Pub Date : 2014-08-01DOI: 10.5702/massspectrometry.S0033
L. Ridder, J. V. D. van der Hooft, S. Verhoeven
The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed.
{"title":"Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa.","authors":"L. Ridder, J. V. D. van der Hooft, S. Verhoeven","doi":"10.5702/massspectrometry.S0033","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0033","url":null,"abstract":"The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"15 1","pages":"S0033"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82337387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-08-01DOI: 10.5702/massspectrometry.S0038
Fumio Matsuda
The CASMI 2013 (Critical Assessment of Small Molecule Identification 2013, http://casmi-contest.org/) contest was held to systematically evaluate strategies used for mass spectrometry-based identification of small molecules. The results of the contest highlight that, because of the extensive efforts made towards the construction of databases and search tools, database-assisted small molecule identification can now automatically annotate some metabolite signals found in the metabolome data. In this commentary, the current state of metabolite annotation is compared with that of transcriptomics and proteomics. The comparison suggested that certain limitations in the metabolite annotation process need to be addressed, such as (i) the completeness of the database, (ii) the conversion between raw data and structure, (iii) the one-to-one correspondence between measured data and correct search results, and (iv) the false discovery rate in database search results.
{"title":"Rethinking Mass Spectrometry-Based Small Molecule Identification Strategies in Metabolomics.","authors":"Fumio Matsuda","doi":"10.5702/massspectrometry.S0038","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0038","url":null,"abstract":"The CASMI 2013 (Critical Assessment of Small Molecule Identification 2013, http://casmi-contest.org/) contest was held to systematically evaluate strategies used for mass spectrometry-based identification of small molecules. The results of the contest highlight that, because of the extensive efforts made towards the construction of databases and search tools, database-assisted small molecule identification can now automatically annotate some metabolite signals found in the metabolome data. In this commentary, the current state of metabolite annotation is compared with that of transcriptomics and proteomics. The comparison suggested that certain limitations in the metabolite annotation process need to be addressed, such as (i) the completeness of the database, (ii) the conversion between raw data and structure, (iii) the one-to-one correspondence between measured data and correct search results, and (iv) the false discovery rate in database search results.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"103 1","pages":"S0038"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88369501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-08-01DOI: 10.5702/massspectrometry.S0034
Andrew G. Newsome, D. Nikolić
The Critical Assessment of Small Molecule Identification (CASMI) contest was initiated in 2012 to evaluate manual and automated strategies for the identification of small molecules from raw mass spectrometric data. The authors participated in both category 1 (molecular formula determination) and category 2 (molecular structure determination) of the second annual CASMI contest (CASMI 2013) using slow but effective manual methods. The provided high resolution mass spectrometric data were interpreted manually using a combination of molecular formula calculators, fragment and neutral loss analysis, literature consultation, manual database searches, deductive logic, and experience. The authors submitted correct formulas as lead candidates for 16 of 16 challenges and submitted correct structure solutions as lead candidates for 14 of 16 challenges. One structure submission (Challenge 3) was very close but not exact (N (2)-acetylglutaminylisoleucinamide instead of the correct N (2)-acetylglutaminylleucinamide). A solution for one (Challenge 13) was not submitted due to an inability to reconcile the provided fragmentation pattern with any known structures with the provided molecular composition.
