Hi!
I’m trying to streamline my workflow in Skyline Batch by using a previously prepared template (normal skyline document) to process a second batch of samples. The issue I’m facing is that I receive a constant error when attempting to apply the saved template to new chromatograms.

First Batch Processing:

We imported a transition list and raw files into a normal Skyline file.
A colleague manually reviewed chromatograms, identified the best peaks, and applied them to all samples for each analyte.
This Skyline file was saved and intended to be used as a template for future batches.
We also created an iRT calculator from this data.
A report was generated using a pivoted table with peak areas for all samples.

Applying This to a Second Batch:

Now, I want to use Skyline Batch to apply the same retention time borders, peak selections, and chromatogram alignment from the first batch to a second batch.
The issue is that the raw file names are different in the second batch. Could this be the cause of the error?
Instead of manually reviewing and selecting peaks for each new batch, we want this process to be automated so all batches are processed consistently.
My Questions:
Is it possible to use a Skyline file (with manually adjusted peaks and applied retention times) as a template in Skyline Batch for processing a new batch of raw files?
Does the difference in raw file names between batches create an issue?
What is the best approach to automate this process so we don’t have to manually realign peaks for every new batch while using the same transition list?
Is there a better way to set up the Skyline Batch or Skyline workflow to ensure peak alignment and selection are consistently applied across multiple batches?
We are trying to reduce human error and ensure that each batch is processed in the same way. Any advice or best practices would be greatly appreciated!