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update RAW file tools page #261

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Jan 6, 2025
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update RAW file tools page #261

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11 changes: 7 additions & 4 deletions _posts/2023-01-04-Reading-ThermoFischer-XCaliber-RAW-Files.md
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Expand Up @@ -13,7 +13,7 @@ _[Sarah Maurer](https://directory.ccsu.edu/person/sarah-maurer) asks: I'm using

I found a [thorough (70 minute) YouTube video describining how to do this](https://www.youtube.com/watch?v=Aj5rd6p1Q1s)

The video mentions [mzXML](http://tools.proteomecenter.org/wiki/index.php?title=Formats%3AmzXML#Thermo.2FXCalibur)
The video mentions [mzXML](http://tools.proteomecenter.org/wiki/index.php?title=Formats%3AmzXML#Thermo.2FXCalibur)...

But instead prefers to use Thermo's [MSFileReader software (reference manual)](https://tools.thermofisher.com/content/sfs/manuals/Man-XCALI-97542-MSFileReader-30-Ref-ManXCALI97542-A-EN.pdf) There's a download link provided in the youtube video comments, but you need a Thermo registration.

Expand Down Expand Up @@ -54,6 +54,9 @@ Note that RawTools appears to be a standalone tool with a GUI, so it can probabl

# Continued readings and gleanings

- (20 Jan 2023) Haas CP, Lübbesmeyer M, Jin EH, McDonald MA, Koscher BA, Guimond N, et al. Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening. ChemRxiv 2022. [doi:10.26434/chemrxiv-2022-0pv2d](https://dx.doi.org/10.26434/chemrxiv-2022-0pv2d) --- describes a python library for reading and processing and extracting information from a variety of HPLC machines/vendors. Subsequently published as MoccA in [ACS Central Sci 2023](https://pubs.acs.org/doi/10.1021/acscentsci.2c01042)
- (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 [ChemRxiv 2024](https://dx.doi.org/10.26434/chemrxiv-2024-nmnzp)---upgrade to MoccA (consider this the latest version)
- (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.
- (20 Jan 2023) Haas CP, Lübbesmeyer M, Jin EH, McDonald MA, Koscher BA, Guimond N, et al. Open-Source Chromatographic Data Analysis for Reaction Optimization and Screening. ChemRxiv 2022. [doi:10.26434/chemrxiv-2022-0pv2d](https://dx.doi.org/10.26434/chemrxiv-2022-0pv2d) --- describes a python library for reading and processing and extracting information from a variety of HPLC machines/vendors. Subsequently published as MoccA in [ACS Central Sci 2023](https://pubs.acs.org/doi/10.1021/acscentsci.2c01042). **Limitation: Only the UV chromatogram, not mass spec**
- (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)
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