For MS2 chromatograms, the "Chromatogram Information Unavailable" typically means that there were no MS2 spectra in the .raw file which matched the precursor m/z.
One reason that this could happen with a PRM method is that the mass spectrometer method really did not include the precursor m/z that you needed. Sometimes that m/z was included in the method, but it is not exactly the same as what Skyline thinks the m/z is. The closeness that the m/z in the .raw file and in the Skyline document need to be is controlled by the "Method match tolerance m/z" setting at "Settings > Transition Settings > Instrument".

Another thing to check is the "Retention time filtering" setting at "Settings > Transition Settings > Full Scan". For a PRM method, that should typically be set to "Include all matching scans" because your instrument method has already told the mass spectrometer when you want data collected for your molecules of interest and you want Skyline to make use of all of the available spectra.

Another thing to check is whether you have set the "Explicit Retention Time" on any of your molecules. If the extracted chromatogram does not overlap with the explicit retention time then Skyline discards the chromatogram.

If you would like you can send us your Skyline document and some of your .raw files and we can tell you what is going on.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms. The "Share Skyline Document" dialog also allows you to include .raw files in the .zip file, or you can upload them separately.

Files which are less than 50 MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick

Thanks for helping sir.

Regards,
PN

Thank you for sending that Skyline document.
Can you also send me one of your .raw files, for instance "SI benzyl 5 mg_L_16.raw"?
That file will probably be too large to attach to this support request so you should upload it here:
https://skyline.ms/files.url
-- Nick

It is shared Nick!

Thank you so much.
PN

I think you just need to tell Skyline to extract chromatograms again and then you will see the chromatograms for that molecule.
Skyline is not smart enough to re-extract chromatograms when you change the settings, or add things to the Targets tree.
You usually need to tell Skyline to extract chromatograms again by doing one of the following:

1. Go to "Edit > Manage Results", select all of the replicates and push the "Reimport" button.
Doing things this way preserves any manually adjusted peak boundaries.

Alternatively:
2. Go to "Edit > Manage Results", push the "Remove All". Then, after you OK the Manage Results dialog, you need to save the document so the extracted chromatograms are deleted from disk, and then you can import them again by doing "File > Import > Results".

I think if you tell Skyline to extract chromatograms again you will see chromatograms for your internal standard.
-- Nick

Yeah!!!!!!!!!!!! It is working :) Thank you so so much Nick. Have a great week-end.

Hey Nick!
Sorry to bother you again. I have another question.
I am trying to get the ion area for each of my compounds for each ion.
 I see that I can get them through the graph Area per compound by copying the graph data.
I was wondering if there is a more easy way to collect those information. Basically everything in one table (sample name, compounds, ions, area, tr, etc). I had tried with the result/report grid but did not succeed.
Is there a way to do that? I had looked at pdf available online, but it did not help me to achieve my goal.
Thanks!

If you want to get lists of numbers out of Skyline you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

If you have two groups of replicates (e.g. healthy and diseased) and you want to know which molecules are changing between the two groups you should look at the Group Comparison tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped

-- Nick

Hi again,
I am a little confused about the columns available when I am trying to get a customized report.
I selected molecule, precursor (or precursor m/z and adduct) but when it comes to the area I am a little confused about what to take ...
I thought first to get the area of all the product ions and do a sum to get an area for my precursors. Kind of like the graph Peak Areas (replicate comparison). But I don't know what Area to take (which section).
I guess alternatively it may be possible to have directly a total area for my molecule but once again what to take. I tried different Total areas and didn't get the same result.
Also, the areas given, do they take into account the background noise? If I have a blank should I remove the area myself from the area provided? In the same way, has the graph Peak Areas been corrected from the background noise?
I am very sorry to bother you but I want to be sure that the data extracted are the good ones!
Thanks again for your help.

If you are making a report with peak areas in it, you should make sure to include something which tells you which replicate the area came from. One way to do that is to check the checkbox "Pivot Replicate Name" in the "Customize Report" dialog. If you check that checkbox you will get one row per molecule, and the areas will go across horizontally and the column names in those area columns will tell you which replicate the area came from.
Alternatively, if you want one row per molecule and replicate you would leave the "Pivot Replicate Name" checkbox unchecked and then include probably the "Replicate" column (that is, check the checkbox next to "Replicates" in the tree where you choose columns in the Customize Report dialog).

In general, the column that you should add to your report is called "Normalized Area" which can be found in the column chooser in the report editor at:
Molecule Lists > Molecules > Molecule Results > Quantification > Normalized Area
(there is also a binoculars button at the top of the report editor which you can use to search for any column by name).

In your document, the "Normalized Area" column will show the exact same numbers as the "Total Area" column ("Molecule Lists > Molecules > Precursors > Precursor Results > Total Area") because each of your molecules has exactly one precursor and also because you have not chosen a normalization method at "Settings > Molecule Settings > Quantification".

It sounded like you might want to use your "S-benzyl-L-cysteine" molecule for some sort of normalization. If you wanted to do that, you would right-click on that molecule in the Targets tree and choose "Set Standard Type > Global Standard". Then, you should go to "Settings > Molecule Settings > Quantification" and change the Normalization Method to "Ratio to Global Standards".
When you do that, the "Normalized Area" column in the Document Grid will show the total area of the molecule divided by the total area of your global standard in that particular file.

I am not sure why you might be getting "different total areas", but if you send me a screenshot I might be able to tell you what is going on.
Alternatively, you could send me your Skyline document again.
If you are going to send me your Skyline document then you should first go to the "Reports" tab at "Settings > Document Settings" and check the checkbox next to all the reports that you might have questions about. That way, when you do "File > Share" those report definitions will be included in the document and I will be able to see what you were seeing.
-- Nick