of gas-phase fragmentation chemistry of peptides is important for accurate protein identification. Additional product ions obtained by sodiated peptides can provide useful sequence information supplementary to protonated peptides and improve protein identification. In this work, we first demonstrate that the sodiated a3 ions are abundant in the tandem mass spectra of sodium-cationized peptides although observations of a3 ions have rarely been reported in protonated peptides. Quantum chemical calculations combined with tandem mass spectrometry are used to investigate this phenomenon by using a model tetrapeptide GGAG. Our results reveal that the most stable [a3 + Na - H](+) ion is present as a bidentate linear structure in which the sodium cation coordinates to the two backbone carbonyl oxygen atoms. Due to structural inflexibility, further fragmentation of the [a3 + Na - H](+) ion needs to overcome several relatively high energetic barriers to form [b2 + Na - H](+) ion with a diketopiperazine structure. As a result, low abundance of [b2 + Na - H](+) ion is detected at relatively high collision energy. In addition, our computational data also indicate that the common oxazolone pathway to generate [b2 + Na - H](+) from the [a3 + Na - H](+) ion is unlikely. The present work provides a mechanistic insight into how a sodium ion affects the fragmentation behaviors of peptides.

Gas-phase fragmentation of metal adducts of alkali-metal oxalate salts

Upon collisional activation, gaseous metal adducts of lithium, sodium and potassium oxalate salts undergo an expulsion of CO2, followed by an ejection of CO to generate a product ion that retains all three metals atoms of the precursor. Spectra recorded even at very low collision energies (2 eV) showed peaks for a 44-Da neutral fragment loss. Density functional theory calculations predicted that the ejection of CO2 requires less energy than an expulsion of a Na(+) and that the [Na3CO2](+) product ion formed in this way bears a planar geometry. Furthermore, spectra of [Na3C2O4](+) and [(39)K3C2O4](+) recorded at higher collision energies showed additional peaks at m/z 90 and m/z 122 for the radical cations [Na2CO2](+•) and [K2CO2](+•), respectively, which represented a loss of an M(•) from the precursor ions. Moreover, [Na3CO2](+), [(39)K3CO2](+) and [Li3CO2](+) ions also undergo a CO loss to form [M3O](+). Furthermore, product-ion spectra for [Na3C2O4](+) and [(39)K3C2O4](+) recorded at low collision energies showed an unexpected peak at m/z 63 for [Na2OH](+) and m/z 95 for [(39)K2OH](+), respectively. An additional peak observed at m/z 65 for [Na2(18)OH](+) in the spectrum recorded for [Na3C2O4](+), after the addition of some H2(18)O to the collision gas, confirmed that the [Na2OH](+) ion is formed by an ion-molecule reaction with residual water in the collision cell.

Eight new peptaibols from sponge-associated Trichoderma atroviride

Eight new and four known peptaibols were isolated from a strain of the fungus, Trichoderma atroviride (NF16), which was cultured from an Axinellid sponge collected from the East Mediterranean coast of Israel. The structures of the pure compounds were determined using HRMS, MS/MS and one- and two-dimensional NMR measurements. The isolated compounds belong to the trichorzianines, a family of 19-residue linear hydrophobic peptides containing a high proportion of α-aminoisobutyric acid (Aib), an acetylated N-terminus and a C-terminal amino alcohol. These new peptaibols exhibited antimicrobial activity against environmental bacteria isolated from the Mediterranean coast of Israel.

Locating Pb2+ and Zn2+ in zinc finger-like peptides using mass spectrometry

The binding preferences of Pb(2+)and Zn(2+) in doubly charged complexes with zinc finger-like 12-residue peptides (Pep), [Mn(Pep-2(n-1)H)](2+) have been explored using tandem mass spectrometry. The peptides were synthesized strategically by blocking the N-terminus with an acetyl group and with four cysteine and/or histidine residues in positions 2, 5, 8, and 11, arranged in different motifs: CCHH, CHCH, and CCCC. The MS(2) spectra of the Pb(2+) and Zn(2+) complexes show multiple losses of water and a single methane loss and these provide a sensitive method for locating the metal dication and so elucidating its coordination. The elimination of a methane molecule indicated the position of the metal at the Cys2 residue. Whereas lead was observed to preferentially bind to cysteine residues, zinc was found to primarily bind to histidine residues and secondarily to cysteine residues. Preferential binding of lead to cysteine is preserved in the complexes with more than one Pb(2+). Key to the mechanism of the loss of water and methane is the metal dication withdrawing electrons from the proximal amidic nitrogen. This acidic nitrogen loses its hydrogen to an amidic oxygen situated four atoms away leading to formation of a five-member ring and the elimination of water.

