Fixed merge conflicts

cytoscape · Nov 16, 2023 · 7b535f4 · 7b535f4
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diff --git a/presentations/modules/RCy3_primer/module.html b/presentations/modules/RCy3_primer/module.html
@@ -1,5 +1,5 @@
                 <section data-transition="linear" data-transition-speed="default">
-                    <h1>Translating biological data into Cytoscape using RCy3</h1>
+                    <h1>Translating biological data into Cytoscape using RCy3 or py4cytoscape</h1>
                     <div class="slideContent" >
                         <p>Networks offer us a useful way to represent our biological data.  But how do we seamlessly translate our data from R into Cytoscape?</p>
 

diff --git a/presentations/modules/proteomics/ap-ms.png b/presentations/modules/proteomics/ap-ms.png
diff --git a/presentations/modules/proteomics/index.html b/presentations/modules/proteomics/index.html
@@ -25,10 +25,6 @@
 	</head>
 	<body>
 		<div class="reveal">
-			<div class="footer">
-				<img src="../assets/images/Cytoscape.png" style="height:70px;opacity:0.5"> 
-				<version>3.6.0</version>
-			</div>
 			<div class="slides">
 			<!-- this is just a shell to import the sections file -->
 			<section data-external="modules/proteomics/module.html"></section>

diff --git a/presentations/modules/proteomics/module.html b/presentations/modules/proteomics/module.html
@@ -3,7 +3,25 @@ <h1>Proteomics</h1>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+  <h1>Why Study Proteins?</h1>
+  <ul class="fragment">
+    <li>RNA Expression &ne; Protein abundance</li>
+    <li>Allows us to study interactions
+      <ul class="fragment">
+        <li>Even at the structural level</li>
+      </ul>
+    </li>
+    <li>Allows us to study signaling (PTMs)</li>
+    <li>However:
+      <ul>
+        <li>It's much harder than many transcriptomics techniques</li>
+      </ul>
+    </li>
+  </ul>
+</section>
+
+<section>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <p style="text-align:left">Caveats:
   <ul>
     <li>I am not an expert</li>
@@ -14,21 +32,21 @@ <h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <div>
     <img src="modules/proteomics/MassSpec1.png" width="80%">
   </div>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <div>
     <img src="modules/proteomics/CO2-spectra.png" width="80%">
   </div>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <h2 style="font-size:80%">Tandem Mass Spectrometry (MS/MS)</h2>
   <p style="text-align: left; font-size:80%">When dealing with proteins or lots of peptides, the m/z ratios might be too close to distinguish.  Tandem Mass Spectrometry addresses that by
   adding an additional fragmentation step</p>
@@ -38,25 +56,25 @@ <h2 style="font-size:80%">Tandem Mass Spectrometry (MS/MS)</h2>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <h2 style="font-size:80%">Proteomics</h2>
   <div>
     <img src="modules/proteomics/3typesofproteomics.png" width="80%">
   </div>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <h2 style="font-size:80%">Proteomics</h2>
   <p style="text-align: left;font-size:80%">How do we get from spectra to peptide?</p>
   <div>
-    <img src="modules/proteomics/ProteinIdentification.png" width="80%">
+    <img src="modules/proteomics/peptide-identification.png" width="80%">
   </div>
   <p style="text-align: left;font-size:80%">Possible problem: peptides might not uniquely identify a single protein.</p>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
+	<h1 style="font-size:120%">(Very) Brief Intro to Mass Spectrometry</h1>
   <h2 style="font-size:80%">Proteomics</h2>
   <p style="text-align: left;font-size:80%">Protein groups are proteins that share all their peptides with other proteins cannot be unambiguously identified.</p>
   <ul style="font-size:80%">
@@ -71,29 +89,15 @@ <h1>Understanding Proteomics Results</h1>
 </section>
 
