Purification and structural characterization of fengycin homologues produced by <Emphasis Type="Italic">Bacillus subtilis</Emphasis> LSFM-05 grown on raw glycerol

Raw glycerol is a byproduct of biodiesel production that currently has low to negative value for biodiesel producers. One option for increasing the value of raw glycerol is to use it as a feedstock for microbial production. Bacillus subtilis LSFM 05 was used for the production of fengycin in a mineral medium containing raw glycerol as the sole carbon source. Fengycin was isolated by acid precipitation at pH 2 and purified by silica gel column chromatography and characterized using electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) with collision-induced dissociation (CID). The mass spectrum revealed the presence of the ions of m/z 1,435.7, 1,449.9, 1,463.8, 1,477.8, 1,491.8 and 1,505.8, which were further fragmented by ESI-MS/MS. The CID profile showed the presence of a series of ions (m/z 1,080 and 966) and (m/z 1,108 and 994) that represented the different fengycin homologues A and B, respectively. Fengycin homologues A and B are variants that differ at position 6 of the peptide moiety, having either Ala or Val residues, respectively. Mass spectrometry analyses identified four fengycin A and three fengycin B variants with fatty acid components containing 14–17 carbons. These results demonstrate that raw glycerol can be used as feedstock to produce fengycin, and additional work should focus on the optimization of process conditions to increase productivity.     

Characterization of fungal antagonistic bacilli isolated from aerial roots of banyan (Ficus benghalensis) using intact‐cell MALDI‐TOF mass spectrometry (ICMS)

Aims

To characterize fungal antagonistic bacilli isolated from aerial roots of banyan tree and identify the metabolites responsible for their antifungal activity.

Methods and Results

Seven gram positive, endospore‐forming, rod‐shaped endophytic bacterial strains exhibiting a broad‐spectrum antifungal activity were isolated from the surface‐sterilized aerial roots of banyan tree. The isolates designated as K1, A2, A4 and A12 were identified as Bacillus subtilis, whereas isolates A11 and A13 were identified as Bacillus amyloliquefaciens using Biolog Microbial Identification System. The antifungal lipopeptides, surfactins, iturins and fengycins with masses varying in the range from m/z 900 to m/z 1550 could be detected using intact‐cell MALDI‐TOF mass spectrometry (ICMS). On the basis of mass spectral and carbon source utilization profile, all seven endophytes could be distinguished from each other. Furthermore, ICMS analysis revealed higher extent of heterogeneity among iturins and fengycins produced by B. subtilis K1, correlating well with its higher antifungal activity in comparison with other isolates.

Conclusion

Seven fungal antagonistic bacilli were isolated from aerial roots of banyan tree, exhibiting broad spectrum of antifungal activity, among which B. subtilis K1 isolate was found to be most potent. The ICMS analysis revealed that all these isolates produced cyclic lipopeptides belonging to surfactin, iturin and fengycin families and exhibited varying degree of heterogeneity.

Significance and Impact of the study

The endophytes are considered as a potential source of novel bioactive metabolites, and this study describes the potent fungal antagonistic bacilli from aerial roots of banyan tree. The isolates described in this study have a prospective application as biocontrol agents. Also ICMS analysis described in this study for characterization of antifungal metabolites produced by banyan endophytic bacilli may be used as a high throughput tool for screening of microbes producing novel cyclic lipopeptides.     

Isolation and characterization of antifungal peptides produced by <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> LBM5006

Bacillus amyloliquefaciens LBM 5006 produces antagonistic activity against pathogenic bacteria and phytopathogenic fungi, including Aspergillus spp., Fusarium spp., and Bipolaris sorokiniana. PCR analysis revealed the presence of ituD, but not sfp genes, coding for iturin and surfactin, respectively. The antimicrobial substance produced by this strain was isolated by ammonium sulfate precipitation, gel filtration chromatography and 1-butanol extraction. The ultraviolet spectrum was typical of a polypeptide and the infrared spectrum indicates the presence of peptide bonds and acyl group(s). The antimicrobial substance was resistant to proteolytic enzymes and heat treatment, and was reactive with ninhydrin. Mass spectroscopy analysis indicated that B. amyloliquefaciens LBM 5006 produces two antimicrobial peptides, with main peaks at m/z 1,058 Da and 1,464 Da, corresponding to iturin-like and fengycin-like peptides, respectively. B. amyloliquefaciens LBM 5006 showed significant activity against phytopatogenic fungi, showing potential for use as a biocontrol agent or production of antifungal preparations.     

