Analysis of Single Nucleotide Polymorphism in Human Paraoxonase 1 Gene(Q192R) with Matrix-assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry

Introduction Single nucleotide polymorphisms （SNPs） are the most abundant DNA markers in the human genome occurring at a frequency of one in every 500--1000 nucleotides. A variety of methods have been used for the analysis of single nucleotide polymorphisms, including restriction fragment length polymorphism （RFLP）, direct sequencing by using laser-induced fluorescence detectionTM, fluorescence energy transfer, MALDI-TOF MS combined with primer extension or invasive cleavage, and fluorescence polarization. During the past two decades, mass spectrometry has become a very popular tool in the analysis of biomolecules and is perfectly suited to the analysis of single nucleotide polymorphisms （SNPs） due to its speed, low cost, and accuracy. In this work, we used MALDI TOF mass spectrometry to detect the fragments of restriction endonuclease hydrolysis of PCR products flanking a SNP located at paraoxonase 1（Q192R）. Compared with electrophoresis, this method requires less time of analysis and possess a higher accuracy.

A novel sample preparation method of matrix-assisted laser desorption/ionization time of flight mass spectrometry for polystyrene

A novel sample preparation method of matrix-assisted laser desorption/ionization mass spectrometry for polystyrene was reported. Compared to the conventional dried-droplet method, the efficiency of ionization and signal intensity of mass spectra were improved. The mechanism was also analyzed.

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.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry traces the geographical source of Biomphalaria pfeifferi and Bulinus forskali,involved in schistosomiasis transmission

Background Freshwater snails of the genera Bulinus spp.,Biomphalaria spp.,and Oncomelania spp.are the main intermediate hosts of human and animal schistosomiasis.Identification of these snails has long been based on mor-phological and/or genomic criteria,which have their limitations.These limitations include a lack of precision for the morphological tool and cost and time for the DNA-based approach.Recently,Matrix-Assisted Laser Desorp-tion/lonization Time-Of-Flight(MALDI-TOF)mass spectrometry,a new tool used which is routinely in clinical microbi-ology,has emerged in the field of malacology for the identification of freshwater snails.This study aimed to evaluate the ability of MALDI-TOF MS to identify Biomphalaria pfeifferi and Bulinus forskali snail populations according to their geographicalorigin.Methods This study was conducted on 101 Bi.pfeifferi and 81 Bu.forskali snails collected in three distinct geo-graphical areas of Senegal(the North-East,South-East and central part of the country),and supplemented with wild and laboratory strains.Specimens which had previously been morphologically described were identified by MALDl-TOF MS[identification log score values(LSV)≥1.7],after an initial blind test using the pre-existing database.After DNA-based identification,new reference spectra of Bi.pfeiferi(n=10)and Bu.forskali(n=5)from the geographical areas were added to the MALDI-TOF spectral database.The final blind test against this updated database was per-formed to assess identification at the geographic source level.Results MALDI-TOF MS correctly identified 92.1%of 101 Bi.pfeifferi snails and 98.8%of 81 Bu.forskali snails.At the final blind test,88%of 166 specimens were correctly identified according to both their species and sampling site,with LSVs ranging from 1.74 to 2.70.The geographical source was adequately identified in 90.1%of 91 Bi.pfeifferi and 85.3%of 75 Bu.forskalii samples.Conclusions Our findings demonstrate that MALDI-TOF MS can identify and differentiate snail populations according to geographical origin.It outperforms the current DNA-based approaches in discriminating laboratory from wild strains.This inexpensive high-throughput approach is likely to further revolutionise epidemiological studies in areas which are endemic for schistosomiasis.

Mass spectrometry-based serum peptide profiling in hepatocellular carcinoma with bone metastasis

AIM: To investigate the potential of serum peptides as a diagnostic tool for hepatocellular carcinoma (HCC) with bone metastasis.

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.