{"title":"CASMI 2013: Identification of Small Molecules by Tandem Mass Spectrometry Combined with Database and Literature Mining.","authors":"Andrew G. Newsome, D. Nikolić","doi":"10.5702/massspectrometry.S0034","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0034","url":null,"abstract":"The Critical Assessment of Small Molecule Identification (CASMI) contest was initiated in 2012 to evaluate manual and automated strategies for the identification of small molecules from raw mass spectrometric data. The authors participated in both category 1 (molecular formula determination) and category 2 (molecular structure determination) of the second annual CASMI contest (CASMI 2013) using slow but effective manual methods. The provided high resolution mass spectrometric data were interpreted manually using a combination of molecular formula calculators, fragment and neutral loss analysis, literature consultation, manual database searches, deductive logic, and experience. The authors submitted correct formulas as lead candidates for 16 of 16 challenges and submitted correct structure solutions as lead candidates for 14 of 16 challenges. One structure submission (Challenge 3) was very close but not exact (N (2)-acetylglutaminylisoleucinamide instead of the correct N (2)-acetylglutaminylleucinamide). A solution for one (Challenge 13) was not submitted due to an inability to reconcile the provided fragmentation pattern with any known structures with the provided molecular composition.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"42 1","pages":"S0034"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77635561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-08-01DOI: 10.5702/massspectrometry.S0039
T. Nishioka, T. Kasama, T. Kinumi, H. Makabe, Fumio Matsuda, Daisuke Miura, M. Miyashita, Takemichi Nakamura, Kenichi Tanaka, Atsushi Yamamoto
CASMI (Critical Assessment of Small Molecule Identification) is a contest in which participants identify the molecular formula and chemical structure of challenging molecules using blind mass spectra as the challenge data. Seven research teams participated in CASMI2013. The winner of CASMI2013 was the team of Andrew Newsome and Dejan Nikolic, the University of Illinois at Chicago, IL, USA. The team identified 15 among 16 challenge molecules by manually interpreting the challenge data and by searching in-house and public mass spectral databases, and chemical substance and literature databases. MAGMa was selected as the best automated tool of CASMI2013. In some challenges, most of the automated tools successfully identified the challenge molecules, independent of the compound class and magnitude of the molecular mass. In these challenge data, all of the isotope peaks and the product ions essential for the identification were observed within the expected mass accuracy. In the other challenges, most of the automated tools failed, or identified solution candidates together with many false-positive candidates. We then analyzed these challenge data based on the quality of the mass spectra, the dissociation mechanisms, and the compound class and elemental composition of the challenge molecules.
CASMI (Critical Assessment of Small Molecule Identification)是一项竞赛，参赛者使用盲质谱作为挑战数据来识别挑战分子的分子式和化学结构。7个研究团队参与了CASMI2013。CASMI2013的冠军是美国伊利诺斯州芝加哥大学的Andrew Newsome和Dejan Nikolic团队。该团队通过人工解释挑战数据、搜索内部和公共质谱数据库、化学物质和文献数据库，确定了16个挑战分子中的15个。MAGMa被选为CASMI2013的最佳自动化工具。在一些挑战中，大多数自动化工具成功地识别了挑战分子，而不依赖于化合物类别和分子质量的大小。在这些挑战数据中，所有同位素峰和鉴定所需的产物离子都在预期的质量精度范围内观察到。在其他挑战中，大多数自动化工具都失败了，或者识别了解决方案候选以及许多假阳性候选。然后，我们根据质谱的质量、解离机制、挑战分子的化合物类别和元素组成来分析这些挑战数据。
{"title":"Winners of CASMI2013: Automated Tools and Challenge Data.","authors":"T. Nishioka, T. Kasama, T. Kinumi, H. Makabe, Fumio Matsuda, Daisuke Miura, M. Miyashita, Takemichi Nakamura, Kenichi Tanaka, Atsushi Yamamoto","doi":"10.5702/massspectrometry.S0039","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0039","url":null,"abstract":"CASMI (Critical Assessment of Small Molecule Identification) is a contest in which participants identify the molecular formula and chemical structure of challenging molecules using blind mass spectra as the challenge data. Seven research teams participated in CASMI2013. The winner of CASMI2013 was the team of Andrew Newsome and Dejan Nikolic, the University of Illinois at Chicago, IL, USA. The team identified 15 among 16 challenge molecules by manually interpreting the challenge data and by searching in-house and public mass spectral databases, and chemical substance and literature databases. MAGMa was selected as the best automated tool of CASMI2013. In some challenges, most of the automated tools successfully identified the challenge molecules, independent of the compound class and magnitude of the molecular mass. In these challenge data, all of the isotope peaks and the product ions essential for the identification were observed within the expected mass accuracy. In the other challenges, most of the automated tools failed, or identified solution candidates together with many false-positive candidates. We then analyzed these challenge data based on the quality of the mass spectra, the dissociation mechanisms, and the compound class and elemental composition of the challenge molecules.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"43 1","pages":"S0039"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80777287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-08-01DOI: 10.5702/massspectrometry.S0036
Emma L. Schymanski, Michael Gerlich, Christoph Ruttkies, S. Neumann
The second Critical Assessment of Small Molecule Identification (CASMI) contest took place in 2013. A joint team from the Swiss Federal Institute of Aquatic Science and Technology (Eawag) and Leibniz Institute of Plant Biochemistry (IPB) participated in CASMI 2013 with an automatic workflow-style entry. MOLGEN-MS/MS was used for Category 1, molecular formula calculation, restricted by the information given for each challenge. MetFrag and MetFusion were used for Category 2, structure identification, retrieving candidates from the compound databases KEGG, PubChem and ChemSpider and joining these lists pre-submission. The results from Category 1 were used to guide whether formula or exact mass searches were performed for Category 2. The Category 2 results were impressive considering the database size and automated regime used, although these could not compete with the manual approach of the contest winner. The Category 1 results were affected by large m/z and ppm values in the challenge data, where strategies beyond pure enumeration from other participants were more successful. However, the combination used for the CASMI 2013 entries was extremely useful for developing decision-making criteria for automatic, high throughput general unknown (non-target) identification and for future contests.
