Pub Date : 2014-12-01DOI: 10.5702/massspectrometry.S0043
K. Ohshimo, T. Komukai, Tohru Takahashi, Naoya Norimasa, Jenna W. J. Wu, R. Moriyama, K. Koyasu, F. Misaizu
Stable cluster sizes and compositions have been investigated for cations and anions of ionic bond clusters such as alkali halides and transition metal oxides by ion mobility-mass spectrometry (IM-MS). Usually structural information of ions can be obtained from collision cross sections determined in IM-MS. In addition, we have found that stable ion sizes or compositions were predominantly produced in a total ion mass spectrum, which was constructed from the IM-MS measurement. These stable species were produced as a result of collision induced dissociations of the ions in a drift cell. We have confirmed this result in the sodium fluoride cluster ions, in which cuboid magic number cluster ions were predominantly observed. Next the stable compositions, which were obtained for the oxide systems of the first row transition metals, Ti, Fe, and Co, are characteristic for each of the metal oxide cluster ions.
{"title":"Application of Ion Mobility-Mass Spectrometry to the Study of Ionic Clusters: Investigation of Cluster Ions with Stable Sizes and Compositions.","authors":"K. Ohshimo, T. Komukai, Tohru Takahashi, Naoya Norimasa, Jenna W. J. Wu, R. Moriyama, K. Koyasu, F. Misaizu","doi":"10.5702/massspectrometry.S0043","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0043","url":null,"abstract":"Stable cluster sizes and compositions have been investigated for cations and anions of ionic bond clusters such as alkali halides and transition metal oxides by ion mobility-mass spectrometry (IM-MS). Usually structural information of ions can be obtained from collision cross sections determined in IM-MS. In addition, we have found that stable ion sizes or compositions were predominantly produced in a total ion mass spectrum, which was constructed from the IM-MS measurement. These stable species were produced as a result of collision induced dissociations of the ions in a drift cell. We have confirmed this result in the sodium fluoride cluster ions, in which cuboid magic number cluster ions were predominantly observed. Next the stable compositions, which were obtained for the oxide systems of the first row transition metals, Ti, Fe, and Co, are characteristic for each of the metal oxide cluster ions.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"205 1","pages":"S0043"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76961753","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 : 2014-12-01DOI: 10.5702/massspectrometry.S0045
E. Fukusaki
Metabolome, a total profile of whole metabolites, is placed on downstream of proteome. Metabolome is thought to be results of implementation of genomic information. In other words, metabolome can be called as high resolution phenotype. The easiest operation of metabolomics is the integration to the upstream ome information including transcriptome and/or proteome. Those trials have been reported at a certain scientific level. In addition, metabolomics can be operated in stand-alone mode without any other ome information. Among metabolomics tactics, the author's group is particularly focusing on metabolic fingerprinting, in which metabolome information is employed as explanatory variant to evaluate response variant. Metabolic fingerprinting technique is expected not only for analyzing slight difference depending on genotype difference but also for expressing dynamic variation of living organisms. The author introduces several good examples which he performed. Those are useful for easy understanding of the power of metabolomics. In addition, the author mentions the latest technology for analysis of metabolic dynamism. The author's group developed a facile analytical method for semi-quantitative metabolic dynamism. The author introduces the novel method that uses time dependent variation of isotope distribution based on stable isotope dilution.
{"title":"Application of Metabolomics for High Resolution Phenotype Analysis.","authors":"E. Fukusaki","doi":"10.5702/massspectrometry.S0045","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0045","url":null,"abstract":"Metabolome, a total profile of whole metabolites, is placed on downstream of proteome. Metabolome is thought to be results of implementation of genomic information. In other words, metabolome can be called as high resolution phenotype. The easiest operation of metabolomics is the integration to the upstream ome information including transcriptome and/or proteome. Those trials have been reported at a certain scientific level. In addition, metabolomics can be operated in stand-alone mode without any other ome information. Among metabolomics tactics, the author's group is particularly focusing on metabolic fingerprinting, in which metabolome information is employed as explanatory variant to evaluate response variant. Metabolic fingerprinting technique is expected not only for analyzing slight difference depending on genotype difference but also for expressing dynamic variation of living organisms. The author introduces several good examples which he performed. Those are useful for easy understanding of the power of metabolomics. In addition, the author mentions the latest technology for analysis of metabolic dynamism. The author's group developed a facile analytical method for semi-quantitative metabolic dynamism. The author introduces the novel method that uses time dependent variation of isotope distribution based on stable isotope dilution.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"51 1","pages":"S0045"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76649258","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 : 2014-12-01DOI: 10.5702/massspectrometry.S0046
D. Saigusa, Michiyo Okudaira, Jiao Wang, K. Kano, M. Kurano, B. Uranbileg, H. Ikeda, Y. Yatomi, H. Motohashi, J. Aoki
Sph, S1P, and Cer, derived from the membrane sphingolipids, act as intracellular and intercellular mediators, involved in various (path) physiological functions. Accordingly, determining the distributions and concentrations of these sphingolipid mediators in body tissues is an important task. Consequently, a method for determination of sphingolipids in small quantities of tissue is required. Sphingolipids analysis has been dependent on improvements in mass spectrometry (MS) technology. Additionally, decomposition of sphingosine-1-phosphate (S1P) in the tissue samples before preparation for MS has hindered analysis. In the present study, a method for stabilization of liver samples before MS preparation was developed using a heat stabilizer (Stabilizor™ T1). Then, a LC-MS/MS method using a triple-quadrupole mass spectrometer with a C8 column was developed for simultaneous determination of sphingolipids in small quantities of liver specimens. This method showed good separation and validation results. Separation was performed with a gradient elution of solvent A (5 mmol L(-1) ammonium formate in water, pH 4.0) and solvent B (5 mmol L(-1) ammonium formate in 95% acetonitrile, pH 4.0) at 300 μL min(-1). The lower limit of quantification was less than 132 pmol L(-1), and this method was accurate (∼13.5%) and precise (∼7.13%) for S1P analysis. The method can be used to show the tissue distribution of sphingolipids.
