Table of Contents

MacCoss Lab Issues List
Finding and Reporting Software Issues

MacCoss Lab Issues List

If you have any doubt whether the issue you are reporting requires a change to the software to fix, please post to the Support Board first instead of the issues list.

Please be thorough in your investigation of all issues, and provide a concise description of the steps necessary to reproduce your issue.  Attach any files that help clarify your issue, or which are necessary to reproduce it.  If the files are large (greater than 10M) or you do not wish to share them publicly, please simply note you have files, and we will arrange with you to transfer them for our investigation.

Learn more about finding and reporting software issues.

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Finding and Reporting Software Issues

If you are using Skyline-daily, you have agreed to help with finding and reporting issues and bugs in the Skyline software before they reach the public release.  In exchange, you get early access to the latest feature improvements and bug fixes as they are made.

Becoming an effective software tester, finding and reporting software bugs, requires approaching the software you are testing from a new perspective.  In most of your daily software use, you will naturally find yourself attempting to learn ways around the issues you encounter with the software.  If you find that every time your screensaver comes on it causes an important program to crash, you will quickly learn to turn off that screensaver.  In most cases, you have no one to communicate these issues with, and your only option is to find a work-around.

Being a good software tester requires going through software with some amount of your energy tuned to when you notice something unexpected, and rather than looking for the quickest way to overcome the unexpected, you focus in on it like it is a potential new scientific discovery.

For example, imagine you just manually set integration on a peak in Skyline, and you noticed it removed an annotation you had set on the peak.  In normal software use, you might reset the annotation and start reminding yourself to make sure you are satisfied with the integration before setting any annotations in the future.  A good software tester, however, starts attempting to zero in on the problem in order to report it most effectively to a software developer.  An effective bug report will help the issue to be fixed quickly, and allow you and everyone else to perform manual integration without fear of losing annotations.  But, this will require you to temporarily shift your attention from your original goal (adjusting integration and annotating), to that of identifying the source of the unexpected behavior.

The following is an example of the narrowing steps I might take before reporting this issue:

  • Press the Undo button and repeat the integration.  Does the annotation disappear again?
  • Set an annotation on another peptide and try the same operation.  Is this specific to the one peptide?
  • Close and re-open the document and retry the original operation.  Can I expect another person to see the same results with what I know of my operation?

Suppose the answers to my questions were yes, yes and yes.  The next step is to report the problem.  If you are completely sure you have identified a bug, you are welcome to do this through the Skyline Issues List.  You can also start on the Support Board, or by sending email directly to me.

A good bug report for the example issue above might look like the following:


Open the file supplied.
Select the heavy precursor in the peptide DATNVGDEGGFAPNILENK.
On the View menu, click Rseults Grid.
Note that the annotation "Ignore" is checked in the replicate BCX1.
Click and drag beneath the x-axis to change the integration boundaries for replicate BCX1.

Expected: The "Ignore" annotation should remain checked.
Actual:  The "Ignore" annotation is cleared.

With an issue report like this, and the necessary files to reproduce the issue, any bug will nearly always be fixed in the next Skyline-daily release.  When supplying files with an issue report like this, please use the File > Share menu item to create a ZIP file containing all files for your Skyline project.

Thank you very much for your help in keeping Skyline quality high.

Brendan MacLean
Skyline Lead Developer