{"title":"Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS.","authors":"Emma L. Schymanski, Michael Gerlich, Christoph Ruttkies, S. Neumann","doi":"10.5702/massspectrometry.S0036","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0036","url":null,"abstract":"The second Critical Assessment of Small Molecule Identification (CASMI) contest took place in 2013. A joint team from the Swiss Federal Institute of Aquatic Science and Technology (Eawag) and Leibniz Institute of Plant Biochemistry (IPB) participated in CASMI 2013 with an automatic workflow-style entry. MOLGEN-MS/MS was used for Category 1, molecular formula calculation, restricted by the information given for each challenge. MetFrag and MetFusion were used for Category 2, structure identification, retrieving candidates from the compound databases KEGG, PubChem and ChemSpider and joining these lists pre-submission. The results from Category 1 were used to guide whether formula or exact mass searches were performed for Category 2. The Category 2 results were impressive considering the database size and automated regime used, although these could not compete with the manual approach of the contest winner. The Category 1 results were affected by large m/z and ppm values in the challenge data, where strategies beyond pure enumeration from other participants were more successful. However, the combination used for the CASMI 2013 entries was extremely useful for developing decision-making criteria for automatic, high throughput general unknown (non-target) identification and for future contests.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"PP 1","pages":"S0036"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84551448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-04-01DOI: 10.5702/massspectrometry.S0031
Xianglei Kong, Zhaiyi Huo, W. Zhai
Chiral recognition of d- and l-amino acids is achieved by a method combining electrospray ionization (ESI) and in-source collision-induced dissociation (CID) mass spectrometry (MS). Trimeric cluster ions [Cu(II)(A)(ref)2-H](+) are formed by ESI of mixtures of d- or l-analyte amino acid (A), chiral reference (ref) and CuSO4. By increasing the applied voltage in the ESI source region, the trimeric ions become unstable and dissociate progressively. Thus chiral differentiation of the analyte can be achieved by comparing the dependence of their relative intensities to a reference ion on applied voltages. The method does not need MS/MS technique, thus can be readily performed on single-stage MS instruments by turning the voltage of sampling cone.
{"title":"Chiral Differentiation of Amino Acids by In-Source Collision-Induced Dissociation Mass Spectrometry.","authors":"Xianglei Kong, Zhaiyi Huo, W. Zhai","doi":"10.5702/massspectrometry.S0031","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0031","url":null,"abstract":"Chiral recognition of d- and l-amino acids is achieved by a method combining electrospray ionization (ESI) and in-source collision-induced dissociation (CID) mass spectrometry (MS). Trimeric cluster ions [Cu(II)(A)(ref)2-H](+) are formed by ESI of mixtures of d- or l-analyte amino acid (A), chiral reference (ref) and CuSO4. By increasing the applied voltage in the ESI source region, the trimeric ions become unstable and dissociate progressively. Thus chiral differentiation of the analyte can be achieved by comparing the dependence of their relative intensities to a reference ion on applied voltages. The method does not need MS/MS technique, thus can be readily performed on single-stage MS instruments by turning the voltage of sampling cone.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"250 1","pages":"S0031"},"PeriodicalIF":0.0,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76791988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-04-01DOI: 10.5702/massspectrometry.S0028
Pui-kin So, Bin Hu, Z. Yao
Development of electrospray ionization on solid substrates (solid-substrate ESI) avoids the clogging problem encountered in conventional capillary-based ESI, allows more convenient sampling and permits new applications. So far, solid-substrate ESI with various materials, e.g., metals, paper, wood, fibers and biological tissue, has been developed, and applications ranging from analysis of pure compounds to complex mixtures as well as in vivo study were demonstrated. Particularly, the capability of solid-substrate ESI in direct analysis of complex samples, e.g., biological fluids and foods, has significantly facilitated mass spectrometric analysis in real-life applications and led to increasingly important roles of these techniques nowadays. In this review, various solid-substrate ESI techniques and their applications are summarized and the prospects in this field are discussed.
