LC-MS metabolomics · processing · annotation

IPA Studio

Process and annotate untargeted LC-MS data in the browser, in four stages: upload your raw files, turn them into a feature set with XCMS Runner, annotate it in IPA Studio with the Integrated Probabilistic Annotation pipeline, and download the results.

You can also explore the software's capabilities without uploading any data. Sample folders are included for this purpose.

You'll get a fresh workspace.

Work through the stages in order: open a stage, finish there, come back to this page, then open the next. How it works

1 · Upload

Upload files

Put your raw files and sample sheet into your workspace.

Centroided mzML, mzXML, mzData or CDF files, plus one .csv or .tsv sample sheet. Wait until each file has finished, then come back here.

2 · Process

XCMS Runner

Turns your raw files into a feature table.

Peak picking, retention-time alignment, grouping, gap filling and CAMERA, with MS/MS spectra linked to features. Use your upload folder as the project folder, start the run, wait for it to finish, then come back here.

3 · Annotate

IPA Studio

Copies your latest XCMS Runner results into IPA Studio and opens it to annotate them.

Isotope mapping, adduct expansion and the Gibbs sampler, with the evidence for every feature. Without a finished run it opens with sample data. After a new XCMS Runner run, press Launch again to load it.

4 · Download

Download results

Download your results.

XCMS Runner's output and IPA Studio's files, including anything you saved there.

How it works

Each button opens one stage. When you have finished there, come back to this page (your browser's Back button, or the ← All stages link on the upload and download pages) and press the next button. All four stages use the same workspace, so your files carry from one stage to the next.

  1. Upload files. Drop your raw files and sample sheet on the upload page and wait until each one says it has finished. The page shows the folder to use in XCMS Runner, with a Copy button. Back.
  2. Launch XCMS Runner. Paste that folder as the project folder and click use this folder: the raw data, sample sheet and output fields fill in. Start the run and wait until it has finished. Back.
  3. Launch IPA Studio. At this moment your latest finished XCMS Runner results are copied into IPA Studio, which then opens on them. If the run is still going or failed, you are told so and can open IPA Studio with its previous files instead. After a new XCMS Runner run, come back and press Launch IPA Studio again; reloading IPA Studio alone keeps the old results. Back.
  4. Download results. Get XCMS Runner's output and IPA Studio's files, including anything you saved there.

Inside IPA Studio

Run the pipeline

Step through isotope mapping, adduct expansion, first-round annotation and the Gibbs sampler, checking the output at each stage.

Inspect every feature

Extracted ion chromatograms by sample group, pcgroup pseudospectra and candidate structures side by side.

Compare MS/MS spectra

Check measured fragmentation against reference spectra, and see which features may be in-source fragments.

Follow the evidence

See the adduct and fragment network that links features and shapes each posterior probability.

About this demo