Serum proteomic profiling for autism using magnetic bead-assisted matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a pilot study

Background The pathogenesis of autism spectrum disorders remains elusive and currently there are no diagnostic or pre-dictive biomarkers in autism available. Proteomic profiling has been used in a wide range of neurodevelopmental disorder studies, which could produce deeper perceptions of the molecular bases behind certain disease and potentially becomes useful in discovering biomarkers in autism spectrum disorders. Methods Serum samples were collected from autistic children about 3 years old in age (n = 32) and healthy controls (n = 20) in similar age and gender. The samples were identified specific proteins that are diff erentially expressed by magnetic bead-based pre-fractionation and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF-MS). Results Eight protein peaks were significantly different in autistic children from the healthy controls (P < 0.0001). The two peaks with the most significant diff erences were 6428 and 7758 Da in size. Conclusion According to diff erences in serum protein profiles between the autistic children and healthy controls, this study identified a set of diff erentially expressed proteins those are significant for further evaluation and might function as biomark-ers in autism.

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.

MALDI coupled with laser-postionization and trapped ion mobility spectrometry contribute to the enhanced detection of lipids in cancer cell spheroids

Cancer cell spheroids(CCS) are a valuable three-dimensional cell model in cancer studies because they could replicate numerous characteristics of solid tumors. Increasing researches have used matrix-assisted laser desorption/ionization mass spectrometry imaging(MALDI-MSI) to investigate the spatial distribution of endogenous compounds(e.g., lipids) in CCS. However, only limited lipid species can be detected owing to a low ion yield by using MALDI. Besides, it is still challenging to fully characterize the structural diversity of lipids due to the existence of isomeric/isobaric species. Here, we carried out the initial application of MALDI coupled with laser-postionization(MALDI-2) and trapped ion mobility spectrometry(TIMS) imaging in HCT116 colon CCS to address these challenges. We demonstrated that MALDI-2 is capable of detecting more number and classes of lipids in HCT116 colon CCS with higher signal intensities than MALDI. TIMS could successfully separate numerous isobaric/isomeric species of lipids in CCS. Interestingly, we found that some isomeric/isobaric species have totally different spatial distributions in colon CCS. Further MS/MS imaging analysis was employed to determine the compositions of fatty acid chains for isomeric species by examining disparities in signal intensities and spatial distributions of product ions. This work stresses the robust ability of TIMS and MALDI-2 imaging in analyzing endogenous lipids in CCS, which could potentially become powerful tools for future cancer studies.

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.

Using MALDI-TOF MS coupled with a high-mass detector to directly analyze intact proteins in thyroid tissues

Protein analysis is vital for biological and clinical research, but the measurement of unseparated, intact and high-mass proteins is also a challenging task by mass spectrometry-based methods. Here, we present a protocol for rapid and high-throughput analysis of intact proteins in tissue samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry（MALDITOF MS） combined with a high-mass detector platform. The method involves tissue specimens that undergo a simple protein extraction before MALDI-MS analysis. Using this method, the high abundance proteins in human thyroid carcinoma and paracarcinoma tissues were successfully investigated, and the mass spectra of the tissues of the 30 illustrated thyroid cancers showed remarkable differences. The peak intensity revealed a significant increase in human albumin in thyroid carcinoma tissues（p＆lt;0.05）. To validate the feasibility and credibility of this method, label-free proteomics quantitative analysis and Western blotting were used to relatively quantify the proteins in these tissues. Those results demonstrated a nearly 3-fold difference in human albumin levels between thyroid carcinoma and para-carcinoma tissues, which were consistent with the results of our method. The advantages of our method are easy sample handling, remarkable reproducibility and the ability to analyze high-mass proteins without digestion, which make them have the potential to be used in biological research and in clinical practice.

