Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ThermoRawParser, ProteoWizard, PythoMS #262

Merged
merged 1 commit into from
Jan 6, 2025
Merged

ThermoRawParser, ProteoWizard, PythoMS #262

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions _posts/2023-01-04-Reading-ThermoFischer-XCaliber-RAW-Files.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@ Note that RawTools appears to be a standalone tool with a GUI, so it can probabl

[RawFileReader](https://github.com/thermofisherlsms/RawFileReader) is a group of .Net Assemblies written in C# used to read Thermo Scientific RAW files. The assemblies can be used to read RAW files on Windows, Linux, and MacOS using C# or other languages that can acces a .Net assembly.

[ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser) (see also [paper](https://pubmed.ncbi.nlm.nih.gov/31755270/)) is a 3rd party command line wrapper around RawFileReader


# Other resources found in my readings

Expand All @@ -58,5 +60,6 @@ Note that RawTools appears to be a standalone tool with a GUI, so it can probabl
- (06 Jan 2024) Hillenbrand et al, Automated Processing of Chromatograms: A comprehensive Python Package with GUI for Intelligent Peak Identification and Deconvolution in Chemical Reaction Analysis [Digital Discovery 2024](https://dx.doi.org/10.1039/D4DD00214H)---upgrade to MoccA (consider this the latest version) **Limitation: Only the UV chromatogram, not mass spec**
- (06 Jan 2024) McDonald et al, "Calibration-free reaction yield quantification by HPLC with a machine-learning model of extinction coefficients" [Chem Sci 2024] (https://doi.org/10.1039/D4SC01881H) --- perhaps not strictly necessary, but useful task to remember.
- (06 Jan 2024) It seems that many packages for working with mass spec in python like [Mass-Suite](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00741-9) and [pyOpenMS](https://github.com/OpenMS/pyopenms-docs) use mzML file formats, not .raw.
- [PythoMS](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00055) and [github](https://github.com/larsyunker/PythoMS) seems to support converting from RAW to mzML as well as doing processing, but hasn't been maintained since 2020
- [ProteoWizard](https://proteowizard.sourceforge.io) is another recommend tool for converting from RAW to mzML. [youtube video tutorial](https://www.youtube.com/watch?v=sudY7UtkMQg)
- [PythoMS](https://pubs.acs.org/doi/10.1021/acs.jcim.9b00055) and [github](https://github.com/larsyunker/PythoMS) seems to support converting from RAW to mzML as well as doing processing, but hasn't been maintained since 2020. Also, [under the hood](https://github.com/larsyunker/PythoMS/blob/master/pythoms/mzml.py) it is just calling [ProteoWizard](https://proteowizard.sourceforge.io) to call the conversion, and only works under windows
- [ProteoWizard](https://proteowizard.sourceforge.io) is another recommend tool for converting from RAW to mzML. [youtube video tutorial](https://www.youtube.com/watch?v=sudY7UtkMQg). But appears to only exist for Windows and maybe Linux.
- [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser) (see also [paper](https://pubmed.ncbi.nlm.nih.gov/31755270/)) is a wrapper around thermo's RawFileReader framework (see section above)
Loading