Detection of phosphodiester adducts formed by the reaction of benzo[a]pyrene diol epoxide with 2'-deoxynucleotides using collision-induced dissociation electrospray ionization tandem mass spectrometry

In this study, we investigated the products formed following the reaction of benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (B[a]PDE) with 2′-deoxynucleoside 3′-monophosphates. The B[a]PDE plus 2′-deoxynucleotide reaction mixtures were purified using solid phase extraction (SPE) and subjected to HPLC with fluorescence detection. Fractions corresponding to reaction product peaks were collected and desalted using SPE prior to analysis for the presence of molecular ions corresponding to m/z 648, 632, 608 and 623 [M−H]⁻ consistent with B[a]PDE adducted (either on the base or phosphate group) 2′-deoxynucleotides of guanine, adenine, cytosine and thymine, respectively, using LC-ESI-MS/MS collision-induced dissociation (CID). Reaction products were identified having CID product ion spectra containing product ions at m/z 452, 436 and 412 [(B[a]Ptriol+base)−H]⁻, resulting from cleavage of the glycosidic bond between the 2′-deoxyribose and base, corresponding to B[a]PDE adducts of guanine, adenine and cytosine, respectively. Further reaction products were identified having unique CID product ion spectra characteristic of B[a]PDE adduct formation with the phosphate group of the 2′-deoxynucleotide. The presence of product ions at m/z 399 and 497 were observed for all four 2′-deoxynucleotides, corresponding to [(B[a]Ptriol+phosphate)−H]⁻ and [(2′-deoxyribose+phosphate+B[a]Ptriol)−H]⁻, respectively. In conclusion, this investigation provides the first direct evidence for the formation of phosphodiester adducts by B[a]PDE following reaction with 2′-deoxynucleotides.     

Identification of novel serum peptides biomarkers for female breast cancer patients in Western China

This study aimed to identify novel serum peptides biomarkers for female breast cancer (BC) patients. We analyzed the serum proteomic profiling of 247 serum samples from 96 BC patients, 48 additional paired pre‐ and postoperative BC patients, 39 fibroadenoma patients as benign disease controls, and 64 healthy controls, using magnetic‐bead‐based separation followed by MALDI‐TOF MS. ClinProTools software identified 78 m/z peaks that differed among all analyzed groups, ten peaks were significantly different (P < 0.0001), with Peaks 1–6 upregulated and Peaks 7–10 downregulated in BC. Moreover, three peaks of ten (Peak 1, m/z: 2660.11; Peak 2, m/z: 1061.09; Peak 10, m/z: 1041.25) showed a tendency to return to healthy control values after surgery. And these three peptide biomarkers were identified as FGA605‐629, ITIH4 347–356, and APOA2 43–52. Methods used in this study could generate serum peptidome profiles of BC, and provide a new approach to identify potential biomarkers for diagnosis as well as prognosis of this malignancy.     

