Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry

MOTIVATION: The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. RESULTS: This paper provides a promising approach to utilizing the correlative information for improving the peptide identification accuracy. The kernel trick, rooted in the statistical learning theory, is exploited to address this issue with low computational effort. The common scoring method, the tandem mass spectral dot product (SDP), is extended to the kernel SDP (KSDP). Experiments on a dataset reported previously demonstrate the effectiveness of the KSDP. The implementation on consecutive fragments shows a decrease of 10% in the error rate compared with the SDP. Our software tool, pFind, using a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html     

Peptaibols and related peptaibiotics of Trichoderma. A review

Peptaibols and the related peptaibiotics are linear, amphipathic polypeptides. More than 300 of these secondary metabolites have been described to date. These compounds are composed of 5-20 amino acids and are generally produced in microheterogeneous mixtures. Peptaibols and peptaibiotics with unusual amino acid content are the result of non-ribosomal biosynthesis. Large multifunctional enzymes known as peptide synthetases assemble these molecules by the multiple carrier thiotemplate mechanism from a remarkable range of precursors, which can be N-methylated, acylated or reduced. Peptaibols and peptaibiotics show interesting physico-chemical and biological properties including the formation of pores in bilayer lipid membranes, as well as antibacterial, antifungal, occasionally antiviral activities, and may elicit plant resistance. The three-dimensional structure of peptaibols and peptaibiotics is characterized predominantly by one type of the helical motifs alpha-helix, 3(10)-helix and beta-bend ribbon spiral. The aim of this review is to summarize the data available about the biosynthesis, biological activity and conformational properties of peptaibols and peptaibiotics described from Trichoderma species.     

Somatic embryogenesis and mass spectrometric identification of proteins related to somatic embryogenesis in Eruca sativa

Several different proteins expressed in embryogenic and nonembryogenic Eruca sativa calli were identified by combining one-dimensional SDS-PAGE protein mapping with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. By querying the widely recognized MASCOT search engine, it was found that three of the proteins that were particularly strongly expressed in the embryogenic callus represented sucrose synthase, phospholipase D, and enolase, respectively. RT-PCR analysis also confirmed that the gene coding for enolase was transcribed especially strongly in the embryogenic callus but not in nonembyogenic callus. Finally, the relationship between the three proteins and somatic embryogenesis is discussed.     

Ultra-high intra-spectrum mass accuracy enables unambiguous identification of fragment reporter ions in isobaric multiplexed quantitative proteomics

Isobaric tagging using reagents such as tandem mass tags (TMT) and isobaric tags for relative and absolute quantification (iTRAQ) have become popular tools for mass spectrometry based quantitative proteomics. Because the peptide quantification information is collected in tandem mass spectra, the accuracy and precision of this method largely depend on the resolution with which precursor ions can be selected for the fragmentation and the specificity of the generated reporter ion. The latter can constitute an issue if near isobaric ion signals are present in such spectra because they may distort quantification results. We propose a simple remedy for this problem by identifying reporter ions via the accurate mass differences within a single tandem mass spectrum instead of applying fixed mass error tolerances for all tandem mass spectra. Our results show that this leads to unambiguous reporter ion identification and complete removal of interfering signals. This mode of data processing is easily implemented in software and offers advantages for protein quantification based on few peptides.     

Mutagenicity of 43 structurally related heterocyclic compounds and its relationship to their carcinogenicity.

