Issue with Data Processing in MetaboAnalyst 6.0 – Seeking Guidance

[jeff.xia]

Adapted from an email excerpt

… I am encountering issues with data processing and alignment. I have attached screenshots for your reference.

I have converted my raw files to mzML format in centroid mode for upload and have ensured that the I see detectable peaks through MZmine, but I am uncertain about the best peak alignment parameters given that my dataset contains a limited number of detectable peaks. Additionally, I am unsure about the optimal m/z and RT weight settings for peak alignment to improve feature detection.

I would greatly appreciate any guidance you could provide on resolving this issue, particularly regarding preprocessing recommendations, and alignment settings best suited for MetaboAnalyst 6.0.

[jeff.xia]

Since there is no detailed information provided for troubleshooting request, here are some comments based on the screenshots

1. The HPLC-Orbitrap is a high resolution instrument, and you should NOT use MatchedFiltered which is mainly designed for low-resolution instrument.

2. For LC-Orbitrap, our tool can perform automated parameter optimization - just leave the “centWave-auto” (default)

3. If you want to do manual tuning, start from the default parameters for “centWave-manual” assuming you are very familiar with the instument & experiment

You can read these two publications for more detail:

1. Algorithm for Parameter Optimization: MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics.
2. Nature Protocols: Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

[gourab]

There is still an issue with peak picking. Can you please provide some alternate suggestions.