MicrobMatcher: a microbial comparison software based on matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry

Matrix-assisted Laser Desorption/Ionization with Time-of-flight Mass Spectrometry (MALDI-TOFMS) was investigated as a method for the rapid identifica-tion of species. Current demand in microbial identi-fication is how to compare unknown strains to the known one quickly, semi-automatically and accurately. In this paper, we present a software tool that allows flexibly microbial matching in a user-friendly way, by letting the users to customize comparison parameters including: in vitro transcription enzyme, mass tolerance,minimum fragment length, intensity threshold and corresponding weights. We provide three spectral scoring functions to compute the affin-ity between the species. Therefore, the precision of microbial comparison increases. To test and verify this tool, we employed experimental spectral data based on MALDI-TOFMS and the gene sequences of E.coli and Salmonella. This software is written in Java for cross-platform intention.

Detection of Sialylated N-Linked Glycans by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Native and methyl-esterified sialylated glycans were analyzed with 2,4,6-trihydroxyacetophenone（THAP）and 2,5-dihydroxybenzoic acid（DHB）as matrix by a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer（MALDI-TOF MS）.High quality negative-ion spectra of commercial sialylated glycan were obtained with THAP as matrix.Detection limit of the glycan was less than 0.1 pmol.After methyl esterification of sialic acid（SA）residue,sialylated glycans were detected sensitively in the positive-ion mode using DHB as matrix.Neutral and sialylated glycans from the mixture of asialofetuin and fetuin were methylesterified and simultaneously recognized in one manipulation.Methyl esterification of SA residue offers a convenient and sensitive way to identify the structure of N-linked glycans for glycan profiling.

Radial Basis Function Networks Applied in Bacterial Classification Based on MALDI-TOF-MS

The radial basis function networks were applied to bacterial classification based on the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF-MS) data. The classification of bacteria cultured at different time was discussed and the effect of the network parameters on the classification was investigated. The cross-validation method was used to test the trained networks. The correctness of the classification of different bacteria investigated changes in a wide range from 61.5% to 92.8%. Owing to the complexity of biological effects in bacterial growth, the more rigid control of bacterial culture conditions seems to be a critical factor for improving the rate of correctness for bacterial classification.

Identification of serum biomarkers for diagnosing stage Ⅰ lung adenocarcinoma by MALDI-TOF mass spectrometry

Objective To identify specific biomarkers that could improve early diagnosis of lung adenocarcinoma using matrix-assisted laser desorption/ionization (MALDI) technology. Methods Serum samples were isolated from 17 patients with stage Ⅰ lung adenocarcinoma and 17 age-and sex-matched healthy controls,and the serum proteomic profiles were obtained by matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry. Results Compared with healthy control group,two highly expressed potential biomarkers were identified with the relative molecular weights of 6 631.64 Da and 4 964.21 Da. The two best novel protein peaks were automatically chosen for the system training and the development of the constructed model. The constructed model was then used to test an independent set of masked serum samples from 15 lung adenocarcinoma patients and 22 healthy individuals. The analysis yielded a sensitivity of 93.3%,and a specificity of 95.5%. Conclusion These results suggest that MALDI-TOF-MS ProteinChip technology is a quick,convenient,and high-output analyzing method that is capable of selecting several relatively potential biomarkers from the serum of lung adenocarcinoma patients and may have a clinical value in the future,and will provide clues to identifying new serologic biomarkers of lung adenocarcinoma.

利用基质辅助激光解吸电离飞行时间质谱快速鉴定产气荚膜梭菌

分别采用基质辅助激光解吸电离飞行时间质谱方法(matrix-assisted laser desorption/ionization time-offlight mass spectrometry,MALDI-TOF MS)、16S rRNA基因测序、VITEK 2 COMPACT和传统生化方法(牛乳汹涌发酵实验)鉴定实验室保存的51株产气荚膜梭菌,以评估MALDI-TOF MS方法是否适用于产气荚膜梭菌的快速鉴定。MALDI-TOF MS方法将51株菌均鉴定为产气荚膜梭菌且鉴定分值在2. 300以上,达到鉴定到种的要求。16S rRNA基因序列比对结果与MALDI-TOF MS方法结果一致。VITEK 2 COMPACT将49株菌鉴定为产气荚膜梭菌,2株菌未能成功鉴定。47株菌的牛乳汹涌发酵实验呈阳性,4株菌为牛乳汹涌发酵实验阴性,且这4株菌经其他3种方法均鉴定为产气荚膜梭菌。结果表明,无论是牛乳汹涌发酵实验还是VITEK 2 COMPACT,在检测产气荚膜梭菌时都有可能发生漏检。相比牛乳汹涌发酵实验、VITEK 2 COMPACT和16S rRNA测序方法,MALDI-TOF MS方法更加快速、准确和低成本,适用于产气荚膜梭菌的快速鉴定。