{"title":"Simultaneous Quantification of Sphingolipids in Small Quantities of Liver by LC-MS/MS.","authors":"D. Saigusa, Michiyo Okudaira, Jiao Wang, K. Kano, M. Kurano, B. Uranbileg, H. Ikeda, Y. Yatomi, H. Motohashi, J. Aoki","doi":"10.5702/massspectrometry.S0046","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0046","url":null,"abstract":"Sph, S1P, and Cer, derived from the membrane sphingolipids, act as intracellular and intercellular mediators, involved in various (path) physiological functions. Accordingly, determining the distributions and concentrations of these sphingolipid mediators in body tissues is an important task. Consequently, a method for determination of sphingolipids in small quantities of tissue is required. Sphingolipids analysis has been dependent on improvements in mass spectrometry (MS) technology. Additionally, decomposition of sphingosine-1-phosphate (S1P) in the tissue samples before preparation for MS has hindered analysis. In the present study, a method for stabilization of liver samples before MS preparation was developed using a heat stabilizer (Stabilizor™ T1). Then, a LC-MS/MS method using a triple-quadrupole mass spectrometer with a C8 column was developed for simultaneous determination of sphingolipids in small quantities of liver specimens. This method showed good separation and validation results. Separation was performed with a gradient elution of solvent A (5 mmol L(-1) ammonium formate in water, pH 4.0) and solvent B (5 mmol L(-1) ammonium formate in 95% acetonitrile, pH 4.0) at 300 μL min(-1). The lower limit of quantification was less than 132 pmol L(-1), and this method was accurate (∼13.5%) and precise (∼7.13%) for S1P analysis. The method can be used to show the tissue distribution of sphingolipids.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"37 1","pages":"S0046"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85360468","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 : 2014-11-01DOI: 10.5702/massspectrometry.S0040
H. Sasaki, Yoshifumi Kobashi, T. Nagai, M. Maeda
For the development and optimization of materials processing a collection of thermodynamic information concerning substances that participate in the reactions is important. One fundamental way to obtain such information is to measure the vapor pressure of gas species under conditions where they are in equilibrium with the condensed phases. Over the past 60 years Knudsen cell mass spectrometry has been used to identify and quantitatively determine gas species at high temperatures. This article describes thermodynamic foundation and examples of measurements in order to demonstrate the use of mass spectrometry focusing on the field of process metallurgy and recycling processes.
{"title":"Thermodynamic Measurements of Alloys and Compounds by Double Knudsen Cell Mass Spectrometry and Their Application to Materials Processing.","authors":"H. Sasaki, Yoshifumi Kobashi, T. Nagai, M. Maeda","doi":"10.5702/massspectrometry.S0040","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0040","url":null,"abstract":"For the development and optimization of materials processing a collection of thermodynamic information concerning substances that participate in the reactions is important. One fundamental way to obtain such information is to measure the vapor pressure of gas species under conditions where they are in equilibrium with the condensed phases. Over the past 60 years Knudsen cell mass spectrometry has been used to identify and quantitatively determine gas species at high temperatures. This article describes thermodynamic foundation and examples of measurements in order to demonstrate the use of mass spectrometry focusing on the field of process metallurgy and recycling processes.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"28 1","pages":"S0040"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78848709","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 : 2014-10-01DOI: 10.5702/massspectrometry.A0031
Yuki Ohta, Shinichi Iwamoto, S. Kawabata, Ritsuko Tanimura, Koichi Tanaka
Mass spectrometry (MS) is a highly sensitive analytical technique that is often coupled with liquid chromatography (LC). However, some buffering salts used in LC (e.g., phosphate and tris(hydroxymethyl)aminomethane (Tris)) are incompatible with MS since they cause ion-source contamination and signal suppression. In this study, we examined salt tolerance of MALDI and applied a matrix additive methylenediphosphonic acid (MDPNA) to reduce salt-induced signal suppression. MDPNA significantly improved the salt tolerance of MALDI-MS. Using ammonium formate buffer at pH 5.0, the effective range of buffering salt concentration in MALDI-MS using MDPNA was estimated up to 250 mM. MDPNA reduced signal suppression caused by buffering salts at pH 4.0 to 8.0. We observed that MDPNA effectively worked over a wide range of buffer conditions. MDPNA was further applied to hydrophilic interaction chromatography (HILIC) and chromatofocusing-MALDI-MS. As a result, the analytes in the eluent containing high-concentration salts were detected with high sensitivity. Thus, our study provides simple and fast LC-MALDI-MS analysis technique not having strict limitation of buffering condition in LC by using matrix additive MDPNA.