Sequencing of the thirteen structurally isomeric quartets of N‐terminal dipeptide motifs in peptides by collision‐induced dissociation

N‐terminal sequencing of protonated peptides is challenging, since each b₂ ion represents two sequence isomers, e.g., NE and EN. Additionally the occurrence of compositional isomers, such as NE and QD, further increases the number of isomers to four (NE, EN, QD, DQ). This leads to a subset of 13 b₂ ion masses where each value represents four individual species. The b₂ ions within such a quartet are characterized by the same elemental composition. To test the utility of CID for differentiation of isomeric b₂ ions, the CID spectra of 52 small synthetic peptides were recorded, representing the 13 isomeric b₂ ion quartets, which may be formed from unmodified amino acid residues. The CID spectra of protonated peptides containing these quartets were carefully inspected for N‐terminal sequence information. Below the m/z value of the b₂ ion, individual differences were found in the b₂ fragment ion signatures (neutral loss of CO, H₂O, NH₃, and other less common units). Recognition of N and Q in second position from the N‐terminus is based on c₁ ion formation. Relative intensities of immonium ions were also used for differentiation between sequence isomers. In the complementary high‐mass regions above the m/z value of the y_max‐2 ion, individual differences were observed in the formation of y_max‐1, x_max‐1 and z_max‐1 ions, which could be correlated to the complementary low‐mass ions. In summary, de novo sequencing of the N‐terminal dipeptide motif is feasible by considering all available sequence information present in CID spectra of protonated peptides.     

Localization of ferruginol,a diterpene phenol,in <Emphasis Type="Italic">Cryptomeria japonica</Emphasis> heartwood by time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) was applied to the investigation of heartwood extractives in Sugi (Cryptomeria japonica). Sugi heartwood tissue generated secondary ions that were not produced from sapwood tissue by TOF-SIMS. Among the peculiar ions generated from heartwood, two positive ions of m/z 285 and 301 were remarkable due to their appearance in a larger mass range and with a high intensity. These two ions were not generated from heartwood tissue preextracted with n-hexane, and the n-hexane extract of Sugi heartwood produced both ions. Gas chromatography-mass spectrometry of the n-hexane extract demonstrated that ferruginol, a diterpene phenol, the molecular weight of which is 286, constituted one of the predominant constituents of the extract. Authentic ferruginol also generated both ions by TOF-SIMS. The molecular formula of the m/z 285 ion generated from Sugi heartwood tissue was estimated to be C₂₀H₂₉O, which corresponds well with that of ferruginol, i.e. C₂₀H₃₀O, by peak identification. All these results strongly suggest that the m/z 285 ion generated from Sugi heartwood tissue originated significantly from ferruginol in Sugi heartwood. By TOF-SIMS imaging, the m/z 285 ion was detected uniformly in the tracheid cell walls, in the cell walls of the axial parenchyma cells and ray parenchyma cells, and also inside these parenchyma cells. These results indicate that ferruginol was distributed almost evenly in Sugi heartwood tissue.     

Balancing robust quantification and identification for iTRAQ: Application of UHR‐ToF MS

iTRAQ reagents allow the simultaneous multiplex identification and quantification of a large number of proteins. Success depends on effective peptide fragmentation in order to generate both peptide sequence ions (higher mass region, 150–2200 m/z) and reporter ions (low mass region, 113–121 m/z) for protein identification and relative quantification, respectively. After collision‐induced dissociation, the key requirements to achieve a good balance between the high and low m/z ions are effective ion transmission and detection across the MS/MS mass range, since the ion transmission of the higher m/z range competes with that of the low m/z range. This study describes an analytical strategy for the implementation of iTRAQ on maXis UHR‐Qq‐ToF instruments, and discusses the impact of adjusting the MS/MS ion transmission parameters on the quality of the overall data sets. A technical discussion highlights a number of maXis‐specific parameters, their impact of quantification and identification, and their cross‐interactions.     