Sequential determination of new peptaibols asperelines G-Z12 produced by marine-derived fungus Trichoderma asperellum using ultrahigh pressure liquid chromatography combined with electrospray-ionization tandem mass spectrometry

Thirty-eight short peptaibols in a microheterogeneous mixture derived from the fermentation broth of a marine-derived fungus Trichoderma asperellum were determined using ultrahigh pressure liquid chromatography in combination with electrospray-ionization tandem mass spectrometry (UHPLC-ESIMS/MS) techniques, including thirty-two new peptaibols namely asperelines G-Z13. The C-terminus bonded to proline (aspereline Z9) or hydroxyprolinol (aspereline Z12) is rarely found in nature. So far, it is the largest number of peptaibols to be detected at once on the basis of the selected ion monitoring (SIM) mode coupled to precursor scan techniques.

Minutissamides E-L, antiproliferative cyclic lipodecapeptides from the cultured freshwater cyanobacterium cf. Anabaena sp

The extract of UIC 10035, a strain obtained from a sample collected near the town of Homestead, South Florida, showed antiproliferative activity against MDA-MB-435 cells. Bioassay-guided fractionation led to the isolation of a series of cyclic lipodecapeptides, named minutissamides E-L (1-8). The planar structures were determined by analysis of HRESIMS, tandem MS, and 1D and 2D NMR data, and the stereoconfigurations were assigned by LC-MS analysis of the Marfey's derivatives after acid hydrolysis. Minutissamides E-L (1-8) exhibited antiproliferative activity against MDA-MB-435 cells with IC(50) values ranging between 1 and 10 μM. The structures of minutissamides E-L (1-8) were closely related with those of the previously reported lipopeptides, puwainaphycins A-E and minutissamides A-D, characterized by the presence of a lipophilic β-amino acid and three non-standard amino acids NMeAsn, OMeThr and Dhb (α,β-dehydro-α-aminobutyric acid). The strain UIC 10035 was designated as cf. Anabaena sp. on the basis of morphological and 16S rRNA gene sequence analyses.

A pseudo MS3 approach for identification of disulfide-bonded proteins: uncommon product ions and database search

It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs.

Mass spectrometry in India

This review emphasizes the mass spectrometry research being performed at academic and established research institutions in India. It consists of three main parts covering the work done in organic, atomic and biological mass spectrometry. The review reveals that the use of mass spectrometry techniques started in the middle of the 20th century and was applied to research in the fields of organic, nuclear, geographical and atomic chemistry. Later, with the advent of soft and atmospheric ionization techniques it has been applied to pharmaceutical and biological research. In due course, several research centers with advanced mass spectrometry facilities have been established for specific areas of research such as gas-phase ion chemistry, ion-molecule reactions, proscribed chemicals, pesticide residues, pharmacokinetics, protein/peptide chemistry, nuclear chemistry, geochronological studies, archeology, petroleum industry, proteomics, lipidomics and metabolomics. Day-by-day the mass spectrometry centers/facilities in India have attracted young students for their doctoral research and other advanced research applications.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical 'b-ion' series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the 'b' or/and the 'y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the 'y-type'. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Differentiation of α- or β-aspartic isomers in the heptapeptides by the fragments of [M + Na]+ using ion trap tandem mass spectrometry

Electrospray ionization coupled with low energy collision induced dissociation (CID) in an ion trap mass spectrometer was used to examine the fragmentation patterns of the [M + Na](+) of eight pairs of heptapeptides containing α- or β-Asp residues in second and sixth amino acid positions, respectively. Selective cleavages at the peptide backbone C-terminal to two Asp residues were observed, which generated a series of C-terminal y(5) ions and N-terminal b(6) ions. Two typical ions: [y5 + Na - H]+ and [b6 + Na + OH]+, produced by α-Asp containing peptides were noted to be much more abundant than those of the peptides with β-Asp, which could be used for distinction of the isomers in Asp2 and Asp6, respectively. In addition, a series of internal ions generated by simultaneous cleavages at Asp residues were detected. Competitive reactions of carboxylic groups occurred between Asp6 side chain and C-terminus. Formation mechanisms of most product ions are proposed. The results obtained in this work are significant since low energy CID has been demonstrated to be effective for the distinction of Asp isomers.