Nocardia cyriacigeorgica infection in a patient with repeated fever and CD4+T cell deficiency:A case report

BACKGROUND Nocardia pneumonia shares similar imaging and clinical features with pulmonary tuberculosis and lung neoplasms,but the treatment and anti-infective medication are completely different.Here,we report a case of pulmonary nocardiosis caused by Nocardia cyriacigeorgica(N.cyriacigeorgica),which was misdiagnosed as community-acquired pneumonia(CAP)with repeated fever.CASE SUMMARY A 55-year-old female was diagnosed with community-acquired pneumonia in the local hospital because of repeated fever and chest pain for two months.After the anti-infection treatment failed in the local hospital,the patient came to our hospital for further treatment.Enhanced computed tomography showed multiple patchy,nodular and strip-shaped high-density shadows in both lungs.A routine haematological examination was performed and showed abnormalities in CD19+B cells and CD4+T cells.Positive acid-fast bifurcating filaments and branching gram-positive rods were observed in the bronchoalveolar lavage fluid of the patient under an oil microscope,which was identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry as N.cyriacigeorgica.The patient’s condition quickly improved after taking 0.96 g compound sulfamethoxazole tablets three times a day.CONCLUSION The antibiotic treatment of Nocardia pneumonia is different from that of common CAP.Attention should be given to the pathogenic examination results of patients with recurrent fever.Nocardia pneumonia is an opportunistic infection.Patients with CD4+T-cell deficiency should be aware of Nocardia infection.

Bacterial flora concurrent with Helicobacter pylori in the stomach of patients with upper gastrointestinal diseases

AIM： To investigate the non-He/icobacterpy/ori （H. pylori） bacterial flora concurrent with H. pylori infection.METHODS： A total of 103 gastric biopsy specimens from H. pylori positive patients were selected for bacterial culture. All the non-H, pylori bacterial isolates were identified by matrix assisted laser desorption ionization time-of-flight mass spectrometry （MALDI-TOF MS）.RESULTS： A total of 201 non-H, pyiori bacterial isolates were cultivated from 67 （65.0%） of the 103 gastric samples, including 153 isolates identified successfully at species level and 48 at genus level by MALDI-TOF MS. The dominant species were Streptococcus, Neisseria, Rothla and Staphylococcus, which differed fromthe predominantly acid resistant species reported previously in healthy volunteers. The prevalence of non-H. pylori bacteria was higher in non-ulcer dyspepsia group than in gastric ulcer group （100% vs 42.9%, P 〈 0.001）. Six bacterial species with urease activity （Staphylococcus epidermidis, Staphylococcus warneri, Staphylococcus capitis, Staphylococcus aureus, Brevibacteriurn spp. and Klebsiella pneumoniae） were also isolated.CONCLUSION： There is a high prevalence of the non-H, pylori bacteria concurrent with H. pylori infection, and the non-H, pylori bacteria may also play important as-yet-undiscovered roles in the pathogenesis of stomach disorders.

Diagnostic model of saliva protein finger print analysis of patients with gastric cancer

AIM:To explore the method for early diagnosis of gastric cancer by screening the expression spectrum of saliva protein in gastric cancer patients using mass spectrometry for proteomics.METHODS:Proportional peptide mass fingerprints were obtained by analysis based on proteomics matrix-assisted laser desorption ionization time-of-flight/mass spectrometry.A diagnosis model was established using weak cation exchange magnetic beads to test saliva specimens from gastric cancer patients and healthy subjects.RESULTS:Significant differences were observed in the mass to charge ratio(m/z) peaks of four proteins(1472.78 Da,2936.49 Da,6556.81 Da and 7081.17 Da) between gastric cancer patients and healthy subjects.CONCLUSION:The finger print mass spectrum of saliva protein in patients with gastric cancer can be established using gastric cancer proteomics.A diagnostic model for distinguishing protein expression mass spectra of gastric cancer from non-gastric-cancer saliva can be established according to the different expression of proteins 1472.78 Da,2936.49 Da,6556.81 Da and 7081.17 Da.The method for early diagnosis of gastric cancer is of certain value for screening special biological markers.

