Data import

Upload MS file

Click the dropdown button Import file and upload MS1, MS/MS files, as shown in the structure below. Click the 1. Check input file button to check the data. After confirming correctness, click the 2. Peak picking button for peak picking. This is a relatively lengthy process, and the progress bar will be displayed in the bottom right corner.

Data cleaning

Data cleaning includes: Overview, Remove noisy features, Remove outliers, Missing value imputation, and Normalization.

Overview

First, upload sample information and set parameters, then Update sample information, click Start, and finally open the Interactive plot button to check for missing sample data.

Open the interactive button, then hover the mouse over the image to see detailed information about the samples in the detailed image.

Remove noisy features

First, adjust the parameters for grouping, samples, and QC missing frequency on the left side, click Find noisy features to identify noisy features, and then click Remove and update to update the data.

Remove outliers

First, adjust the parameters on the left side, click Find outliers to identify outliers, open the Interactive plot, hover the mouse over the outlier sample to view outlier sample information, remove outlier values. Then switch to negative spectrum and repeat the operation, then click Remove and update to update the data.

Missing value imputation

Select the method for missing value imputation, such as: knn, rf, mean, median, zero, mininum, bpca, svdlmpute, ppca, etc., click Start to proceed with imputation.

Data standardization

First, adjust the method for filling missing values on the left side, such as svr, total, mean,median, pqn, loess ppca, etc., click Start normalization to standardize the data. Select PCA color grouping. Then click Visualize to visualize the data before and after normalization. Open the Interactive plot button, and you can see the 3D PCA plot. Hovering the mouse over it allows you to see detailed information about the samples. Finally, click the Export normalized data button to download the normalized data.