mzDB: A File Format Using Multiple Indexing Strategies for the Efficient Analysis of Large LC-MS/MS and SWATH-MS Data Sets *

Abstract

The analysis and management of MS data, especially those generated by data independent MS acquisition, exemplified by SWATH-MS, pose significant challenges for proteomics bioinformatics. The large size and vast amount of information inherent to these data sets need to be properly structured to enable an efficient and straightforward extraction of the signals used to identify specific target peptides. Standard XML based formats are not well suited to large MS data files, for example, those generated by SWATH-MS, and compromise high-throughput data processing and storing.We developed mzDB, an efficient file format for large MS data sets. It relies on the SQLite software library and consists of a standardized and portable server-less single-file database. An optimized 3D indexing approach is adopted, where the LC-MS coordinates (retention time and m/z), along with the precursor m/z for SWATH-MS data, are used to query the database for data extraction.In comparison with XML formats, mzDB saves ϳ25% of storage space and improves access times by a factor of twofold up to even 2000-fold, depending on the particular data access. Similarly, mzDB shows also slightly to significantly lower access times in comparison with other formats like mz5. Both C؉؉ and Java implementations, converting raw or XML formats to mzDB and providing access methods, will be released under permissive license. mzDB can be easily accessed by the SQLite C library and its drivers for all major languages, and browsed with existing dedicated GUIs. The mzDB described here can boost existing mass spectrometry data analysis pipelines, offering unprecedented performance in terms of efficiency, portability, compactness, and flexibility. Molecular & Cellular Proteomics 14: 10.1074/ mcp.O114.039115, 771-781, 2015.

Fast, axis-agnostic, dynamically summarized storage and retrieval for mass spectrometry data

“…Here we compare MzTree to leading MS file formats most like it–mzML, mz5 [ 5 ] and mzDB [ 6 ]–in the arenas of data querying, file conversion time and size on disk. Querying comparisons are of two kinds: random and path.…”

“…Because of axis-agnostic design, MzTree is comparably fast in both m/z- and RT-major queries, where competing methods perform relatively worse than in m/z-major queries (see Fig 5(b) ). MzTree’s improved performance is due to axis-agnostic design, as both mz5 [ 5 ] and mzDB [ 6 ] are optimized for m/z-centric queries.…”

“…Recognizing the limitations of native mzML, the community has developed several storage and retrieval systems for MS data, such as mz5 [ 5 ] and mzDB [ 6 ]. mz5 is a queryable MS data store based on the HDF5 database system and provides faster access than XML-based mzML, but still requires iteration through each relevant scan in order to retrieve the subset of individual points in the requested window.…”

mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements

“…The mzDB format 7 uses an alternative database paradigm, the lightweight SQLite relational database. mzDB’s main mechanism of increasing random read performance is in organizing data in small two-dimensional blocks across multiple consecutive spectra (i.e., along both the m / z and retention time axis), enabling a quick reading of XICs.…”

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

“…Regardless, algorithms are limited to taking slices of the data along the retention time (or spectrum) axis only. In contrast, other attempts such as mzDB [4], mzRTree [5], and mzTree [6], focus on random I/O access through the use of an RTree [7] data structure. This allows the data to be accessed along both the m/z (or chromatogram) axis as well as the retention time axis, at the cost of file size or mass accuracy.…”