Proteiomic patterns for endometrial cancer using SELDI-TOF-MS

Serum samples from endometrial cancer (EC) patients and healthy females were analyzed using surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF-MS) to discover the potential diagnostic biomarker for detection of EC. A preliminary training set of spectra derived from 40 EC patients and 30 healthy women were used to develop a proteomic model that effectively discriminated cancer patients from healthy women. The training set had a specificity of 100% and sensitivity of 92.5% in the EC detection. A blind test set, including 20 new cancer cases and 10 healthy women, was used to validate the sensitivity and specificity of this multivariate model, which had a corresponding results of 60% in specificity and 75% in sensitivity, respectively. The combination of SELDI-TOF-MS with bioinformatics tools could help find new biomarkers and establish the detection of EC with high sensitivity and specificity.

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.

Increase in functional groups for POSS by introducing branched phenylglycidylether

In the selected experimental conditions, firstly, the branched products with functional groups, N-（2-hydroxylpropylphenylether） （3-aminopropyl） triethoxysilane （APES-PGE, containing one hydroxyl group） and N-[di（2-hydroxylpropylphenylether）]（3-aminopropyl） triethoxysilane （APES-PGE2, containing two hydroxyl groups）, were synthesized by reacting 1 mole of （3-aminopropyl）triethoxysilane （APES） with 2 mole of phenylglycidylether （PGE）. Then the hydrolytic condensation of APES-PGE and APES-PGE2 was performed by dissolving 1 g of the corresponding silane in 1.5 ml tetrahydrofuran （THF）, adding water and eventually a catalyst （molar ratios: [H2O]/Si=3, [NaOH]/Si=0.05）, and heating at 50 ℃ for 24 h, allowing continuous evaporation of volatiles. The final products with branches containing hydroxyl groups were polyhedral oligomeric silsesquioxanes （POSS）. The products from two reactions were characterized by standard spectroscopic techniques, gel partition chromatography （GPC）, Fourier-transformed infrared spectroscopy （FTIR） and matrix-assisted ultraviolet laser desorption/ionization time-of-flight mass spectrometry （UV-MALDI-TOF MS）. Additionally, a narrow mass distribution of multifunctionalized POSS was shown by UV-MALDI-TOF MS and assignments of the MS peaks.

Insights into glycan biosynthesis in chemically-induced hepatocellular carcinoma in rats: A glycomic analysis

AIM： To evaluate the qualitative and quantitativechanges in N-linked glycosylation, which occurredin association with diethyl nitrosamine-inducedhepatocellular carcinoma （HCC） in rodents.METHODS： Liver tissues of （1） normal （non-tumorbearing）rats; and （2） tumor-bearing rats; were collectedand were used for histological and GlycanMap？ analyses.Briefly, GlycanMap？ analysis is a high-throughputassay that provides a structural and quantitativereadout of protein-associated glycans using a unique,automated 96-well assay technology coupled tomatrix-assisted laser desorption/ionization time-offlightmass spectrometry and custom bioinformatics.Histopathological studies were carried out to ensure thedevelopment of HCC in the tested animals.RESULTS： The N-glycomic analysis revealed 5glycans; Glc1Man9GlcNAc2, Gal2Man3GlcNac4Fuc1Neu1,Man4G l c N a c 2, G a l 2Man3G l c N a c 4Neu3OAc 3, andMan3GlcNac5Fuc1, which showed significant changesin rat HCC tissues when compared with normal livertissues. Four glycans were increased （P 〈 0.05） andGlc1Man9GlcNAc2 was decreased （5.89 ± 0.45 vs 3.54± 0.21, P 〈 0.01） in HCC tissues compared to normal liver tissues. An increase （66.5 ± 1.05 vs 62.7 ± 1.1,P 〈 0.05） in high-mannose structures in HCC rats wasobserved compared to normal rats. Importantly, HCCrats showed an increase （P 〈 0.05） in both tumorassociatedcarbohydrates and in branched glycans. Thechanges in glycans correlated well with glycan flowchanges reported in the glycan biosynthetic pathway,which indicates the importance of enzyme activitiesinvolved in glycan synthesis at different subcellularlocalizations.CONCLUSION： The reported HCC-associated changesin glycan flow and subcellular localization explain theincrease in high mannose glycans and siayl Lewisglycans common in HCC liver tissues.

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.