{"title":"Electrospray Ionization on Solid Substrates.","authors":"Pui-kin So, Bin Hu, Z. Yao","doi":"10.5702/massspectrometry.S0028","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0028","url":null,"abstract":"Development of electrospray ionization on solid substrates (solid-substrate ESI) avoids the clogging problem encountered in conventional capillary-based ESI, allows more convenient sampling and permits new applications. So far, solid-substrate ESI with various materials, e.g., metals, paper, wood, fibers and biological tissue, has been developed, and applications ranging from analysis of pure compounds to complex mixtures as well as in vivo study were demonstrated. Particularly, the capability of solid-substrate ESI in direct analysis of complex samples, e.g., biological fluids and foods, has significantly facilitated mass spectrometric analysis in real-life applications and led to increasingly important roles of these techniques nowadays. In this review, various solid-substrate ESI techniques and their applications are summarized and the prospects in this field are discussed.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"127 2 1","pages":"S0028"},"PeriodicalIF":0.0,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77878199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-04-01DOI: 10.5702/massspectrometry.K0006
Yu-Ju Chen, J. Shiea
The first Asia and Oceania Mass Spectrometry Conference (AOMSC) organized by the Mass Spectrometry Society for Japan (MSSJ) was held in Tsukuba, Japan in 2010. The 2nd and 3rd AOMSC were held in Busan, Korea in 2011 and Kyoto, Japan in 2012; with the conferences organized by the Korean Society for Mass Spectrometry (KSMS) and MSSJ, respectively. The continuous effort on the 4th AOMSC, was hosted and organized by Taiwan Society for Mass Spectrometry (TSMS) in July 10–12, 2013, at the Taipei International Convention Center (TICC), Taiwan. More than 800 participants attended the conference, where they contributed 88 oral and 196 poster presentations and discussed current advances in mass spectrometry regarding fundamentals; instrumentation; methodology; interfacing to chromatographs; and a broad range of applications in emerging fields such as the environmental sciences, energy, food safety, forensics, nanomaterials, molecular imaging, clinic diagnoses, pharmaceuticals, biomedicine, quantitative proteomics, post-translational modifications, metabolomics, glycoproteomics, bioinformatics, and inorganic mass spectrometry.
{"title":"Recent Development of Mass Spectrometric Technologies in Asia and Oceania.","authors":"Yu-Ju Chen, J. Shiea","doi":"10.5702/massspectrometry.K0006","DOIUrl":"https://doi.org/10.5702/massspectrometry.K0006","url":null,"abstract":"The first Asia and Oceania Mass Spectrometry Conference (AOMSC) organized by the Mass Spectrometry Society for Japan (MSSJ) was held in Tsukuba, Japan in 2010. The 2nd and 3rd AOMSC were held in Busan, Korea in 2011 and Kyoto, Japan in 2012; with the conferences organized by the Korean Society for Mass Spectrometry (KSMS) and MSSJ, respectively. The continuous effort on the 4th AOMSC, was hosted and organized by Taiwan Society for Mass Spectrometry (TSMS) in July 10–12, 2013, at the Taipei International Convention Center (TICC), Taiwan. More than 800 participants attended the conference, where they contributed 88 oral and 196 poster presentations and discussed current advances in mass spectrometry regarding fundamentals; instrumentation; methodology; interfacing to chromatographs; and a broad range of applications in emerging fields such as the environmental sciences, energy, food safety, forensics, nanomaterials, molecular imaging, clinic diagnoses, pharmaceuticals, biomedicine, quantitative proteomics, post-translational modifications, metabolomics, glycoproteomics, bioinformatics, and inorganic mass spectrometry.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"161 1","pages":"K0006"},"PeriodicalIF":0.0,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86184008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-04-01DOI: 10.5702/massspectrometry.S0025
S. Taira, H. Taguchi, Reiko Fukuda, Kohei Uematsu, Y. Ichiyanagi, Yukie Tanaka, Yutaka Fujii, H. Katano
A specific property of silver oxide-based nanoparticles permits the ionization of an analyte, giving rise to various applications of a smart analytical methodology. The nanoparticles (d=6.7 nm) contained an Ag2O core. The detection of several model componds (a nucleobase and two hair growth promoters) via the use of silver oxide nanoparticles is described. Adducts were produced between the target molecules and the two silver stable isotopes (Ag(107) and Ag(109)), resulting in the formation of specific signals as well as a protonated signal. Thus, it was possible to easily determine whether the given signals were correlated with the target molecule or not.
