Hello,
This issue is not related to a bug report or a feature request, but rather a personal question. I’m not entirely sure if it’s appropriate to raise this as a GitHub issue, but I’m struggling to resolve my problem and was hoping to get some assistance from the authors.
I am researching the microbiome, and this is my first time working on metabolomics analysis. I have HPLC-MS data and analysed it following the instructions of pcpfm suggested by the authors.
Here is my question.
The output generated from level 4 annotation seems to be the empCpds.json file but I am unsure about the purpose of level 4 annotation. I initially thought it might provide more precise information by matching metabolites to HMDB, similar to the pre-annotation results in the Feature_annotation.tsv file. However, since my data is MS1-only, it seems that matching will rely solely on m/z and retention time. Could you explain what additional information can be obtained specifically through level 4 annotation?
Hello, This issue is not related to a bug report or a feature request, but rather a personal question. I’m not entirely sure if it’s appropriate to raise this as a GitHub issue, but I’m struggling to resolve my problem and was hoping to get some assistance from the authors. I am researching the microbiome, and this is my first time working on metabolomics analysis. I have HPLC-MS data and analysed it following the instructions of pcpfm suggested by the authors.
Here is my question. The output generated from level 4 annotation seems to be the empCpds.json file but I am unsure about the purpose of level 4 annotation. I initially thought it might provide more precise information by matching metabolites to HMDB, similar to the pre-annotation results in the Feature_annotation.tsv file. However, since my data is MS1-only, it seems that matching will rely solely on m/z and retention time. Could you explain what additional information can be obtained specifically through level 4 annotation?
I appreciate your help in advance.