MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography
Recent small-angle X-ray scattering (SAXS) for biological macromolecules (BioSAXS) is generally combined with size-exclusion chromatography (SEC-SAXS) at synchrotron facilities worldwide. For SEC-SAXS analysis, the final scattering profile for the target molecule is calculated from a large volume of...
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2023-02-01
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| Series: | Biophysics and Physicobiology |
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| Online Access: | https://doi.org/10.2142/biophysico.bppb-v20.0001 |
| _version_ | 1828034763398578176 |
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| author | Kento Yonezawa Masatsuyo Takahashi Keiko Yatabe Yasuko Nagatani Nobutaka Shimizu |
| author_facet | Kento Yonezawa Masatsuyo Takahashi Keiko Yatabe Yasuko Nagatani Nobutaka Shimizu |
| author_sort | Kento Yonezawa |
| collection | DOAJ |
| description | Recent small-angle X-ray scattering (SAXS) for biological macromolecules (BioSAXS) is generally combined with size-exclusion chromatography (SEC-SAXS) at synchrotron facilities worldwide. For SEC-SAXS analysis, the final scattering profile for the target molecule is calculated from a large volume of continuously collected data. It would be ideal to automate this process; however, several complex problems exist regarding data measurement and analysis that have prevented automation. Here, we developed the analytical software MOLASS (Matrix Optimization with Low-rank factorization for Automated analysis of SEC-SAXS) to automatically calculate the final scattering profiles for solution structure analysis of target molecules. In this paper, the strategies for automatic analysis of SEC-SAXS data are described, including correction of baseline-drift using a low percentile method, optimization of peak decompositions composed of multiple scattering components using modified Gaussian fitting against the chromatogram, and rank determination for extrapolation to infinite dilution. In order to easily calculate each scattering component, the Moore-Penrose pseudo-inverse matrix is adopted as a basic calculation. Furthermore, this analysis method, in combination with UV–visible spectroscopy, led to better results in terms of accuracy in peak decomposition. Therefore, MOLASS will be able to smoothly suggest to users an accurate scattering profile for the subsequent structural analysis. |
| first_indexed | 2024-04-10T15:38:19Z |
| format | Article |
| id | doaj.art-f537fdbce89044659691093acb8b4109 |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-04-10T15:38:19Z |
| publishDate | 2023-02-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-f537fdbce89044659691093acb8b41092023-02-13T01:33:44ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792023-02-012010.2142/biophysico.bppb-v20.0001MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatographyKento Yonezawa0Masatsuyo Takahashi1Keiko Yatabe2Yasuko Nagatani3Nobutaka Shimizu4Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, JapanStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, JapanStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, JapanPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, JapanStructural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, JapanRecent small-angle X-ray scattering (SAXS) for biological macromolecules (BioSAXS) is generally combined with size-exclusion chromatography (SEC-SAXS) at synchrotron facilities worldwide. For SEC-SAXS analysis, the final scattering profile for the target molecule is calculated from a large volume of continuously collected data. It would be ideal to automate this process; however, several complex problems exist regarding data measurement and analysis that have prevented automation. Here, we developed the analytical software MOLASS (Matrix Optimization with Low-rank factorization for Automated analysis of SEC-SAXS) to automatically calculate the final scattering profiles for solution structure analysis of target molecules. In this paper, the strategies for automatic analysis of SEC-SAXS data are described, including correction of baseline-drift using a low percentile method, optimization of peak decompositions composed of multiple scattering components using modified Gaussian fitting against the chromatogram, and rank determination for extrapolation to infinite dilution. In order to easily calculate each scattering component, the Moore-Penrose pseudo-inverse matrix is adopted as a basic calculation. Furthermore, this analysis method, in combination with UV–visible spectroscopy, led to better results in terms of accuracy in peak decomposition. Therefore, MOLASS will be able to smoothly suggest to users an accurate scattering profile for the subsequent structural analysis.https://doi.org/10.2142/biophysico.bppb-v20.0001sec-saxsautomatic data analysisconcentration dependencemoore-penrose pseudo-inverse matrix |
| spellingShingle | Kento Yonezawa Masatsuyo Takahashi Keiko Yatabe Yasuko Nagatani Nobutaka Shimizu MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography Biophysics and Physicobiology sec-saxs automatic data analysis concentration dependence moore-penrose pseudo-inverse matrix |
| title | MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography |
| title_full | MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography |
| title_fullStr | MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography |
| title_full_unstemmed | MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography |
| title_short | MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography |
| title_sort | molass software for automatic processing of matrix data obtained from small angle x ray scattering and uv visible spectroscopy combined with size exclusion chromatography |
| topic | sec-saxs automatic data analysis concentration dependence moore-penrose pseudo-inverse matrix |
| url | https://doi.org/10.2142/biophysico.bppb-v20.0001 |
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