Lipopeptide Antibiotics Produced by the Engineered Strain Bacillus subtilis GEB3 and Detection of Its Bioactivity

MALDI-TOF-MS technology was used for identification of lipopeptide antibiotics producedby GEB3 strain, a derivative of Bacillus subtilis 168 which was transformed by lpaB3gene. The result showed GEB3 only produced lipopeptide antibiotic surfactin. The analysisby LC-MS demonstrated that GEB3 produced standard surfactin isoforms with side chainlengths of 13,14 and 15 carbon atoms. The bioactivity detection of surfactin indicatedthat the surfactin produced by GEB3 had inhibition effect on plant pathogens Rhizoctoniasolani and Pyricularia oryzae.

Obligate aerobic, gram-positive, weak acid-fast, nonmotile bacilli, Tsukamurella tyrosinosolvens: Minireview of a rare opportunistic pathogen

Tsukamurella species are obligate aerobic,gram-positive,weak acid-fast,nonmotile bacilli.They are found in various environments,such as soil,water,sludge,and petroleum reservoir wastewater,and belong to the order Actinomycetales.In 2016,there was a reclassification of species within the genus Tsukamurella,merging the species Tsukamurella tyrosinosolvens(T.tyrosinosolvens)and Tsukamurella carboxydivorans.Tsukamurella species are clinically considered to be a rare opportunistic pathogen,because most reported cases have been related to bacteremia and intravascular prosthetic devices and immunosuppression.To date,it has been isolated only from human specimens,and has always been associated with clinical disease;human infections are very rare.Reported infections have included pneumonia,brain abscesses,catheter-related bloodstream infections,ocular infections,bacteremia,and sepsis presenting with septic pulmonary emboli in patients who are immunocompromised.To date,there is no commercially available test for identification.On the other hand,sequence-based identification,including matrix-assisted laser desorption ionization time-of-flight mass spectrometry,is an alternative method for identifying clinical isolates that are either slow growers or difficult to identify through biochemical profiling.The golden standards for diagnosis and optimal management still remain to be determined.However,newer molecular biological techniques can provide accurate identification,and contribute to the appropriate selection of definitive therapy for infections caused by this organism.Combinations of several antimicrobial agents have been proposed for treatment,though the length of treatment for infections has yet to be determined,and should be individualized according to clinical response.Immunocompromised patients often experience severe cases due to infection,and life-threatening T.tyrosinosolvens events associated with dissemination and/or failure of source control have occurred.Favorable prognoses can be achieved through earlier identification of the cause of infection,as well as successful management,including appropriate antibiotic therapy together with source control.Further analyses of similar cases are required to establish the most adequate diagnostic methods and treatment regimens for infections.

Multiple skin abscesses associated with bacteremia caused by Burkholderia gladioli:A case report

BACKGROUND Burkholderia gladioli(B.gladioli)is regarded as a rare opportunistic pathogen.Only a few patients with abscesses caused by B.gladioli infections have been reported,and these are usually abscesses at the incision caused by traumatic surgery.CASE SUMMARY A 74-year-old male patient with abscesses and pain throughout his body for 1 mo was admitted to our hospital.Some of the abscesses had ruptured with purulent secretions on admission.Color Doppler ultrasound examination of the body surface masses showed mixed masses 75 mm×19 mm,58 mm×17 mm,17 mm×7 mm,and 33 mm×17 mm in size in the muscle tissues of both the right and left forearms,the posterior area of the right knee and the left leg,respectively.Abscess secretions and blood cultures grew B.gladioli.The following 3 methods were used to jointly identify the bacterium:an automatic microbial identification system,matrix-assisted laser desorption/ionization time-of-flight mass spectrometry,and full-length 16 S rDNA sequencing.After 27 d of treatment with meropenem,etimicin,trimethoprim-sulfamethoxazole and other antibiotics,most of his skin abscesses were flat and he was discharged without any symptoms.CONCLUSION This is the first reported case of multiple skin abscesses associated with bacteremia caused by B.gladioli.Our study provides important reference values for the clinical diagnosis and treatment of B.gladioli infections.

