Toffee – a highly efficient, lossless file format for DIA-MS

Abstract

The closed nature of vendor file formats in mass spectrometry is a significant barrier to progress in developing robust bioinformatics software. In response, the community has developed the open mzML format, implemented in XML and based on controlled vocabularies [1]. Widely adopted, mzML is an important step forward; however, it suffers from two challenges that are particularly apparent as the field moves to high-throughput proteomics: a) large increase in file size -and corresponding increase in CPU time devoted to I/O, and b) a largely sequential I/O access pattern. Described here is 'toffee', an open, random I/O format backed by HDF5, with lossless compression that gives file sizes similar to the original vendor format and can be reconverted back to mzML without penalty. In addition to the file format, there are C++ and python libraries for creating and accessing the file format, along with a wrapper around OpenSWATH [2] that enables SWATH-MS data to be analyzed with standard algorithms. Using this library, the files can be accessed in the same manner as the Vendor file (or mzML) in a scan-by-scan manner; however, by accepting a degree of mass approximation (<5 parts per million) toffee enables data to be extracted as a two-dimensional slice analogous to an image, and thus amenable to deep-learning based peptide identification strategies. Documentation and examples are available at https://toffee.readthedocs.io, and all code is MIT licensed at https://bitbucket.org/cmriprocan/toffee.There are many previous attempts at new and open formats for mass spectrometry. Some, such as mzML [1], and mz5 [3], aim to be archival formats that faithfully adopt the HUPO PSI guidelines. * https://cmri.org.au/procan; https://brett-tully.id.au