43 heteropolycyclic compounds belonging to a homologous series were investigated for mutagenicity. The results are compared with carcinogenicity data obtained with the same batches of compounds under conditions identical for all of them. Mutagenicity was tested in the Ames test with Salmonella typhimurium strains TA1535, TA1537 and TA100 in the presence and absence of liver 10 000 g supernatant from rats treated with Aroclor 1254. Carcinogenicity was tested by injection of the compounds into subcutaneous tissue of XVIInc/Z mice. 18 test compounds showed carcinogenic activity, some strongly, others only weakly. Of these, 17 were detected as mutagens: one weak carcinogen did not revert the Salmonella strains. No quantitative correlation was observed between the extents of the mutagenic and the carcinogenic effects. Of the 25 substances that did not produce tumours, 13 showed mutagenicity (12 in the presence, 2 in the absence, of the liver homogenate). The mutagenic effects of these compounds were quantitatively similar to those of the compounds that produced tumours. The most sensitive strain of Salmonella typhimurium was TA100. It detected all 30 mutagens. TA98 was mutated by 25 compounds, TA1537 by 16 compounds. No mutagenic effects were seen with TA1535. Possible reasons for the high percentage of apparently "false positives" in the Ames test and the lack of a quantitative correlation between the potency of the mutagenic and carcinogenic effects are discussed. It is suggested that the complexity of the metabolism of these heterocyclic compounds may lead to critical differences in metabolism in mouse subcutaneous tissue in vivo and in liver homogenates from rats treated with Aroclor. Therefore the present study will be extended to life-long oral and intrahepatic carcinogenicity tests leading to a higher proportion of metabolism in the liver.     

The occurrence of keratinophilic fungi in queensland

Summary Keratinophilic fungi have been isolated and identified in soil samples from 233 sites in Queensland and 12 from the Northern Territory. Total numbers of the fungi isolated are given, together with their occurrence in various broad types of locality.It is noted that populated localities produced a higher incidence of keratinophilic fungi than remote areas. Exceptions to this were found in beach sand, 17 samples of which produced only two growths ofChrysosporium species and no potentially pathogenic fungi.Culture technique, and the method of examination of colonies are discussed, and the morphological features of several of the more commonly occurring species are described.Isolates ofChrysosporium tropicum were made from two samples, one from Alice Springs and one from Brisbane. This is the first time this fungus has been reported in Australia.     

Use of mass spectrometric methods for protein identification in receptor research

In recent years, mass spectrometry has become the method of choice for identifying small amounts of gel separated proteins. Using high mass accuracy peptide mass mapping followed if necessary by nanoelectrospray sequencing, most mammalian proteins can now be identified quickly and sensitively either in amino acid or in EST sequence databases. These methods are illustrated here using an ongoing project in the author's laboratory, a mass spectrometric screen for new mouse brain receptors and their interaction partners.     

The occurrence of fungi in activated sludge

The population of a biological system in a sewage treatment plant is formed of a fortuitous assemblage of microorganisms, members of which are continually dropped out while additional members are recruited. Many of these organisms are active throughout the year. Fewer yeasts than filamentous fungi are found by the plating technique. The population is about evenly divided between species producing their spores in dry states and in wet states. The fungus population includes species which under certain circumstances are able to use a wide variety of substrates from simple sugars to complex carbohydrates and hydrocarbons.

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Zusammenfassung Die Population eines biologischen Systems in einem Kloakenwasser-Behandlungs-werk ist durch ein zufälliges Zusammentreffen von Mikroorganismen geformt, deren Mitglieder fortwährend ausfallen, während andere hinzukommen. Viele dieser Mikroorganismen sind während des ganzen Jahres aktiv. Weniger Hefen denn Fadenpilze sind mit der Plattentechnique gefunden. Die Population ist ungefähr gleichmäßig unter den Arten verteilt, die die Sporen in trockenem wie in feuchtem Zustand produzieren. Die Pilzpopulation umfaßt Arten, die unter gewissen Umständen fähig sind, eine große Varietät von Nährmaterial, von einfachen wie auch komplexen Kohlenstoffhydraten und Kohlenstoffhydraten zu benutzen.

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Much of the material included here was Presented at the 23rd Industrial Waste Conference Purdue University, Lafayette, Indiana May 7–9, 1968     

Tag-mediated isolation of yeast mitochondrial ribosome and mass spectrometric identification of its new components.