Gas chromatographic-mass spectrometric identification and quantitation of urinary phenols after derivatization with 4-carbethoxyhexafluorobutyryl chloride, a novel derivative

Urinary phenol is analyzed widely to determine benzene exposure in humans. Most methods utilize direct measurements of phenols after extraction from urine using gas chromatography or high-performance liquid chromatography. We describe a novel derivatization of urinary phenols using 4-carbethoxyhexafluorobutyryl chloride after extraction from urine and subsequent analysis by gas chromatography-mass spectrometry. The derivative elutes at significantly higher temperature than phenol and the method is free from interferences from more volatile components in urine. We also observed excellent chromatographic properties of these derivatives. In addition, we observed strong molecular ions for the 4-carbethoxyhexafluoro butyryl derivative of phenol (m/z 344), p-cresol (m/z 358) and the internal standard 3,4-dimethylphenol (m/z 372) and other characteristic ions in the electron ionization, thus aiding in unambiguous identification of these compounds. The protonated molecular ions (m/z 373 for derivatized phenol, m/z 359 for derivatized p-cresol and m/z 373 for the internal standard) were the base peaks (relative abundance 100%) in the chemical ionization, although other secondary peaks were less abundant. The assay is linear for phenol concentration of 1–100 mg/l. The within-run and between-run precisions were 4.8% ( ) and 8.1% ( ) respectively, and the detection limit was 0.5 mg/l.     

Monitoring of olanzapine in serum by liquid chromatography–atmospheric pressure chemical ionization mass spectrometry

A selective assay of olanzapine with liquid chromatography atmospheric pressure chemical ionization (LC–APCI–MS, positive ions) is described. The drug and internal standard (ethyl derivative of olanzapine) were isolated from serum using a solid-phase extraction procedure (C₁₈ cartridges). The separation was performed on ODS column in acetonitrile–50 mM ammonium formate buffer, pH 3.0 (25:75). After analysis of mass spectra taken in full scan mode, a selected-ion monitoring detection (SIM) was applied with the following ions: m/z 313 and 256 for olanzapine and m/z 327 and 270 for the internal standard for quantitation. The limit of quantitation was 1 μg/l, the absolute recovery was above 80% at concentration level of 10 to 100 μg/l. The method tested linear in the range from 1 to 1000 μg/l and was applied for therapeutic monitoring of olanzapine in the serum of patients receiving (Zyprexa™) and in one case of olanzapine overdose. Olanzapine in frozen serum samples and in frozen extracts was stable over at least four weeks. The examinations of urine extracts from patients receiving olanzapine revealed peaks of postulated metabolites (glucuronide and N-desmethylolanzapine).     

Isolation and physico-chemical characterisation of extracellular polymeric substances produced by the marine bacterium Vibrio parahaemolyticus

A marine bacterial strain identified as Vibrio parahaemolyticus by 16S rRNA gene (HM355955) sequencing and gas chromatography (GC) coupled with MIDI was selected from a natural biofilm by its capability to produce extracellular polymeric substances (EPS). The EPS had an average molecule size of 15.278 μm and exhibited characteristic diffraction peaks at 5.985°, 9.150° and 22.823°, with d-spacings of 14.76661, 9.29989 and 3.89650 Å, respectively. The Fourier-transform infrared spectroscopy (FTIR) spectrum revealed aliphatic methyl, primary amine, halide groups, uronic acid and saccharides. Gas chromatography mass spectrometry (GCMS) confirmed the presence of arabinose, galactose, glucose and mannose. ¹HNMR (nuclear magnetic resonance) revealed functional groups characteristic of polysaccharides. The EPS were amorphous in nature (CI_xrd 0.092), with a 67.37% emulsifying activity, thermostable up to 250°C and displayed pseudoplastic rheology. MALDI-TOF–TOF analysis revealed a series of masses, exhibiting low-mass peaks (m/z) corresponding to oligosaccharides and higher-mass peaks for polysaccharides consisting of different ratios of pentose and hexose moieties. This is the first report of a detailed characterisation of the EPS produced by V. parahaemolyticus, which could be further explored for biotechnological and industrial use.     

