Identifying unknown analytes

Injection-level unknowns

If you use Mass Spectrometry, Peaksel can help identifying unknown m/z values. When holding Shift, the mass spectrum will center around the mass that you hover over, and the X-axis will turn into offsets relative to that mass:

As for the possible Adducts, when adding an analyte Peaksel adds some by default. Most of them are unchecked for quantification purposes, but even the unchecked ones are used when identifying possible unknowns. So if you want a different set of adducts to be considered:

  1. In the Edit Analyte dialog open Mass Spec Settings

  2. Click on the ions/fragments

  3. Update ions and neutral gains & losses that you potentially are interested in. You don’t need to check them (if you do, they’ll be part of the Extracted Chromatogram). Peaksel just needs to know the list.

You can apply these settings to all the injections in a batch.

Peaksel gathers all possible ions/neutral fragments from all the analytes within the injection. So if you add a new fragment of interest to just one analyte, this will already allow identifying such unknowns.
When hovering over some m/z, that mass is considered as [M+H]+ and [M-H]- respectively. So the rest of the arithmetics works under the assumption that to get M we need to remove/add 1 H.

Batch-level unknowns

The idea is that on the batch level you build charts and tables that show the unknown analytes and the trends across all the injections in a batch. It’s possible that you’ll find the same unknown repeating in many injections.

See the documentation: Batch-level unknowns.

Configure Common Adducts globally

We’d like to provide a global, per-organization list of adducts that will be used by default in every injection for every analyte.

This feature is on our TODO list, you can expedite it by raising a ticket.

Writing custom scripts to identify unknowns

If you want more control or want to test your own ideas on how to identify analytes from spectra, you can write your own scripts using Peaksel SDK. Use this template script as a starting point: it already fetches the injections and calculates the unknown peaks spectra.

You can supply the information about identified analytes (MF/Structure/EMW) back to Peaksel. And as usually, it will automatically build EICs, integrate the peaks and calculate stats.