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Tong J, Lu M, Wang R, An S, Wang J, Wang T, Xie C, Yu C. How Much Storage Precision Can Be Lost: Guidance for Near-Lossless Compression of Untargeted Metabolomics Mass Spectrometry Data. J Proteome Res 2024; 23:1702-1712. [PMID: 38640356 DOI: 10.1021/acs.jproteome.3c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Several lossy compressors have achieved superior compression rates for mass spectrometry (MS) data at the cost of storage precision. Currently, the impacts of precision losses on MS data processing have not been thoroughly evaluated, which is critical for the future development of lossy compressors. We first evaluated different storage precision (32 bit and 64 bit) in lossless mzML files. We then applied 10 truncation transformations to generate precision-lossy files: five relative errors for intensities and five absolute errors for m/z values. MZmine3 and XCMS were used for feature detection and GNPS for compound annotation. Lastly, we compared Precision, Recall, F1 - score, and file sizes between lossy files and lossless files under different conditions. Overall, we revealed that the discrepancy between 32 and 64 bit precision was under 1%. We proposed an absolute m/z error of 10-4 and a relative intensity error of 2 × 10-2, adhering to a 5% error threshold (F1 - scores above 95%). For a stricter 1% error threshold (F1 - scores above 99%), an absolute m/z error of 2 × 10-5 and a relative intensity error of 2 × 10-3 were advised. This guidance aims to help researchers improve lossy compression algorithms and minimize the negative effects of precision losses on downstream data processing.
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Affiliation(s)
- Junjie Tong
- Central Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong, China
- Key Laboratory of Tropical Medicinal Plant Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou 571158, Hainan, China
| | - Miaoshan Lu
- Central Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong, China
| | - Ruimin Wang
- Central Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong, China
- Fudan University, Shanghai 200000, China
- Westlake University, Hangzhou 310024, Zhejiang, China
| | - Shaowei An
- Fudan University, Shanghai 200000, China
- Westlake University, Hangzhou 310024, Zhejiang, China
| | - Jinyin Wang
- Westlake University, Hangzhou 310024, Zhejiang, China
- Zhejiang University, Hangzhou 310009, Zhejiang, China
| | - Tong Wang
- Central Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong, China
| | - Cong Xie
- Central Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong, China
- Key Laboratory of Tropical Medicinal Plant Chemistry of Ministry of Education, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou 571158, Hainan, China
| | - Changbin Yu
- Central Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong, China
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