Determination of perfluorodecalin and perfluoro-N-methylcyclohexylpiperidine in rat blood by gas chromatography–mass spectrometry

A gas chromatography–mass spectrometry method (SIM mode) was developed for the determination of perfluorodecalin (cis and trans isomers, 50% each) (FDC), and perfluoromethylcyclohexylpiperidine (3 isomers) (FMCP) in rat blood. The chromatographic separation was performed by injection in the split mode using a CP-select 624 CB capillary column. Analysis was performed by electronic impact ionization. The ions m/z 293 and m/z 181 were selected to quantify FDC and FMCP due to their abundance and to their specificity, respectively. The ion m/z 295 was selected to monitor internal standard. Before extraction, blood samples were stored at −30°C for at least 24 h in order to break the emulsion. The sample preparation procedure involved sample clean-up by liquid–liquid extraction. The bis(F-butyl)ethene was used as the internal standard. For each perfluorochemical compound multiple peaks were observed. The observed retention times were 1.78 and 1.87 min for FDC, and 2.28, 2.34, 2.48 and 2.56 min for FMCP. For each compound, two calibration curves were used; assays showed good linearity in the range 0.0195–0.78 and 0.78–7.8 mg/ml for FDC, and 0.00975–0.39 and 0.39–3.9 mg/ml for FMCP. Recoveries were 90 and 82% for the two compounds, respectively with a coefficient of variation <8%. Precision ranged from 0.07 to 15.6%, and accuracy was between 89.5 and 111.4%. The limits of quantification were 13 and 9 μg/ml for FDC and FMCP, respectively. This method has been used to determine the pharmacokinetic profile of these two perfluorochemical compounds in blood following administration of 1.3 g of FDC and 0.65 g of FMCP per kg body weight, in emulsion form, in rat.     

ESI LC-MS and MS/MS characterization of antifungal cyclic lipopeptides produced by Bacillus subtilis XF-1

Bacillus subtilis XF-1 (CGMCC No. 2357), a patent strain with good effects for controlling the clubroot of crucifer and many pathogenic fungi, was predicted to produce cyclic lipopeptide (CLP) antibiotics based on its genomic analysis. In this study, the CLPs were purified and determined with the following protocol: the supernatant of XF-1 cultivating mixture was firstly precipitated, then the precipitants were extracted with methanol and further separated by Sephadex LH-20 chromatography to test its antifungal activities. Fungi-inhibiting fractions were further characterized with LC/ESI-MS and LC/ESI-MS/MS. The results show that four molecular ion peaks [M+H]? (m/z 1,464, 1,478, 1,492 and 1,506) from fungi suppression fraction were identified as fengycin A with fatty acid of C??-C??, fengycin B (C??-C??), fengycin C (C??-C??), fengycin D (C??-C??) and fengycin S (C??-C??). Fengycin C (C?? and C??), fengycin D (C??, C?? and C??) and fengycin S (C??, C?? and C??) were reported for the first time. The diversity of the fengycins that exist in this strain will help the elucidation of their biocontrol mechanisms.     

Evaluation of antagonistic activities of Bacillus subtilis and Bacillus licheniformis against wood-staining fungi: In vitro and in vivo experiments

The antifungal activity of bacterial strains Bacillus subtilis EF 617317 and B. licheniformis EF 617325 was demonstrated against sapstaining fungal cultures Ophiostoma flexuosum, O. tetropii, O. polonicum, and O. ips in both in vitro and in vivo conditions. The crude active supernatant fractions of 7 days old B. subtilis and B. licheniformis cultures inhibited the growth of sapstaining fungi in laboratory experiments. Thermostability and pH stability of crude supernatants were determined by series of experiments. FT-IR analysis was performed to confirm the surface structural groups of lipoproteins present in the crude active supernatant. Partial purification of lipopeptides present in the crude supernatant was done by using Cellulose anion exchange chromatography and followed by Sephadex gel filtration chromatography. Partially purified compounds significantly inhibited the sapstaining fungal growth by in vitro analysis. The lipopeptides responsible for antifungal activity were identified by electrospray ionization mass spectrometry after partial purification by ion exchange and gel filtration chromatography. Four major ion peaks were identified as m/z 1023, 1038, 1060, and 1081 in B. licheniformis and 3 major ion peaks were identified as m/z 1036, 1058, and 1090 in B. subtilis. In conclusion, the partially purified lipopeptides may belong to surfactin and iturin family. In vivo analysis for antifungal activity of lipopeptides on wood was conducted in laboratory. In addition, the potential of extracts for fungal inhibition on surface and internal part of wood samples were analyzed by scanning electron microscopy.     