Rapid Determination of Endogenous 20-Hydroxyecdysone in Plants on MALDI-TOF/TOF Mass Spectrometry via Chemical Labeling Based on Boronate Affinity

20-Hydroxyecdysone(20E)derived from plants has a wide range of physiological and pharmacological ef ects on animals and humans,and rapid and sensitive methods for screening of the endogenous 20E in plants are thus required.Herein,a matrixassisted laser desorption/ionization time-of-f ight tandem mass spectrometry(MALDI-TOF/TOF MS)method is described for rapid and sensitive determination of endogenous 20E in plants.It is based on the use of the(3-(acridin-9-ylamino)phenyl)boronic acid(AYPBA)as the mass tag to assist the MS and tandem MS(MS^(n))analysis of 20E on MALDI-TOF/TOF MS.Good linearity was obtained with a determination coef cient(R^(2))larger than 0.99 in the range of 0.025–2.5μΜ.The limit of detection(LOD)was 2.4 fmol.Acceptable precision and accuracy were gained by intra-and inter-day analysis with relative standard deviations less than 19.5%and relative recoveries ranging from 85.7 to 105.2%.In addition,the AYPBA labeled 20E produced abundant characteristic fragment ions under the high energy collision-induced dissociation,which facilitated the identif cation of 20E by MS^(2)analysis on MALDI-TOF/TOF MS.Using the method,we enabled the identif cation and quantif cation of endogenous 20E in four herbs including Cyanotis arachoidea,Achyranthes bidentata,Spinacia oleracea and Chenopodium quinoa willd.,demonstrating the feasibility of the proposed method for screening of the endogenous 20E in plants.

Proteomic Alterations of Antarctic Ice Microalga Chlamydomonas sp.Under Low-Temperature Stress

Antarctic ice microalga can survive and thrive in cold channels or pores in the Antarctic ice layer. In order to understand the adaptive mechanisms to low temperature, in the present study we compared two-dimensional polyacrylamide gel electrophoresis （2-DE） profiles of normal and low temperature-stressed Antarctic ice microalga Chlamydomonas sp. cells. In addition, new protein spots induced by low temperature were identified with peptide mass fingerprinting based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-TOF-MS） and database searching. Well-resolved and reproducible 2-DE patterns of both normal and low temperature-stressed cells were acquired. A total of 626 spots was detected in control cells and 652 spots were detected in the corresponding low temperature-stressed cells. A total of 598 spots was matched between normal and stressed cells. Two newly synthesized proteins （a and b） in low temperature-stressed cells were characterized. Protein spot A （53 kDa, pl 6.0） was similar to isopropylmalate/homocitrate/citramalate synthases, which act in the transport and metabolism of amino acids. Protein spot b （25 kDa, pl 8.0） was related to glutathione S-transferase, which functions as a scavenger of active oxygen, free radicals, and noxious metabolites. The present study is valuable for the application of ice microalgae, establishing an ice microalga Chlamydomonas sp. proteome database, and screening molecular biomarkers for further studies.

Identification of Biomarkers for Endometriosis Using Clinical Proteomics

Background：We investigated possible biomarkers for endometriosis （EM） using the ClinProt technique and proteomics methods.Methods：We enrolled 50 patients with EM,34 with benign ovarian neoplasms and 40 healthy volunteers in this study.Serum proteomic spectra were generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MS） combined with weak cationic exchange （WCX） magnetic beads.Possible biomarkers were analyzed by a random and repeat pattern model-validation method that we designed,and ClinProtools software,results were refined using online liquid chromatography-tandem MS.Results：We found a cluster of 5 peptides （4210,5264,2660,5635,and 5904 Da）,using 3 peptides （4210,5904,2660 Da） to discriminate EM patients from healthy volunteers,with 96.67％ sensitivity and 100％ specificity.We selected 4210 and 5904 m/z,which differed most between patients with EM and controls,and identified them as fragments of ATP1B4,and the fibrinogen alpha （FGA） isoform 1/2 of the FGA chain precursor,respectively.Conclusions：ClinProt can identify EM biomarkers,which-most notably-distinguish even early-stage or minimal disease.We found 5 stable peaks at 4210,5264,2660,5635,and 5904 Da as potential EM biomarkers,the strongest of which were associated with ATP1B4 （4210 Da） and FGA （5904 Da）; this indicates that ATP1B4 and FGA are associated with EM pathogenesis.

