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shuzhao-li-lab / asari

asari, metabolomics data preprocessing
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How can we get MSII merged from all samples mgf file output (like xcms) and can also related to precursor in asari ? #93

Open YUANMENG-1 opened 2 months ago

YUANMENG-1 commented 2 months ago

How can we get MSII merged from all samples mgf file output (like xcms) and can also related to precursor in asari ?

jmmitc06 commented 2 months ago

Currently the Asari feature table is only for ions detected in MS1 only.

The issue of outputting the MS2 data in mgf or other format is in the to-do list for future versions of Asari or another tool in the Asari ecosystem. In the meantime, you can work with DDA data using the pcpfm pipeline based on Asari: https://github.com/shuzhao-li-lab/PythonCentricPipelineForMetabolomics.

YUANMENG-1 commented 2 months ago

I've learned the complete pipeline you mentioned several times before. However, when directly processing the input mzML files, the output includes annotated results, but it doesn't have a merged MGF output like XCMS does.

For instance, if I want to use the MSI quantification table generated by Asari and annotate it with another pipeline, it cannot be done (because Asari or PCPFM cannot directly output MSII MGF files)?

jmmitc06 commented 2 months ago

True, neither tool outputs the MS2 data in mgf format. For the time being though, the empirical compounds generated by PCPFM will have the MS2 spectra associated with them in the JSON files. From those data, it should be possible to convert them to mgf. However, any MS2 spectra that could not be mapped to a feature will be excluded.

Ill have to think about how best to implement this and where. For instance, should it be in Asari or the pipeline and how should mutliple MS2 spectra be combined when they represent the same ion.

On Thu, Jun 27, 2024, 9:47 PM Circle Dram 1 @.***> wrote:

I've learned the complete pipeline you mentioned several times before. However, when directly processing the input mzML files, the output includes annotated results, but it doesn't have a merged MGF output like XCMS does.

For instance, if I want to use the first-level quantification table generated by Asari and annotate it with another pipeline, it cannot be done (because Asari or PCPFM cannot output second-level MGF files)?

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