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shuzhao-li-lab / asari

asari, metabolomics data preprocessing
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Earnestly request validation form for SZ22dataset #103

Open YUANMENG-1 opened 1 week ago

YUANMENG-1 commented 1 week ago

Table S2. Manually verified true features in credentialed E. coli samples. I want to use the data set of your article for other verification. It seems that only the verification form of SZ22 has not been made public at present. If it can be made public, can I get it from you

shuzhao-li commented 1 week ago

I think it can be recreated by following the published notebook: https://github.com/shuzhao-li-lab/data/blob/main/notebooks/TrueDetection_credentialed_ecoli.ipynb

If you look for isotope labeling data to use, several were released with https://pubs.acs.org/doi/10.1021/jasms.4c00175 I.e., zenodo, DOI: 10.5281/zenodo.11068202. Metabolomics Workbench (metabolomicsworkbench.org) as study ST003387.

YUANMENG-1 commented 1 week ago

I'm sorry to bother you again, but we need 74 features of 6 ecoil samples (3 C13, 3 C12) that you have verified.

image

A subset of E. coli metabolites were labeled by 13C isotope during the cell culture, and they were selected by elevated 13C/ 91 12C ratio and manual inspection of raw data (Table S2). Asari successfully detected 71 out of 74 of these credentialed features (Figure 2E). Two of the missed features were of low intensity and one of incomplete elution peak. These data indicate that the feature detection by asari is at least on par with XCMS performance.

YUANMENG-1 commented 1 week ago

I'm sorry to bother you again, but we need 74 features of 6 ecoil samples (3 C13, 3 C12) that you have verified. image

A subset of E. coli metabolites were labeled by 13C isotope during the cell culture, and they were selected by elevated 13C/ 91 12C ratio and manual inspection of raw data (Table S2). Asari successfully detected 71 out of 74 of these credentialed features (Figure 2E). Two of the missed features were of low intensity and one of incomplete elution peak. These data indicate that the feature detection by asari is at least on par with XCMS performance.

shuzhao-li commented 1 week ago

You are looking at an obsolete version on Biorxiv? The published version is here (open access): https://www.nature.com/articles/s41467-023-39889-1

YUANMENG-1 commented 1 week ago

You are looking at an obsolete version on Biorxiv? The published version is here (open access): https://www.nature.com/articles/s41467-023-39889-1

Sorry, I looked at the published version first, but since no vertified tables were found for this Ecoli data, I tried to find some information from the preprint，Could I find the "71 out of 74 of these credentialed features" ? Even in source data I can't.