mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data
Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These ‘dirty data’ problems increase the difficulty of performing MS analyses beca...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2017-07-01
|
| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/2211-5463.12247 |
| _version_ | 1798018906153025536 |
|---|---|
| author | Geunho Lee Hyun Beom Lee Byung Hwa Jung Hojung Nam |
| author_facet | Geunho Lee Hyun Beom Lee Byung Hwa Jung Hojung Nam |
| author_sort | Geunho Lee |
| collection | DOAJ |
| description | Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These ‘dirty data’ problems increase the difficulty of performing MS analyses because they lead to performance degradation when statistical or machine‐learning tests are applied to the data. Thus, we have developed missing values preprocessor (mvp), an open‐source software for preprocessing data that might include duplicate records and missing values. mvp uses the property of MS data in which identical chemical species present the same or similar values for key identifiers, such as the mass‐to‐charge ratio and intensity signal, and forms cliques via graph theory to process dirty data. We evaluated the validity of the mvp process via quantitative and qualitative analyses and compared the results from a statistical test that analyzed the original and mvp‐applied data. This analysis showed that using mvp reduces problems associated with duplicate records and missing values. We also examined the effects of using unprocessed data in statistical tests and examined the improved statistical test results obtained with data preprocessed using mvp. |
| first_indexed | 2024-04-11T16:32:00Z |
| format | Article |
| id | doaj.art-e15c06d1be4d46a490c815c3cfa9b053 |
| institution | Directory Open Access Journal |
| issn | 2211-5463 |
| language | English |
| last_indexed | 2024-04-11T16:32:00Z |
| publishDate | 2017-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj.art-e15c06d1be4d46a490c815c3cfa9b0532022-12-22T04:14:01ZengWileyFEBS Open Bio2211-54632017-07-01771051105910.1002/2211-5463.12247mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry dataGeunho Lee0Hyun Beom Lee1Byung Hwa Jung2Hojung Nam3School of Electrical Engineering and Computer Science Gwangju Institute of Science and Technology (GIST) KoreaMolecular Recognition Research Center Korea Institute of Science and Technology (KIST) Seoul KoreaMolecular Recognition Research Center Korea Institute of Science and Technology (KIST) Seoul KoreaSchool of Electrical Engineering and Computer Science Gwangju Institute of Science and Technology (GIST) KoreaMass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These ‘dirty data’ problems increase the difficulty of performing MS analyses because they lead to performance degradation when statistical or machine‐learning tests are applied to the data. Thus, we have developed missing values preprocessor (mvp), an open‐source software for preprocessing data that might include duplicate records and missing values. mvp uses the property of MS data in which identical chemical species present the same or similar values for key identifiers, such as the mass‐to‐charge ratio and intensity signal, and forms cliques via graph theory to process dirty data. We evaluated the validity of the mvp process via quantitative and qualitative analyses and compared the results from a statistical test that analyzed the original and mvp‐applied data. This analysis showed that using mvp reduces problems associated with duplicate records and missing values. We also examined the effects of using unprocessed data in statistical tests and examined the improved statistical test results obtained with data preprocessed using mvp.https://doi.org/10.1002/2211-5463.12247dirty dataduplicate recordmass spectrometrymissing valueMS data preprocessorR package |
| spellingShingle | Geunho Lee Hyun Beom Lee Byung Hwa Jung Hojung Nam mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data FEBS Open Bio dirty data duplicate record mass spectrometry missing value MS data preprocessor R package |
| title | mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
| title_full | mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
| title_fullStr | mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
| title_full_unstemmed | mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
| title_short | mvp – an open‐source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
| title_sort | mvp an open source preprocessor for cleaning duplicate records and missing values in mass spectrometry data |
| topic | dirty data duplicate record mass spectrometry missing value MS data preprocessor R package |
| url | https://doi.org/10.1002/2211-5463.12247 |
| work_keys_str_mv | AT geunholee mvpanopensourcepreprocessorforcleaningduplicaterecordsandmissingvaluesinmassspectrometrydata AT hyunbeomlee mvpanopensourcepreprocessorforcleaningduplicaterecordsandmissingvaluesinmassspectrometrydata AT byunghwajung mvpanopensourcepreprocessorforcleaningduplicaterecordsandmissingvaluesinmassspectrometrydata AT hojungnam mvpanopensourcepreprocessorforcleaningduplicaterecordsandmissingvaluesinmassspectrometrydata |