著者

Fumio Matsuda Shuka Komori Yuki Yamada Daiki Hara Nobuyuki Okahashi

出版者

The Mass Spectrometry Society of Japan

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

pp.A0106, (Released:2022-11-05)

参考文献数

44

被引用文献数

1

---

In metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured m/z value is also one of the bottlenecks to narrowing down the candidate compositional formula. In this study, we report that averaging multiple product ion spectra can improve m/z precision as well as the reliability of fragment ions that are observed in such spectra. A graph-based method was applied to cluster a set of similar spectra from multiple DDA data files resulting in creating an averaged product-ion spectrum. The error levels for the m/z values declined following the central limit theorem, which allowed us to reduce the number of candidate compositional formulas. The improved reliability and precision of the averaged spectra will contribute to a more efficient annotation of product ion spectral data.

著者

Fumio Matsuda

出版者

日本質量分析学会

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

vol.3, no.Special_Issue_2, pp.S0038-S0038, 2014-08-01 (Released:2014-08-16)

参考文献数

38

被引用文献数

4 14

---

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.

著者

Fumio Matsuda

出版者

The Mass Spectrometry Society of Japan

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

vol.12, no.1, pp.A0138, 2023-12-08 (Released:2023-12-08)

参考文献数

37

---

Non-targeted metabolome analysis studies comprehensively acquire product ion spectra from the observed ions by the data-dependent acquisition (DDA) mode of tandem mass spectrometry (MS). A DDA dataset redundantly contains closely similar product ion spectra of metabolites commonly existing among the biological samples analyzed in a metabolome study. Moreover, a single DDA data file often includes two or more closely similar raw spectra obtained from an identical precursor ion. The redundancy of product ion spectra has been used to generate an averaged product ion spectrum from a set of similar product ion spectra recorded in a DDA dataset. The spectral averaging improved the accuracy of m/z values and signal-to-noise levels of product ion spectra. However, the origins of redundancy, variations among datasets, and these effects on the spectral averaging procedure needed to be better characterized. This study investigated the nature of the redundancy by comparing the averaging results of eight DDA datasets of non-targeted metabolomics studies. The comparison revealed a significant variation in redundancy among datasets. The DDA datasets obtained by the quadrupole (Q)-Orbitrap-MS datasets had more significant intrafile redundancy than that of the Q-time-of-flight-MS. For evaluating the similarity score between two product ion spectra, the optimal threshold level of the cosine-product method was approximately 0.8–0.9. Moreover, contamination of biological samples such as plasticizers was another origin of spectral redundancy. The results will be the basis for further development of methods for processing of product ion spectra data.

著者

Fumio Matsuda Shuka Komori Yuki Yamada Daiki Hara Nobuyuki Okahashi

出版者

The Mass Spectrometry Society of Japan

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

vol.11, no.1, pp.A0106, 2022-12-15 (Released:2022-12-15)

参考文献数

44

被引用文献数

1

---

In metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured m/z value is also one of the bottlenecks to narrowing down the candidate compositional formula. In this study, we report that averaging multiple product ion spectra can improve m/z precision as well as the reliability of fragment ions that are observed in such spectra. A graph-based method was applied to cluster a set of similar spectra from multiple DDA data files resulting in creating an averaged product-ion spectrum. The error levels for the m/z values declined following the central limit theorem, which allowed us to reduce the number of candidate compositional formulas. The improved reliability and precision of the averaged spectra will contribute to a more efficient annotation of product ion spectral data.

著者

Nobuyuki Okahashi Shuichi Kawana Junko Iida Hiroshi Shimizu Fumio Matsuda

出版者

The Mass Spectrometry Society of Japan

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

vol.8, no.1, pp.A0073, 2019-08-30 (Released:2019-08-30)

参考文献数

15

被引用文献数

1 18

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Isotope labeling measurements using mass spectrometry can provide informative insights on the metabolic systems of various organisms. The detailed identification of carbon positions included in the fragment ions of dicarboxylic and tricarboxylic acids in central carbon metabolism is needed for precise interpretation of the metabolic states. In this study, fragment ions containing the carbon backbone cleavage of dicarboxylic and tricarboxylic in the Krebs cycle were investigated by using gas chromatography (GC)-electron ionization (EI)-MS and GC-EI-MS/MS. The positions of decarboxylation in the dicarboxylic and tricarboxylic acids were successfully identified by analyses using position-specific 13C-labeled standards prepared by in vitro enzymatic reactions. For example, carboxyl groups of C1 and C6 of trimethylsilyl (TMS)- and tert-butyldimethylsilyl (TBDMS)-derivatized malic and citric acids were primarily cleaved by EI. MS/MS analyses were also performed, and fragment ions of TBDMS-citric and α-ketoglutaric acids (αKG) with the loss of two carboxyl groups in collision-induced dissociation (CID) were observed.

著者

Nobuyuki Okahashi Shuichi Kawana Junko Iida Hiroshi Shimizu Fumio Matsuda

出版者

The Mass Spectrometry Society of Japan

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

pp.A0073, (Released:2019-08-01)

参考文献数

15

被引用文献数

18

---

Isotope labeling measurements using mass spectrometry can provide informative insights on the metabolic systems of various organisms. The detailed identification of carbon positions included in the fragment ions of dicarboxylic and tricarboxylic acids in central carbon metabolism is needed for precise interpretation of the metabolic states. In this study, fragment ions containing the carbon backbone cleavage of dicarboxylic and tricarboxylic in the Krebs cycle were investigated by using gas chromatography (GC)-electron ionization (EI)-MS and GC-EI-MS/MS. The positions of decarboxylation in the dicarboxylic and tricarboxylic acids were successfully identified by analyses using position-specific 13C-labeled standards prepared by in vitro enzymatic reactions. For example, carboxyl groups of C1 and C6 of trimethylsilyl (TMS)- and tert-butyldimethylsilyl (TBDMS)-derivatized malic and citric acids were primarily cleaved by EI. MS/MS analyses were also performed, and fragment ions of TBDMS-citric and α-ketoglutaric acids (αKG) with the loss of two carboxyl groups in collision-induced dissociation (CID) were observed.

著者

Fumio Matsuda

出版者

日本質量分析学会

雑誌

Mass Spectrometry (ISSN:2187137X)

巻号頁・発行日

vol.5, no.2, pp.S0052-S0052, 2016-11-23 (Released:2016-11-25)

参考文献数

105

被引用文献数

37

---

Metabolomics is a strategy for analysis, and quantification of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scientific research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10–100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and specific instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism.