Updated teachinmodule.qmd and split of module into three files

TeachingModule/AnalysisMSData_FragPipe.qmd

@@ -109,32 +109,40 @@ Next, we can launch FragPipe, which is located on the desktop. In this tutorial,
 Now that we have launched FragPipe, we need to configure the settings prior to running the analysis. Therefore, we have provided some guiding questions to help you set up the settings in FragPipe:
 
 ### Getting started with FragPipe
+
+::: {.callout-note}
+Some of the information you will need in this section can be found in **Supplementary Information** to the study. Open the **Supplementary Information**  and go to page 25, **Supplementary Methods**.
+:::
+
 Go to the “Workflow” tab to set up the workflow for the analysis and import the data you have just downloaded.
 
 ::: {.question}
-Which workflow should you select? HINT: How many TMT tags are listed in the table in Supplementary Data 1?
+Which workflow should you select? **Hint**: What labeling method was used in the study?
 :::
 
 
-Click ‘Load workflow’ after you have found and selected the correct workflow to be used.
+::: {.question}
+How does the labeling method affect data processing?
+:::
+
+Click "Load workflow" after you have found and selected the correct workflow to be used.
 
 Next, add your files by clicking on “Add files” and locate them in the designated folder for your raw files that you previously created. Assign each file to a separate *experiment* by clicking "Consecutive".
 
 Go to the "Quant (Isobaric)" tab. Here, you need to provide annotations for TMT channels. Use the five pool annotations that you downloaded from this page.
 You will need to upload them to Ucloud and specify the corresponding annotation file for each experiement in order.
 
-Now you should relocate to the “Database” tab. Here you can either download or browse for an already preexisting database file. In this case, we will simply download the latest database file by clicking the "Download" button in FragPipe.
+Now you should relocate to the “Database” tab. Here you can either download or browse for an already preexisting database file.
+In this case, we will simply download the latest database file by clicking the "Download" button in FragPipe. Add contaminants and decoys.
 
 ::: {.question}
 What is the purpose of the database file used in FragPipe, and why is it important?
 :::
 
-
 ::: {.question}
 Which organism should you choose when downloading the database file?
 :::
 
-
 ::: {.question}
 Describe the relationship between decoys and false discovery rate (FDR) by answering the following questions:
 
@@ -145,28 +153,29 @@ Describe the relationship between decoys and false discovery rate (FDR) by answe
 </ul>
 :::
 
+Next, you can go to the "MSFragger" tab to adjust the parameter settings for the search and matching of the theoretical and experimental peptide spectra.
+The search parameters to be used are listed in **Supplementary Methods**.
 
-Next, you can go to the MSFragger tab to adjust the parameter settings for the search and matching of the theoretical and experimental peptide spectra.
-
-Most of the settings used for MSFragger can be obtained from the paper *NAME OF PAPER*, which is referred to in the Methods and Materials section.
+::: {.question}
+What parameters did you set?
+:::
 
 When all settings have been obtained, MSFragger should look something like this:
 
 ::: {.question}
-What is MSFragger?
+What is MSFragger? What does it do?
 :::
 
 
 ::: {.question}
 How does MSFragger operate?
 :::
 
-
-::: {.question}
-Why is it essential to run MSFragger for this analysis?
+::: {.callout-note}
+You can also skip configuring MSFragger manually and just use this [parameter file](https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/fragger.params).
+You will need to upload it to UCloud and then load it on the "MSFragger" tab in FragPipe.
 :::
 
-
 Finally, we can navigate to the “Run” tab and run the analysis. For that, we must choose an output directory for the results of the search made by FragPipe. Once you have adjusted that, you are ready to click on “Run”.
 
 This process might take some time, so make sure that you still have enough hours allocated on your job on UCloud—otherwise, it will get terminated. Meanwhile, you can answer these questions:
@@ -182,7 +191,7 @@ Can the output from this analysis be reliably used for downstream applications g
 
 
 ::: {.question}
-What does it signify that the sample tissues have been fractionated as described in *PAPER*?
+What does it signify that the sample tissues have been fractionated as described in **Supplementary Information**?
 :::
 <ul>
     <li>Outline the fractionation process utilized.</li>
@@ -225,4 +234,4 @@ OmicsQ can be used to facilitate the processing of quantitative data from Omics
 Guide and introduction to Omics Q
 Questions about Omics Q
 Questions about output and interpretations of results from OmicsQ
--->
+-->

TeachingModule/Preliminarywork.qmd

@@ -9,14 +9,36 @@ Before delving into the actual analysis of the data in FragPipe, we must initial
 
 To better understand the paper, we have formulated some questions that should help clarify the study design, aim, and overall scope of the work. These questions are listed below:
 
-- …
-- …
-- …
+::: {.question}
+What are the primary research goals of this study?
+:::
+
+::: {.question}
+How is the study design structured to achieve the study objective?
+:::
+
+::: {.question}
+What role does LC-MS/MS play in this study, and why was it chosen as a method?
+:::
+
+::: {.question}
+What novel insights were gained from the proteogenomic approach used in this study?
+:::
 
 
 ### Supplementary Data
 
-Before we proceed and download the data available from the paper, we must first delve into some of the details in Supplementary Data 1. This is a large table containing the quantitative proteome data from the Oslo2 breast cancer cohort, which includes 45 subgroups of cancer tumors and relates to Figures 1-6 in the paper.
+Before we proceed and download the data available from the paper, we must first delve into some of the details in Supplementary Data.
+Your first task is to look through the Supplementary Data and find the annotation relating the tumor types to the isotopic labels used.
+
+::: {.question}
+How did you find the required information? Describe the steps you took. How much time did it take?
+:::
+
+::: {.callout-note collapse="true"}
+#### Hint
+If you have not been able to find the annotations, open Supplementary Data 1, and then go to the tab called "Tumor annotations".
+:::
 
 To better understand the supplementary data, we have prepared guiding questions to aid in interpreting the table. You can find the supplementary data in the paper [here](https://www-nature-com.proxy1-bib.sdu.dk/articles/s41467-019-09018-y#Sec15).
 
@@ -39,7 +61,10 @@ Briefly describe TMT-labeled mass spectrometry proteomics data and explain the e
 #### TMT10-Tags and Tumor IDs
 
 Fill in the table below by entering the corresponding TMT10-tags and Tumor IDs. Once submitted, you'll get instant feedback on whether your input is correct.
+
+::: {.callout-note}
 When you have filled the whole table correctly, download the annotation files, **you will need them later**.
+:::
 
 <form id="tmtForm">
   <table style="width: 100%; border-collapse: collapse;">
@@ -203,4 +228,4 @@ What is in TMT131?
 What is the purpose of using this type of sample?
 :::
 
-Now that we better understand the workflow of the study and the content of the data, we are ready to move on to the analysis performed by FragPipe in the next section.
+Now that we better understand the workflow of the study and the content of the data, we are ready to move on to the analysis performed by FragPipe in the next section.