Analyze Your Data: Multivariate Comparisons

Example Use Cases

  • Check your data against public data by comparing the chemicals annotated in your samples, analyzed by principal components analysis (PCA), versus chemicals annotated in similar chemicals viz. does my urine data look like urine data collected by others?
  • Explore if interesting differences exist in your data compared to the public data at the highest-level. For example, does urine from my cohort of diabetes subjects looks similar to other data from different diseases?


The common denominator of all mass spectrometry data is the chemicals detected. In spite of the numerious confounders (e.g. instrument type, user, year, and extraction method), the chemicals that are detected and annotated from samples is the ground truth of any experiment. The MS2 data, specifically product ion scans, are extracted from the public data and analyzed de novo in GNPS, and in doing so provide the chemical annotations based on library spectral matching for each file. Principal components analysis (PCA) was used to analyze the results in an unsupervised manner. The results are plotted using Emperor visualization which provides interactive plotting capabilities to explore the data via a PCA score plot. Using the task ID from the GNPS job previously run, your data will be projected on to a precalculated PCA of all ReDU data.


  1. Log into a GNPS account and perfrom a library search. Once the job has finished running, make note of the task ID found in the URL.

    Find Task ID

  2. Navigate to the ReDU-MS2 homepage and click "Compare Your Data to Public Data via Multivariate Analysis" under the Analyze Your Data Section.

    Homepage Image Public Multivariate

  3. Enter the task ID of the previously run GNPS job into the bar, and click the "Create PCA".

    Enter Task ID

  4. For cababilities of data exploration tool, please view Global Multivariate Analysis Documentation