Getting Started with Scaffold DIA Part 2

The following is a continuation of Getting Started with Scaffold DIA Part 1. In that document, library selection, installing Scaffold DIA and load data was covered. This document introduces what data can be found in the Scaffold DIA user interface. 

Viewing Results

The Scaffold DIA user interface is structured very similarly to our other programs, each portion of the data analysis process is broken up into one of 6 views.

The Samples View displays what proteins were identified during the search and their associated quantitative values in each sample. When GO terms or statistical tests are added, the resulting information will also be displayed in the Samples View. The Display Type dropdown can be used to change the quantitative value displayed. Scaffold DIA has numerous options for filtering data available here. There are also multiple Excel formatted exports available using the Export dropdown menu. 

 

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Figure 1. The Samples View

 

The Organize View allows you to organize your samples according to your experimental design and the experimental organization scheme can be changed as needed. For more information, check out this video on how to organize samples. The video uses Scaffold perSPECtives but the process and interface are exactly the same.

 

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Figure 2. The Organize View

 

The Proteins View allows you to do a deep dive into a single protein identification. Here you can see peptide sequences for those peptides assigned to this protein as well as the chromatogram used to identify that peptide. The Proteins View also includes a protein sequence coverage map, protein level quant charts and modification information.

 

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Figure 3. The Organize View

 

The Visualize View contains charts and graphs related to quantitation. Here you can see numerous scatterplots as well as GO term charts and a heatmap. Scaffold DIA also has principal component analysis built in and available here.

 

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Figure 4. The Visualize View

 

The Analysis View provides a visual representation of your chromatography for each sample. This can be used to detect samples that had chromatography issues.

 

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Figure 5. The Analysis View

 

Finally, the Publish View collapses experimental metadata down to a single page. This can be used for starting the methods section of a publication.

 

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Figure 6. The Publish View

 

Beyond Your First Scaffold DIA Run

Loading a few files against existing data is just the start. Next, think about creating your own chromatogram library specific to your instrumentation. Also, once you are familiar with the Organize View, setting up larger more complex experiments will be a breeze. Of course, if you have any questions feel free to contact our tech support department for assistance.

 

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