Generation of gas-phase sodiated arenes such as [(Na3(C6H4)+] from benzene dicarboxylate salts

Upon collision-induced activation, gaseous sodium adducts generated by electrospray ionization of disodium salts of 1,2- 1,3-, and 1,4-benzene dicarboxylic acids (m/z 233) undergo an unprecedented expulsion of CO(2) by a rearrangement process to produce an ion of m/z 189 in which all three sodium atoms are retained. When isolated in a collision cell of a tandem-in-space mass spectrometer, and subjected to collision-induced dissociation (CID), only the m/z 189 ions derived from the meta and para isomers underwent a further CO(2) loss to produce a peak at m/z 145 for a sodiated arene of formula (Na(3)C(6)H(4))(+). This previously unreported m/z 145 ion, which is useful to differentiate meta and para benzene dicarboxylates from their ortho isomer, is in fact the sodium adduct of phenelenedisodium. Moreover, the m/z 189 ion from all three isomers readily expelled a sodium radical to produce a peak at m/z 166 for a radical cation [(*C(6)H(4)CO(2)Na(2))(+)], which then eliminated CO(2) to produce a peak at m/z 122 for the distonic cation (*C(6)H(4)Na(2))(+).

The production and characterisation of trichotoxin peptaibols, by Trichoderma asperellum

Trichoderma spp. are regularly found as a constituent of the mycoflora of many soils and are noted for their antagonistic activity against bacteria and other fungi. This latter property is the basis for the widespread interest in their use in the biological control of soil-borne fungal plant pathogens. This antagonism is partly based on their ability to produce an impressive inventory of secondary metabolites. An important group of bioactive metabolites produced by Trichoderma spp. are the non-ribosomal peptides (NRPs), especially the peptaibols. A virulent antagonistic strain, T. asperellum, which had been used in biological control strategies in Malaysia and previously examined for mycolytic enzyme production, has been studied for its potential for peptaibol production. The present research demonstrated the ability of T. asperellum to produce at least two metabolites which were identified as acid trichotoxin 1704E (Ac-Aib-Gly-Aib-Leu-Aib-Gln-Aib-Aib-Aib-Ala-Ala-Aib-Pro-Leu-Aib-Iva-Glu-Vol) and neutral trichotoxin 1717A (Ac-Aib-Gly-Aib-Leu-Aib-Gln-Aib-Aib-Aib-Ala-Aib-Aib-Pro-Leu-Aib-Iva-Gln-Vol). Addition of free Aib to the culture medium enhanced the production of trichotoxins. Biological activity of these substances was investigated against Bacillus stearothermophilus. The general characteristics of peptaibols, also found in the trichotoxins, include the presence of high proportions of the uncommon amino acid Aib, the protection of the N- and C-termini by an acetyl group and reduction of the C-terminus to 2-amino alcohols, respectively, amphipathy and microheterogeneity.

Determination of peptaibol trace amounts in marine sediments by liquid chromatography/electrospray ionization-ion trap-mass spectrometry

Extraction followed by reverse phase liquid chromatography (LC)/electrospray ionization-ion trap-mass spectrometry (ESI-IT-MS) analysis has been successfully developed for the determination of peptaibols, fungal toxic metabolites, in marine sediments. Spiking experiments showed that the mean recovery of target compounds exceeded 85% at a spiking level of 10 ng/g of sediment (wet weight). Detection and quantification limits were 250 and 830 pg/g of sediment, respectively. The method developed constituted the first sensitive assay for quantification of peptaibol trace amounts in a natural environment. A concentration of 5 ng/g in sediment samples collected from Fier d'Ars was found.

Peptaibols of trichoderma

The fungal genus Trichoderma has various applications in industry and in medicine, and several species have economic importance as sources of enzymes, antibiotics, plant growth promoters, decomposers of xenobiotics, and as commercial biofungicides. Peptaibiotics and peptaibols are a class of linear peptides synthesized by such fungi, and more than 300 have been described to date. Of this class, those compounds exhibiting antimicrobial activity are referred to as antibiotic peptides. In this review, the biosynthesis, fermentation, structure elucidation (by MS and NMR techniques in particular) and biological activity of antibiotic peptides from Trichoderma species are described.

Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides

The software Peptide Fragment Ion Analyser (PFIA) aids in the analysis and interpretation of tandem mass spectrometric data of peptides. The software package has been designed to facilitate the analysis of product ions derived from acyclic and cyclic peptide natural products that possess unusual amino acid residues and are heavily post-translationally modified. The software consists of two programmes: (a) PFIA-I lists the amino acid compositions and their corresponding product ion types for 'a queried m/z value' (z = +1) and (b) PFIA-II displays fragmentation pattern diagram(s) and lists all sequence-specific product ion types for the protonated adduct of 'a queried sequence'. The unique feature of PFIA-II is its ability to handle cyclic peptides. The two programmes used in combination can prove helpful for deriving peak assignments in the de novo sequencing of novel peptides.