Hiding Unassigned Peaks in Protein Metrics

In this guide, I’ll show you how I modified the default Javascript Label Script in Protein Metrics to hide annotations for unassigned peaks in deconvoluted mass spectra—a task I managed to do with no prior Javascript knowledge. In Protein Metrics’ Intact Workflows, you can customize the annotations on deconvoluted mass plots using Label Scripts. These are Javascript snippets that control what information is displayed for each peak.

I wanted to declutter my deconvoluted mass spectrum by hiding annotations for peaks that weren’t assigned. The default settings show proposed protein names and delta-mass information for unassigned, low relative-intensity peaks (often deconvolution artifacts/noise), even when the proposed assignment is wrong. I asked the Microsoft Copilot for help, and here’s the path that worked.

What I started with

The original Label Script showed both protein and delta mass names whenever either value was present.

• Problem: Unassigned peaks still showed text, cluttering the plot and misleading users.
• Original script:

<script>
  (function () {
    var proteinName = templateFunctionsManager.detectValue('[ProteinAccessionName]').trim();
    var deltaName = templateFunctionsManager.detectValue('[DeltaMassName]').trim();
    if (!proteinName && !deltaName) {
      return '';
    }
    return '[ProteinAccessionName], [DeltaMassName]';
  })();
</script>

Copilot’s key nudge

It pointed me to the built-in scripts under the annotation editor (gear icon → Edit annotations → Load): Intact_MonoMassIfAssigned, Intact_MonoMassIfAssignedAndNamed, and Intact_MonoMassIfNamed.

That was the helpful bit: Intact_MonoMassIfAssigned adds a filter. Despite my lack of Javascript knowledge, I could see that the change required was simply adding this filter to the beginning of the default annotation script.

The simple fix

Add the assigned check and return nothing for everything else:

<script>
  (function () {
    var isValidCandidate = templateFunctionsManager.detectValue('[IsValidCandidate]') == 2;
    if (!isValidCandidate) {
      return '';
    }
    var proteinName = templateFunctionsManager.detectValue('[ProteinAccessionName]').trim();
    var deltaName = templateFunctionsManager.detectValue('[DeltaMassName]').trim();
    if (!proteinName && !deltaName) {
      return '';
    }
    return '[ProteinAccessionName], [DeltaMassName]';
  })();
</script>

• Result: Only assigned peaks show labels; unassigned peaks are hidden.

References

• Protein Metrics Support: Adding Custom Labels to Deconvoluted Mass Plots in the Intact Workflows