Custom Reporting -Small Molecule

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Custom Reporting -Small Molecule davis  2019-02-13 16:21
 

Hi Skyline Community!

I would like to report my small mole data in the following reporting format (see excel for an example of preferred reporting format). I have reviewed Skylines custom reporting tutorial but it is not clear if this format is achievable? Has anyone generated a report like this using Skyline or would I have to copy and paste each species into excel to achieve this reporting format?

Thank you! Sonnet Davis

 
 
Nick Shulman responded:  2019-02-13 16:53
The columns in the Document Grid are named based on what makes sense for peptides, but they do still work for small molecules for the most part.

These are the columns that I would add to your report:
Name : Proteins > Peptides
Precursor : Proteins > Peptides > Precursors > Precursor Mz
Product : Proteins > Peptides > Precursors > Transitions > Product Mz
RT: Proteins > Peptides > Explicit Retention Time

I'm not sure what to do about the IonMode column (which is just always "ES+" for every row) or the Internal Standards column.

The Internal Standards column is a little bit like the "Normalization Method" column.
The Normalization Method column is at:
Proteins > Peptides > Normalization Method

However, the Normalization Method looks more like "Ratio to Sphingosine d17:1".

If you want to associate extra information with your molecules, you can define an Annotation. Annotations are described on page 27 of the Custom Reports tutorial.

You can rename the columns in the document grid by bringing up the View Editor and clicking slowly on the column name in the column list.

-- Nick
 
Brian Pratt responded:  2019-02-13 17:04
I think you'd have to write teh precursor adduct in the Ion Mode column: "ES+" is implying that everything is positively ionized, probably [M+H].

Between that and "Ratio to..." there might be some light post processing needed to get exactly this result.

- Brian
 
davis responded:  2019-02-13 17:08
Hi Nick,

I apologize. I attached the wrong reporting file in my previous submission. Please find the correct reporting file format we are hoping to achieve.

Thanks for your assistance.

Best! Sonnet
 
Nick Shulman responded:  2019-02-13 17:27
It looks like you want to have one row per Replicate, and have each Molecule in a separate column.

Skyline makes it easy to create a report that goes the other way: one row per Molecule and the Replicates in separate columns. There is a checkbox at the bottom of the "View Editor" which is "Pivot Replicate Name", which does that.

You can make it so that the different molecules appear in different columns using the Pivot Editor.

To do that, you would add the following columns to your report:
Replicates > Files > File Name
Replicates > Sample ID (assuming you have defined a Replicate Annotation called "Sample ID").
Protein > Peptides > Molecule Name
Protein > Peptides > Peptide Results > Quantification > Normalized Area

Then, when you are looking at the results in the Document Grid, press the "Group/Total" button (it's next to the Views dropdown).
In the Pivot Editor, add the following columns as Row Headers:
File Name
Sample ID
Add the following column as Column Header:
Molecule Name
And, choose "Mean" in the dropdown and add Normalized Area as a Value.

You can find more information about the Pivot Editor here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor

-- Nick
 
davis responded:  2019-02-13 18:23
Thank you! The steps provided gave me the MVA table I was looking for. Thanks again! Sonnet