Toffee: a highly compressed file format for mass spectrometry
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There is a need for a high performance, open, random IO, compressed file format for representing mass spectrometry data. We introduce Toffee -- a tool developed at ProCan, Children's Medical Research Institute in Sydney -- that produces files slightly smaller than vendor files.
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Toffee: a highly compressed file format for mass spectrometry
- 1. A highly compressed file format for Time of Flight and Orbitrap DIA-MS David Clarke, Akila Seneviratne, Brett Tully @brett_tully
- 2. 2,000 injections per month 20 TB of mzML per month!
- 3. mzML Format 1 GB vendor file ο 10 GB open XML file 70,000 samples ~ 150,000 files 1,500 TB petabytes of data $30,000 /month On-going storage cost in Amazon S3 Toffee Data Format 1 GB vendor file ο 1 GB toffee file 70,000 samples ~ 150,000 files 150 TB terabytes of data $3,000 /month On-going storage cost in Amazon S3 @brett_tully
- 4. @brett_tully In a given spectrum, the spacing of mass over charge is proportional to π π§
- 5. @brett_tully Work done by electric field: ππ = π§π Change in kinetic energy: ΞπΈ π = 1 2 ππ£2 = π π Re-arrange to give time of arrival at detector π‘ = π 2π π π§
- 6. @brett_tully β π π§ π π§ Ξβ π π§ Similar to ResearchGate PDF from Veritomyx (Schneider 2016)
- 7. @brett_tully Raw profile data described by triplets: retention time, mass over charge, intensity As integers, these can be stored as a Compressed Sparse Row matrix in an HDF5 file
- 9. @brett_tully Retention time: lossless Intensity: lossless Mass over charge: <4 ppm MS1 mass error <6 ppm MS2 mass error
- 10. @brett_tully C++ engine / Python library / Docker https://bitbucket.org/cmriprocan/toffee HDF5 ο window by window random access RTree ο efficient spatial searching
- 11. @brett_tully Load a toffee file Load an MS2 window
- 12. @brett_tully
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- 17. @brett_tully Open, efficient β same size as vendor files Near lossless m/z transfer function Presents new opportunities for using raw DIA data Better testing, image-based analysis
- 18. Acknowledgements Co-Directors: Prof. Roger Reddel & Prof. Phil Robinson Pathology: Prof. Rosemary Balleine & team Proteomics: Dr Peter Hains & team Software Engineering: Dr Brett Tully & team Data Science: Dr Qing Zhong & team
- 19. @brett_tully Transfer function to describe π π§ in integer space ππ π§π = πΌ[ππΌππ+πΎ] + π½ 2
- 20. @brett_tully
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