As proteomics methods are developed and refined, multiple documents are often produced that need to be tracked and linked together. For example, a first runs attempt may include many proteins, precursors, and transitions, which later run attempts will progressively narrow down to the best performing ones. In order to track the method development, documents can be marked with comments and linked together as series of different versions.

Automatically Link Skyline Documents

The server will automatically link Skyline documents together at import time (beginning with LabKey Server 16.1), provided that the Skyline documents provide a document ID. When importing a Skyline document whose ID matches one already in the folder, the incoming document will automatically be linked to the previous document(s) as the newest version in the document chain.

The document’s import log file will indicate if it was attached as a new version in the document chain. This functionality is now part of the Skyline-daily builds (beta), and will be part of the next regular release (Skyline 3.6).

Document Details

You can view a detailed profile for each document in Panorama by clicking the document name in Targeted MS Runs web part.

The profile provides:

  • a Document Summary panel showing key data points. (Click the pencil icon to rename the document.)
  • a Document Versions panel which shows the document's position in the series of versions. (Click the versions link.)
  • a Precursor List/Transition List panel which shows different views of the protein/peptide breakdown. (Click the transitions link.)

Link Document Versions

To chain together a series of document versions, select them in the Targeted MS Runs web part and click Link Versions.

The Link Versions panel will appear. You can drag and drop the documents into the preferred order and click Save.

Note that an individual document can be incorporated into only one document series -- it cannot be incorporated into different document series simultaneously.

Add Comments

To add comments to a document, click in the Flag column.

The Review panel will appear. Enter the comment and click Ok.

Comments are displayed in the Document Versions panel as notes.

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