A Study on Immonium Ions and Immonium-Related Ions Depending on Different Collision Energies as Assessed by Q-TOF MS

Immonium ions and immonium-related ions commonly appear in the mass spectra of peptide precursor ions. An overall understanding of the variation of the abundance of these ions is beneficial for the identification of unknown peptides. Here, four peptides from mass spectrometry (MS) of sucrose phosphorylase were selected as precursor ions, and the frequency of immonium ions and immonium-related ions in a dataset containing 130 MS/MS spectra were examined. Immonium ions and immonium-related ions were mainly produced from the further fragmentation of a-, b-, and y-ions. At the optimal collision energy (CE), the immonium ions of leucine at m/z 86, isoleucine at m/z 86, glutamine at m/z 101, arginine at m/z 129, tryptophan at m/z 159, proline at m/z 70, valine at m/z 72, glutamic acid at m/z 102, phenylalanine at m/z 120, and tyrosine at m/z 136, as well as the immonium-related ions of methionine at m/z 61, lysine at m/z 84, glutamine at m/z 84, and tyrosine at m/z 91 existed in higher abundance and had higher confidence level, therefore suggesting the presence of corresponding amino acid residues well. However, the immonium ions of serine at m/z 60 and threonine at m/z 74, although showing lower abundance, were stable at high CE and had higher confidence level, indicating the presence of serine and threonine residues, respectively. The immonium ion of asparagine at m/z 87 also was a good indicator for the existence of asparagine residue.     

Erratum: Rondelli,I., Corsaletti,R., Redenti,E., Acerbi,D., Delcanale,M., Amari,G., Ventura,P. New method for the resolution of the enatiomers of 5,6-dihydroxy-2-methyl-aminotetralin by selective derivatization and HPLC. Chirality 8:381–389, 1996

In the article listed above, the caption for Figure 5 should read as “Ionspray mass spectra of the negatively charged [DPB-CHF 1024] (A) and [DPB-CHF 1024 urea derivative] (B) complexes. The m/z values referred to the normal masses of ions.” rather than “Collision-activated dissociation spectrum of….”. The authors apologize for the error.     

Molecular mapping of stomatal‐conductance‐related traits in durum wheat (Triticum turgidum ssp. durum)

The most promising traits identified in wheat to raise yield potential via an increase in biomass accumulation are stomatal conductance and stomatal‐conductance‐related traits, such as carbon isotope discrimination (CID) and photosynthetic rate. The evaluation of the extent of genetic variation and the mapping of chromosomal regions controlling these traits are essential for the development of effective breeding strategies in durum wheat. A population of 161 F2‐derived, F8–F9 recombinant inbred lines obtained from a cross between durum wheat (Triticum turgidum ssp. durum) cultivars Ofanto and Cappelli was phenotyped for heading date, plant height, leaf porosity, CID and chlorophyll concentration (estimated through the SPAD index) for 2007/2008 and 2008/2009 seasons, at Ottava, Sardinia (Italy) under irrigated conditions. The genotype mean heritability for leaf porosity, CID and chlorophyll concentration was moderate in size. Six quantitative trait loci were detected for leaf porosity, four for chlorophyll concentration, but only one for CID, because of the small variation expressed in the population for this trait under these experimental conditions. The quantitative trait loci for leaf porosity located on chromosome 3B appear to be more stable with respect to the others, and different microsatellite markers are positioned within the interval of the quantitative trait loci, or in their vicinity, that represent useful tools in programmes for selection assisted by molecular markers.     

