Combined wiff files or multiple injections in one wiff file
What happens when you import the data in WebIDQ, the wiff files are converted into .mzML data files. Since mzML doesn’t support combined spectra, they are split into two separate files. WebIDQ should always take the most recent file imported, so this will be the last injection as the wiff spectra are organized by time.
However, if you want to be extra certain of which file is uploaded, you can convert the files before uploading to WebIDQ using the msconvert tool:
Using these settings:
This will create separate .mzML files for each injection ordered by time labeled: (1), (2), etc. Then you can just upload the files you want to include.