We’re looking for testers for our updated end-to-end protocol on MetaboAnalyst 6.0. The protocol is published on (protocols.io or dropbox)
What the protocol covers
The protocols provide step-by-step instructions on how to use MetaboAnalyst 6.0 for exposomics data analysis, including: LC-MS/MS spectra processing and compound identification (Stage 1); exposomics data processing and exploratory analysis (Stage 2); dose-response modeling to study metabolic responses to exposure levels (Stage 3); and leveraging known genetic associations for causal inference (Stage 4). We demonstrate Stages 1-3 using data from a recent blood exposomics study concerning electronic waste exposure. Stage 4 is illustrated through an investigation of the potential causal link between L-Isoleucine and type 2 diabetes. Stage 1 may take approximately two hours to complete depending on server load, and the remaining stages may be executed in a total of approximately 90 minutes.
Input Data:
Stages 1 - 3 utilize a subset of an exposomics dataset derived from electronic waste (e-waste) workers. LC-MS1 and MS2 spectra were acquired using an Q-Exactive Orbitrap system. The metadata table contains blood concentration levels of various heavy metals, including cadmium (Cd), lanthanum (La), and lead (Pb), along with age, body mass index (BMI), smoking status, and alcohol consumption. No input file is required for Stage 4.
● Stage 1: Exposomics raw spectra processing and compound annotation:
https://www.xialab.ca/api/download/metaboanalyst/NP_exposome_raw.zip
This demo dataset comprises a subset of LC-MS spectra of whole blood samples from 10 e-waste workers and 6 individuals who served as controls. Users can optionally download the complete LC-MS spectra from 100 e-waste workers and 6 QC samples. Three DDA-MS2 files, acquired from the pooled QC samples, were included for compound identification.
● Stage 2: Data processing and exploratory data analysis
https://www.xialab.ca/api/download/metaboanalyst/ewaste_data_QC.csv
https://www.xialab.ca/api/download/metaboanalyst/ewaste_metadata.csv
This is a subset of LC-MS peak intensity data from the whole blood samples of individuals working in e-waste recycling sites. The “ewaste_data_QC.csv” contains 100 samples including 6 QCs. Its associated metadata is “ewaste_metadata.csv”. The primary exposure of interest is “BCd_group” describing categorical blood concentration level of cadmium (low/medium/high).
● Stage 3: Dose response analysis:
https://www.xialab.ca/api/download/metaboanalyst/ewaste_data.csv
https://www.xialab.ca/api/download/metaboanalyst/ewaste_metadata_dose.csv
The “ewaste_data_dose.csv” has gone through data filtering and missing values imputation already, with QCs samples removed. Its associated metadata is “ewaste_metadata_dose.csv”. The primary exposure of interest is “BCd” describing the blood cadmium concentrations.
● No input file is required for Stage 4.
What we need from you
Please reply in this thread (or DM @xia.lab if you’d rather share privately) with:
- Which stage(s) you ran
- OS / browser
- The step number where anything failed, plus the error text or a screenshot
- Approximate time per stage