{"title":"Silver Oxide Based Nanoparticle Assisted Laser Desorption/Ionization Mass Spectrometry for the Detection of Low Molecular Weight Compounds.","authors":"S. Taira, H. Taguchi, Reiko Fukuda, Kohei Uematsu, Y. Ichiyanagi, Yukie Tanaka, Yutaka Fujii, H. Katano","doi":"10.5702/massspectrometry.S0025","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0025","url":null,"abstract":"A specific property of silver oxide-based nanoparticles permits the ionization of an analyte, giving rise to various applications of a smart analytical methodology. The nanoparticles (d=6.7 nm) contained an Ag2O core. The detection of several model componds (a nucleobase and two hair growth promoters) via the use of silver oxide nanoparticles is described. Adducts were produced between the target molecules and the two silver stable isotopes (Ag(107) and Ag(109)), resulting in the formation of specific signals as well as a protonated signal. Thus, it was possible to easily determine whether the given signals were correlated with the target molecule or not.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"7 1","pages":"S0025"},"PeriodicalIF":0.0,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87462026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-04-01DOI: 10.5702/massspectrometry.S0030
E. W. Y. Ng, H. S. Lam, P. Ng, T. Poon
Parallel Fragmentation Monitoring (PFM), which is an analogue of selected reaction monitoring (SRM), is a recently developed method for quantification of small molecules by MALDI-TOF/TOF mass spectrometry (MS). It is well known that isobaric interference substances can be occasionally present in complex biological samples, and affect the accuracy of measurement by SRM. Unfortunately, by design it is not possible to assess whether isobaric interference happens in a SRM analysis. In contrast, the unique design of PFM should allow quick inspection for isobaric interference and subsequent correction. In this study, using arginine as an example, interference effect of isobaric structural analogs on the quantification of citrulline by PFM was evaluated. Our results showed that the presence of arginine affected the measured concentrations of citrulline standard solutions in a concentration dependent manner. Such interference could be observed readily in the MS/MS spectra, and contributed by [arginine+H-NH3](+) fragment ion. Because of having highly similar mass, (13)C-isotope of [arginine+H-NH3](+) fragment ion overlapped with monoisotope of [citrulline+H-NH3](+) fragment ion, which was used as the report ion for quantification. However, such interference could be mathematically eliminated or minimized through estimation of the signal intensity of the (13)C-isotopic peak of [arginine+H-NH3](+) from the intensity of the corresponding monoisotopic peak according to isotope distribution of elements. Furthermore, the presence of interfering fragment ions could be avoided by optimizing MALDI ionization condition. In conclusion, isobaric interference can happen in PFM, but can be easily identified in the mass spectra and eliminated (minimized) with simple methods.
{"title":"Study of Isobaric Interference in Quantification of Citrulline by Parallel Fragmentation Monitoring.","authors":"E. W. Y. Ng, H. S. Lam, P. Ng, T. Poon","doi":"10.5702/massspectrometry.S0030","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0030","url":null,"abstract":"Parallel Fragmentation Monitoring (PFM), which is an analogue of selected reaction monitoring (SRM), is a recently developed method for quantification of small molecules by MALDI-TOF/TOF mass spectrometry (MS). It is well known that isobaric interference substances can be occasionally present in complex biological samples, and affect the accuracy of measurement by SRM. Unfortunately, by design it is not possible to assess whether isobaric interference happens in a SRM analysis. In contrast, the unique design of PFM should allow quick inspection for isobaric interference and subsequent correction. In this study, using arginine as an example, interference effect of isobaric structural analogs on the quantification of citrulline by PFM was evaluated. Our results showed that the presence of arginine affected the measured concentrations of citrulline standard solutions in a concentration dependent manner. Such interference could be observed readily in the MS/MS spectra, and contributed by [arginine+H-NH3](+) fragment ion. Because of having highly similar mass, (13)C-isotope of [arginine+H-NH3](+) fragment ion overlapped with monoisotope of [citrulline+H-NH3](+) fragment ion, which was used as the report ion for quantification. However, such interference could be mathematically eliminated or minimized through estimation of the signal intensity of the (13)C-isotopic peak of [arginine+H-NH3](+) from the intensity of the corresponding monoisotopic peak according to isotope distribution of elements. Furthermore, the presence of interfering fragment ions could be avoided by optimizing MALDI ionization condition. In conclusion, isobaric interference can happen in PFM, but can be easily identified in the mass spectra and eliminated (minimized) with simple methods.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"224 1","pages":"S0030"},"PeriodicalIF":0.0,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79070666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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