Simultaneous determination of buprenorphine, norbuprenorphine, and buprenorphine–glucuronide in plasma by liquid chromatography–tandem mass spectrometry

For the first time, an LC–MS–MS method has been developed for the simultaneous analysis of buprenorphine (BUP), norbuprenorphine (NBUP), and buprenorphine–glucuronide (BUPG) in plasma. Analytes were isolated from plasma by C₁₈ SPE and separated by gradient RP-LC. Electrospray ionization and MS–MS analyses were carried out using a PE-Sciex API-3000 tandem mass spectrometer. The m/z 644→m/z 468 transition was monitored for BUPG, whereas for BUP, BUP-d₄, NBUP, and NBUP-d₃ it was necessary to monitor the surviving parent ions in order to achieve the required sensitivity. The method exhibited good linearity from 0.1 to 50 ng/ml (r²≥0.998). Extraction recovery was higher than 77% for BUPG and higher than 88% for both BUP and NBUP. The LOQ was established at 0.1 ng/ml for the three analytes. The method was validated on plasma samples collected in a controlled intravenous and sublingual buprenorphine administration study. Norbuprenorphine–glucuronide was also tentatively detected in plasma by monitoring the m/z 590→m/z 414 transition.     

Differentiation of Bacillus pumilus and Bacillus safensis Using MALDI-TOF-MS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification, still present limitations in which concerns the differentiation of closely related species. Bacillus pumillus and Bacillus safensis, are species of biotechnological and pharmaceutical significance, difficult to differentiate by conventional methodologies. In this study, using a well-characterized collection of B. pumillus and B. safensis isolates, we demonstrated the suitability of MALDI-TOF-MS combined with chemometrics to accurately and rapidly identify them. Moreover, characteristic species-specific ion masses were tentatively assigned, using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and primary literature. Delineation of B. pumilus (ions at m/z 5271 and 6122) and B. safensis (ions at m/z 5288, 5568 and 6413) species were supported by a congruent characteristic protein pattern. Moreover, using a chemometric approach, the score plot created by partial least square discriminant analysis (PLSDA) of mass spectra demonstrated the presence of two individualized clusters, each one enclosing isolates belonging to a species-specific spectral group. The generated pool of species-specific proteins comprised mostly ribosomal and SASPs proteins. Therefore, in B. pumilus the specific ion at m/z 5271 was associated with a small acid-soluble spore protein (SASP O) or with 50S protein L35, whereas in B. safensis specific ions at m/z 5288 and 5568 were associated with SASP J and P, respectively, and an ion at m/z 6413 with 50S protein L32. Thus, the resulting unique protein profile combined with chemometric analysis, proved to be valuable tools for B. pumilus and B. safensis discrimination, allowing their reliable, reproducible and rapid identification.     

Development of novel mass spectrometric methods for identifying HOCl‐induced modifications to proteins

Protein oxidation is thought to contribute to a number of inflammatory diseases, hence the development of sensitive and specific analytical techniques to detect oxidative PTMs (oxPTMs) in biological samples is highly desirable. Precursor ion scanning for fragment ions of oxidized amino acid residues was investigated as a label‐free MS approach to mapping specific oxPTMs in a complex mixture of proteins. Using HOCl‐oxidized lysozyme as a model system, it was found that the immonium ions of oxidized tyrosine and tryptophan formed in MS² analysis could not be used as diagnostic ions, owing to the occurrence of isobaric fragment ions from unmodified peptides. Using a double quadrupole linear ion trap mass spectrometer, precursor ion scanning was combined with detection of MS³ fragment ions from the immonium ions and collisionally‐activated decomposition peptide sequencing to achieve selectivity for the oxPTMs. For chlorotyrosine, the immonium ion at 170.1 m/z fragmented to yield diagnostic ions at 153.1, 134.1, and 125.1 m/z, and the hydroxytyrosine immonium ion at 152.1 m/z gave diagnostic ions at 135.1 and 107.1 m/z. Selective MS³ fragment ions were also identified for 2‐hydroxytryptophan and 5‐hydroxytryptophan. The method was used successfully to map these oxPTMs in a mixture of nine proteins that had been treated with HOCl, thereby demonstrating its potential for application to complex biological samples.