Comparative Proteomic Analysis of Arabidopsis Mature Pollen and Germinated Pollen

Proteomic analysis was applied to generating the map of Arabidopsis mature pollen proteins and analyzing the differentially expressed proteins that are potentially involved in the regulation of Arabidopsis pollen germination. By applying 2-D electrophoresis and silver staining, we resolved 499 and 494 protein spots from protein samples extracted from pollen grains and pollen tubes, respectively. Using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry method, we identified 189 distinct proteins from 213 protein spots expressed in mature pollen or pollen tubes, and 75 new identified proteins that had not been reported before in research into the Arabidopsis pollen proteome. Comparative analysis revealed that 40 protein spots exhibit reproducible significant changes between mature pollen and pollen tubes. And 21 proteins from 17 downregulated and six upregulated protein spots were identified. Functional category analysis indicated that these differentially expressed proteins mainly involved in signaling, cellular structure, transport, defense/stress responses, transcription, metabolism, and energy production. The patterns of changes at protein level suggested the important roles for energy metabolism-related proteins in pollen tube growth, accompanied by the activation of the stress response pathway and modifications to the cell wall.

Serum peptidome profiling for identifying pathological patterns in patients with primary nephrotic syndrome

Background Renal biopsy is necessary for diagnosing the pathological changes of primary nephrotic syndrome （NS）. However, it is invasive, time-consuming and can not be performed frequent on the same patient. Thus, development of a non-invasive and rapid diagnostic method may improve clinical patient management. Methods Proteomic tool magnetic bead-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MB-based MALDI TOF MS） was applied to serum to determine peptidome patterns that are characteristic of different pathological changes. Results Serum specimen from 114 patients with NS （62 were minimal change disease （MCD）, 30 were membranous nephropathy （MN）, and 22 were focal segmental glomerulosclerosis （FSGS）） and 60 normal individuals were analyzed using MB-based MALDI TOF MS. The peptidome pattern was generated by genetic algorithms using a training set of 31 MCD, 15 MN, 11 FSGS and 30 normal individuals and was validated by an independent testing set of the remaining samples. The serum peptidome pattern, based on a panel of 14 peaks, accurately recognized samples from MCD, MN, FSGS and healthy control with sensitivities of 93.5%, 86.7%, 63.6% and 90.0%, and specificities of 98.2%, 94.4%, 100% and 89.5%, respectively. Moreover, one peptide from peptidome pattern was identified by liquid chromatography tandem mass spectrometry （LC MS/MS） as fibrinogen A. Conclusion Detection of the serum peptidome pattern is a rapid, non-invasive, high-throughout, and reproducible method for identifying the pathological patterns of patients with nephrotic syndrome.

Sol-gel-derived Poly（dimethylsiloxane） Enzymatic Reactor for Microfluidic Peptide Mapping

The silica-based poly（dimethylsiloxane） （PDMS） microfluidic enzymatic reactor was reported along with its analytical features in coupling with MALDI TOF and ESI MS. Microfluidic chip was fabricated using PDMS casting and O2-plasma techniques, and used for the preparation of enzymatic reactor. Plasma oxidation for PDMS enabled the channel wall of microfluidics to present a layer of silanol （SiOH） groups. These SiOH groups as anchors onto the microchannel wall were linked covalently with the hydroxy groups of trypsin-encapsulated sol matrix. As a result, the leakage of sol-gel matrix from the microchannel was effectively prevented. On-line protein analysis was performed with the microfluidic enzymatic reactor by attachment of stainless steel tubing electrode and replaceable tip, The success of trypsin encapsulation was investigated by capillary electrophoresis （CE） detection, and MALDI TOF and ESI MS analysis. The lab-made device provided excellent extent of digestion even at the fast flow rate of 7.0 μL/min with very short residence time of ca. 2 s. In addition, the encapsulated trypsin exhibits increased stability even after continuous use. These features are the most requisite for high-throughput protein identification.

Proteomics analysis of cerebral cortex in Wistar rats

To analyze the protein expression pattern of the cerebral cortex in Wistar rats using the proteomics approach,proteins were separated by two-dimensional gel electrophoresis,stained with Coomassie brilliant blue and digested with trypsin.Then,we analyzed the peptide section using a matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS)and identified the protein by indexing special database(SwissProt)according to the finger printing of the peptide quality.Eighty-four protein spots were identified,including metabolic enzymes,skeleton proteins,heat shock proteins,antioxidant proteins,signaling proteins,proteasome related proteins,neuron and glial specific proteins and serum associated proteins.The result of this study enriches the database of the proteome in the cerebral cortex of rats and lays a foundation for further research of neurological disorders in rat models.