{"title":"Salt Tolerance Enhancement of Liquid Chromatography-Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Using Matrix Additive Methylenediphosphonic Acid.","authors":"Yuki Ohta, Shinichi Iwamoto, S. Kawabata, Ritsuko Tanimura, Koichi Tanaka","doi":"10.5702/massspectrometry.A0031","DOIUrl":"https://doi.org/10.5702/massspectrometry.A0031","url":null,"abstract":"Mass spectrometry (MS) is a highly sensitive analytical technique that is often coupled with liquid chromatography (LC). However, some buffering salts used in LC (e.g., phosphate and tris(hydroxymethyl)aminomethane (Tris)) are incompatible with MS since they cause ion-source contamination and signal suppression. In this study, we examined salt tolerance of MALDI and applied a matrix additive methylenediphosphonic acid (MDPNA) to reduce salt-induced signal suppression. MDPNA significantly improved the salt tolerance of MALDI-MS. Using ammonium formate buffer at pH 5.0, the effective range of buffering salt concentration in MALDI-MS using MDPNA was estimated up to 250 mM. MDPNA reduced signal suppression caused by buffering salts at pH 4.0 to 8.0. We observed that MDPNA effectively worked over a wide range of buffer conditions. MDPNA was further applied to hydrophilic interaction chromatography (HILIC) and chromatofocusing-MALDI-MS. As a result, the analytes in the eluent containing high-concentration salts were detected with high sensitivity. Thus, our study provides simple and fast LC-MALDI-MS analysis technique not having strict limitation of buffering condition in LC by using matrix additive MDPNA.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"51 1","pages":"A0031"},"PeriodicalIF":0.0,"publicationDate":"2014-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79802517","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.S0035
D. L. Sweeney
The combination of partitioning and systematic bond disconnection has been used to identify compounds from accurate-mass fragmentation data. This combination is very effective in excluding wrong answers that occur by chance. However, both processes are CPU intensive. This paper describes a novel data structure for representing molecules in a computer readable format that is conducive to very rapid mass spectral searching while still retaining the advantages of partitioning and systematic bond disconnection.
{"title":"A Data Structure for Rapid Mass Spectral Searching.","authors":"D. L. Sweeney","doi":"10.5702/massspectrometry.S0035","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0035","url":null,"abstract":"The combination of partitioning and systematic bond disconnection has been used to identify compounds from accurate-mass fragmentation data. This combination is very effective in excluding wrong answers that occur by chance. However, both processes are CPU intensive. This paper describes a novel data structure for representing molecules in a computer readable format that is conducive to very rapid mass spectral searching while still retaining the advantages of partitioning and systematic bond disconnection.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"22 1","pages":"S0035"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78058839","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.S0037
Kai Dührkop, Franziska Hufsky, Sebastian Böcker
We present the results of a fully automated de novo approach for identification of molecular formulas in the CASMI 2013 contest. Only results for Category 1 (molecular formula identification) were submitted. Our approach combines isotope pattern analysis and fragmentation pattern analysis and is completely independent from any (spectral and structural) database. We correctly identified the molecular formula for ten out of twelve challenges, being the best automated method competing in this category.
{"title":"Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.","authors":"Kai Dührkop, Franziska Hufsky, Sebastian Böcker","doi":"10.5702/massspectrometry.S0037","DOIUrl":"https://doi.org/10.5702/massspectrometry.S0037","url":null,"abstract":"We present the results of a fully automated de novo approach for identification of molecular formulas in the CASMI 2013 contest. Only results for Category 1 (molecular formula identification) were submitted. Our approach combines isotope pattern analysis and fragmentation pattern analysis and is completely independent from any (spectral and structural) database. We correctly identified the molecular formula for ten out of twelve challenges, being the best automated method competing in this category.","PeriodicalId":18243,"journal":{"name":"Mass spectrometry","volume":"1 3","pages":"S0037"},"PeriodicalIF":0.0,"publicationDate":"2014-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5702/massspectrometry.S0037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72406532","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.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}
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