Data-dependent acquisition (DDA) with Product Ion Scan

Tandem instruments like Orbitrap and QTOF can run a Data-dependent Acquisition (DDA) with Product Ion Scan (aka Product Scan). If you’re not familiar with the workflow, read Mass Spectrometry: types, modes, data processing.

There are problems that we had to address when dealing with DDA + PIS:

  1. Typical mass spec Scans show only the analyte masses, while Product Ion Scan deals both with precursors and products. How do we measure a Total chromatogram for such detector? Two points on a chromatogram would represent completely different measurements. That’s why we split DDA into 2 runs: Scan and ProductScan.

  2. DDAs are often set up to run Product Ion Scan for the highest precursors found in a Scan. So the precursors can vary from scan to scan. Then how do we extract a chromatogram from such Product Ion Scan if it represents many different analytes? For this reason:

    1. During extraction of Product Scan, only points where precursor matches Analyte’s mass are used for the new chromatogram. The rest of the points are skipped. So 2 EICs have different number of points and don’t share the Retention Time.

    2. Each EIC is shown on a separate card

Note, that the total Product Scan chromatogram still contains all the points for all precursors. It usually has a seesaw look because different precursors usually have very different intensities.

How precursor ions are chosen for Product Ion Scan?

So during extraction, for each Analyte we select only points where precursor matches the Analyte’s m/z. But which m/z? The analytes usually have many ions.

When an Analyte is registered, Peaksel calculates the ion distribution and chooses the most abundant ion (EMW) to be the precursor. But it’s possible to change this manually:

  • You can either select a different m/z

  • Or select multiple ions. In which case the EIC may contain more points because during DDA more than 1 precursor could’ve been selected for the Product Ion Scan.

How the intensity of Product Ion Scan EIC is calculated?

Currently, Peaksel sums up all the fragments of the precursor when EIC is generated. You can’t select Quantifier fragments.

Neither you can select Qualifier fragments and match with the libraries are used. This is going to change in the future, let us know if you’re interested in the library search for targeted and untargeted analyses.