Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files

Abstract

Mass spectrometers typically output data in proprietary binary formats. While converter suites and standardized XML formats have been developed in response, these conversion steps come with non-negligible computational time and storage space overhead. As a result, simple, everyday data inspection tasks are often beyond the skills of the mass spectrometrist, who is unable to freely access the acquired data. We therefore here describe the unthermo library for convenient, platform-independent access to Thermo Scientific RAW files and the associated online playground to transform small and easily understandable scriptlets into executable programs for end-users. By fostering the provision of code examples and snippet exchange, the interested mass spectrometrist or researcher can use this playground to quickly assemble custom scripts for their particular purpose. In this way, the data in these RAW files can be mined much more readily and directly by the user, and fast, automated raw data extraction or analysis can finally become part of the daily routine of the mass spectrometrist.

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

“…An important driver for this bias has been the lack of cross-platform libraries to access instrument output data files (RAW files) from major instrument providers . Several approaches have been devised to overcome this challenge, including the use of dedicated Windows machines in workflows for conversion to RAW data to standard file formats such as mzML, the encapsulation of Windows tools such as ReAdW and msconvert into WineHQ () to make these tools Linux-compatible, and even the creation of reverse-engineered RAW file readers …”

“…9 Several approaches have been devised to overcome this challenge, including the use of dedicated Windows machines in workflows 10 for conversion to RAW data to standard file formats such as mzML, 11 the encapsulation of Windows tools such as ReAdW 12 and msconvert 13 into WineHQ (http:// tools.proteomecenter.org/wiki/index.php?title=Msconvert_ Wine) to make these tools Linux-compatible, and even the creation of reverse-engineered RAW file readers. 14 An important breakthrough was achieved in 2016 when Thermo Scientific released the first cross-platform application programming interface (API) that enables access to Thermo RAW files from all their instruments on all commonly used operating systems (e.g., Linux/Unix, Mac OX, or Microsoft Windows). Importantly, this provides the enticing possibility to move proteomics into Linux/UNIX environments, including scalable clusters and cloud environments.…”

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

“…An important driver for this bias has been the lack of cross-platform libraries to access instrument output data files (RAW files) from major instrument providers (10). Several approaches have been devised to overcome this challenge, including the use of dedicated Windows machines in workflows (11) for conversion to RAW data to standard file formats such as mzML (12), the encapsulation of Windows tools such as ReAdW (13) and msconvert (14) into WineHQ (http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine) to make these tools Linux-compatible, and even the creation of reverse-engineered RAW file readers (15).…”

Update on the moFF Algorithm for Label-Free Quantitative Proteomics

“…The access library for Thermo raw files was also updated. In the original version of moFF, the extraction of data from Thermo raw files was supported by the Unthermo library, 7 which allows full accessibility to these raw files on both Microsoft Windows and Linux environments. Whereas the performance of the Unthermo library is quite good, it is based on reverse engineering of the Thermo format, which means that more recent Thermo instruments, with updated raw file formats, were not fully supported.…”