### DDA and DIA data for ViMMS 2.0

This dataset contains the mzML  files produced from liquid chromatography tandem mass spectrometry (LC-MS/MS) measurements of 6 beer samples. Data acquisition was performed using newly developed Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) controllers in the ViMMS 2.0 framework. For DDA this includes the fullscan, Top-N and all methods introduced in the TopNEXt paper. For DIA this includes the AIF and SWATH methods used for the DDA vs. DIA comparison paper.

Please extract the compressed mzML.zip file. This contains the following folders. Files 1a - 1d are used for validation for the DDA vs. DIA comparison paper. Files 3b are used to generate the Multi-injection spectral library for the DDA vs. DIA paper. All other files are used for the multi-sample (TopNEXt) paper.

1. `results_1` contains the mzML files generated by the following ViMMS controllers:
    a. Fullscan                  (6 beers x 1 replicate)
    b. Top-N                     (6 beers x 1 replicate)
    c. AIF                       (6 beers x 1 replicate)
    d. SWATH                     (6 beers x 1 replicate)

2. `results_2` contains the mzML files generated by the following ViMMS controllers:
    a. Fullscan                  (6 beers x 1 replicate)
    b. Intensity Non-overlap     (6 beers x 4 replicates)
    c. Non-overlap               (6 beers x 4 replicates)
    d. Top-N Exclusion           (6 beers x 4 replicates)

3. `results_3` contains the mzML files generated by the following ViMMS controllers:
    a. Fullscan                  (6 beers x 1 replicate)
    b. Intensity Non-overlap     (6 beers x 10 replicates)
    c. Non-overlap               (1 beer x 10 replicates)
    d. Top-N Exclusion           (1 beer x 10 replicates)

4. `results_4` contains the mzML files generated by the following ViMMS controllers:
    a. Fullscan                  (6 beers x 1 replicate)
    b. Hard RoI Exclusion        (6 beers x 4 replicates)
    c. Intensity RoI Exclusi     (6 beers x 4 replicates)
    d. Top-N                     (6 beers x 4 replicates)