Mitochondrial ribosomal proteins (mrps) of the budding yeast, Saccharomyces cerevisiae, have been extensively characterized genetically and biochemically. However, the list of the genes encoding individual mrps is still not complete and quite a few of the mrps are only predicted from their similarity to bacterial ribosomal proteins. We have constructed a yeast strain in which one of the small subunit proteins, termed Mrp4, was tagged with S-peptide and used for affinity purification of mitochondrial ribosome. Mass spectrometric analysis of the isolated proteins detected most of the small subunit mrps which were previously identified or predicted and about half of the large subunit mrps. In addition, several proteins of unknown function were identified. To confirm their identity further, we added tags to these proteins and analyzed their localization in subcellular fractions. Thus, we have newly established Ymr158w (MrpS8), Ypl013c (MrpS16), Ymr188c (MrpS17) and Ygr165w (MrpS35) as small subunit mrps and Img1, Img2, Ydr116c (MrpL1), Ynl177c (MrpL22), Ynr022c (MrpL50) and Ypr100w (MrpL51) as large subunit mrps.     

The occurrence of keratinophilic fungi in texas soil

Summary A total of 137 soils, 27 coming from caves and 110 from outdoor lands of Texas, were examined for the presence of keratinophilic fungi by the use of the ToKaVa hairbaiting technique. Twenty three and 69 fungal isolates, respectively, were recovered from these areas. Microsporon gypseum was the most common isolate, followed byTrichophyton mentagrophytes, andT. terrestre. M. gypseum was recovered from caves in a very high frequency (67 %), in comparison to its presence in the outdoor soils (10 %).Fifteen strains ofChrysosporium, belonging to four species, were isolated. Fourteen of these isolates were recovered from shady areas under trees. None of these had been isolated from Texas soil before.     

Predicting molecular formulas of fragment ions with isotope patterns in tandem mass spectra

A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well generalized to the component prediction of fragment ions in tandem mass spectra. In this paper, a new method, FFP (fragment ion formula prediction), is presented to predict elemental component formulas of fragment ions. In the FFP method, the prediction of the best formulas is converted into the minimization of the distance between theoretical and observed isotope patterns. And, then, a novel local search model is proposed to generate a set of candidate formulas efficiently. After the search, FFP applies a new multiconstraint filtering to exclude as many invalid and improbable formulas as possible. FFP is experimentally compared with the previous enumeration methods, and shown to outperform them significantly. The results of this paper can help to improve the reliability of de novo in the identification of peptide sequences.     

The occurrence of fungi in hospital and community potable waters

The prevalence of fungi was investigated in 126 potable water samples (84 hospital and 42 community samples), in parallel with the standard pollution indicator micro-organisms. Filamentous fungi were isolated from 104 of 126 (82.5%) samples and yeasts from 14 (11.1%), whereas their mean counts were 36.6 and 4.4, respectively. Fungi were isolated from 95.2% of community and 76.2% of hospital water samples, with the difference being statistically significant (P < 0.05), while yeasts were isolated from 9.5 and 11.9%, respectively. Prevailing genera were Penicillium spp., isolated from 64, Aspergillus spp., from 53, and Candida, from nine of the examined samples. Colony-forming units of yeasts were significantly correlated with those of total and faecal coliforms, whereas the counts of filamentous fungi were significantly correlated with total heterotrophic bacteria counts. These results suggest that tap water is a potential transmission route for fungi both in hospitals and the community in the examined region and may pose a health hazard mainly for the immunocompromised host.     

Liquid chromatography-tandem mass spectrometric determination of ceramides and related lipid species in cellular extracts

A liquid chromatography-electrospray ionization tandem mass spectrometric (LC-MS/MS) method was developed for the simultaneous qualitative and quantitative determination of sphingolipid metabolites such as ceramides, sphingisine, sphinganine, sphingomyelins, and ceramide 1-phosphates in the extracts of human promyelocytic leukemia cells (HL-60). The assay uses C(4) ceramide as an internal standard; simple liquid extraction; a short XTerra MS C(18) (3 microm, 50 mm x2.0 mm) column; a gradient mobile phase of 5mM ammonium formate (pH 4.0)/methanol/tetrahydrofuran (5/2/3-->1/2/7); mass spectrometric detection using electrospray ionization. This LC-MS/MS method allowed the identification of 22 sphingolipid derivatives at pmol levels. In addition, this technique was successfully applied to analyze the changes of the sphingolipids profiles in cancer cells treated with apoptosis inducing agents, C(2) ceramide and H(2)O(2).