Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time

Miaoshan Lu; Shaowei An; Ruimin Wang; Jinyin Wang; Changbin Yu

doi:10.1186/s12859-021-04490-0

Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time

BMC Bioinformatics. 2022 Jan 12;23(1):35. doi: 10.1186/s12859-021-04490-0.

Authors

Miaoshan Lu^{1

2

3

4}, Shaowei An^{5

6

7

4}, Ruimin Wang^{2

3

7

4}, Jinyin Wang^{1

5

6

4}, Changbin Yu⁸

Affiliations

¹ Zhejiang University, Hangzhou, 310009, Zhejiang Province, China.
² School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
³ Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
⁴ Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China.
⁵ School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
⁶ Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.
⁷ Fudan University, Shanghai, China.
⁸ Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China. yu_lab@sdfmu.edu.cn.

Abstract

Background: With the precision of the mass spectrometry (MS) going higher, the MS file size increases rapidly. Beyond the widely-used open format mzML, near-lossless or lossless compression algorithms and formats emerged in scenarios with different precision requirements. The data precision is often related to the instrument and subsequent processing algorithms. Unlike storage-oriented formats, which focus more on lossless compression rate, computation-oriented formats concentrate as much on decoding speed as the compression rate.

Results: Here we introduce "Aird", an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate. Aird provides a novel compressor called Zlib-Diff-PforDelta (ZDPD) for m/z data. Compared with Zlib only, m/z data size is about 55% lower in Aird average. With the high-speed decoding and encoding performance of the single instruction multiple data technology used in the ZDPD, Aird merely takes 33% decoding time compared with Zlib. We have downloaded seven datasets from ProteomeXchange and Metabolights. They are from different SCIEX, Thermo, and Agilent instruments. Then we convert the raw data into mzML, mgf, and mz5 file formats by MSConvert and compare them with Aird format. Aird uses JavaScript Object Notation for metadata storage. Aird-SDK is written in Java, and AirdPro is a GUI client for vendor file converting written in C#. They are freely available at https://github.com/CSi-Studio/Aird-SDK and https://github.com/CSi-Studio/AirdPro .

Conclusions: With the innovation of MS acquisition mode, MS data characteristics are also constantly changing. New data features can bring more effective compression methods and new index modes to achieve high search performance. The MS data storage mode will also become professional and customized. ZDPD uses multiple MS digital features, and researchers also can use it in other formats like mzML. Aird is designed to become a computing-oriented data format with high scalability, compression rate, and fast decoding speed.

Keywords: Aird; Compressor; DDA; DIA; Mass spectrometry; Metabolomics; Proteomics; ZDPD.

MeSH terms

Algorithms
Data Compression*
Humans
Mass Spectrometry
Software