In the Internal Standard Concentration column, add the known amount of fmol for each heavy labeled peptide (see the annex at the end of this tutorial). Now, again from the window “Document Grid” Go to Ratio in the quantification column you have the “View” “Peptide Results”. Now, amount of each endogenous peptide calculated with the single point calibration method. Now the should look like this: “Document grid” Statistical comparison between conditions Annotating samples with group information To perform statistical analysis of the results we first need to annotate which samples are replicates. Skyline allows you to associate additional information with the runs in the document by defining custom annotations. To view the Annotation Settings form, perform the following steps: On the menu, click “Settings” “Document Settings”. In the click “Annotations” Tab “Add”. Name the new as “Annotation” “Condition” Type: Value List each on a new Values: “G1”, “G2M”, “S”, line (without “ ”) Applies To: “Replicates” Click “OK”. Generate another following the same steps as “Annotation” named “BioReplicate” above. Name the new as “Annotation” “BioReplicate” Type: Value List Values: each on a new “1”, “2”, “3”…”9” line (without “ ”) Applies To: “Replicates” Click the button. “OK” Select both in the tab. “Annotations” “Annotations” Editing the annotation values in Skyline is done using the “Document Grid”. To bring up the Document Grid go to the menu and click Grid “View” “Document Go to “View” ”Replicates” → as shown in the table below. Annotate “Condition”, “BioReplicate” Close the Document Grid Save the Skyline file as in folder. PRM_Annotated.sky Skyline Webinar
In the Internal Standard Concentration column, add the known amount of fmol for each heavy labeled peptide (see the annex at the end of this tutorial). Now, again from the “Document Grid” window Go to “View” “Peptide Ratio Results”. Now, in the quantification column you have the amount of each endogenous peptide calculated with the single point calibration method. Now the “Document grid” should look like this: Statistical comparison between conditions Annotating samples with group information To perform statistical analysis of the results we first need to annotate which samples are replicates. Skyline allows you to associate additional information with the runs in the document by defining custom annotations. To view the Annotation Settings form, perform the following steps: On the “Settings” menu, click “Document Settings”. In the “Annotations” Tab click “Add”. Name the new “Annotation” as “Condition” Type: Value List Values: “G1”, “G2M”, “S”, each on a new line (without “ ”) Applies To: “Replicates” Click “OK”. Generate another “Annotation” named “BioReplicate” following the same steps as above. Name the new “Annotation” as “BioReplicate” Type: Value List Values: “1”, “2”, “3”…”9” each on a new line (without “ ”) Applies To: “Replicates” Click the “OK” button. Select both “Annotations” in the “Annotations” tab. Editing the annotation values in Skyline is done using the “Document Grid”. To bring up the Document Grid go to the “View” menu and click “Document Grid Go to “View” → ”Replicates” Annotate “Condition”, “BioReplicate” as shown in the table below. Close the Document Grid Save the Skyline file as PRM_Annotated.sky in Skyline Webinar folder.
Webinar%2017%20%28Chiva%29.docx