 <section>
-	<h1 style="font-size:100%">(Very) Brief Intro to Mass Spectrometry</h1>
-  <p style="text-align:left">Resources for learning more:
-  <ul>
-    <li><a href="https://www.youtube.com/watch?v=hvKbAoKkSM8">Georgia Tech Video on Fundamentals of Mass Spectrometry</a></li>
-    <li><a href="https://www.khanacademy.org/science/ap-chemistry-beta/x2eef969c74e0d802:atomic-structure-and-properties/x2eef969c74e0d802:mass-spectrometry-of-elements/v/mass-spectrometry">Kahn Academy Video on Mass Spectrometry</a></li>
-    <li><a href="https://masspec.scripps.edu/learn/ms/">Scripps Center for Metabolimics</a>.  A more thorough discussion of current techniques.</li>
-    <li><a href="https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Spectroscopy/Mass_Spectrometry">LibreTexts Chemistry Chapter</a>.  Another pretty thorough discussion.</li>
-    <li><a href="https://www.youtube.com/watch?v=wx4F6kGy1Fs">Simple overview of proteomics from Lars Juhl Jensen</a></li>
-    <li><a href="https://www.youtube.com/watch?v=ZgwNWRul98o">More detailed presentation of proteomics from Lennart Martens</a></li>
-    <li><a href="https://www.youtube.com/watch?v=2BDYcoVB45U&t=1s">EMBL-EBI Training presentation on proteomics</a></li>
-  </ul>
-</section>
-
-<section>
-  <h1>Understanding Proteomics Results</h1>
+  <h1 style="font-size:120%">Understanding Proteomics Results</h1>
   <h2 style="font-size:80%">MaxQuant proteinGroups.txt</h2>
   <div>
     <img src="modules/proteomics/ProteinGroups.png" width="80%">
   </div>
 </section>
 
 <section>
-  <h1>Understanding Proteomics Results</h1>
+  <h1 style="font-size:120%">Understanding Proteomics Results</h1>
   <h2 style="font-size:80%">MaxQuant Columns</h2>
   <p style="text-align:left; font-size: 80%">The most important columns that every proteinGroups.txt file contains are:
 
@@ -119,19 +123,71 @@ <h2 style="font-size:80%">MaxQuant Columns</h2>
 </section>
 
 <section>
-  <h1>Analyzing Proteomics Data</h1>
+  <h1 style="font-size:120%">Understanding Proteomics Results</h1>
+  <p>Overview of analytical pipeline</p>
+  <div>
+    <img src="modules/proteomics/pipeline.jpg" >
+  </div>
+  <a style="font-size: large;" href="https://doi.org/10.3389/fmed.2021.747333">https://doi.org/10.3389/fmed.2021.747333</a>
+</section>
+
+<section>
+  <h1 style="font-size:120%">Understanding Proteomics Results</h1>
+  <p>Example dataset after identification and quantitation</p>
+  <div>
+    <img src="modules/proteomics/spreadsheet.png" title="add image here" >
+  </div>
 </section>
 
 <section>
-  <h2>Analyzing Abundance Data</h1>
+  <h1 style="font-size:120%">Analyzing Proteomics Data</h1>
+  <p>R packages for proteomics analysis</p>
+  <ul>
+    <li><a href="https://bioconductor.org/packages/devel/BiocViews.html#___MassSpectrometry">MS packages at Bioconductor</a></li> 
+    <li><a href="https://bioconductor.org/packages/devel/BiocViews.html#___Proteomics">Proteomics packages at Bioconductor</a></li> 
+    <li><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05360-7">tidyproteomics</a> - an open-source R package and data object for quantitative proteomics post analysis and visualization</li> 
+    <li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10010602/">promor</a> - a comprehensive R package for label-free proteomics data analysis and predictive modeling</li> 
+    <li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10088014/">prolfqua</a> - a Comprehensive R-Package for Proteomics Differential Expression Analysis</li> 
+  </ul>
 </section>
 
 <section>
   <h2>Analyzing PTM Data</h1>
-</section>
+    <p>Peptide identification must account for the masses of potential post-translational modifications (PTMs)</p>
+    <div>
+      <img src="modules/proteomics/ptm-spectra.png" >
+    </div>
+    <ul>
+      <li><a href="https://bioconductor.org/packages/devel/bioc/html/MSstatsPTM.html">MSstatsPTM</a> - Statistical Characterization of Post-translational Modifications</li> 
+    </ul>
+  </section>
 
 <section>
   <h2>Analyzing AP/MS or BioID Data</h1>
+	<p>AP/MS and BioID results are a list of interactions</p>
+    <div>
+      <img src="modules/proteomics/ap-ms.png" width="70%">
+    </div>
+  <a style="font-size: large;" href="https://doi.org/10.1038/nature10719">https://doi.org/10.1038/nature10719</a>
+</section>
+
+<section>
+  <h1 style="font-size:120%">Proteomics</h1>
+  <p style="text-align:left">Resources for learning more:
+  <ul>
+    <li><a href="https://www.youtube.com/watch?v=hvKbAoKkSM8">Georgia Tech Video on Fundamentals of Mass Spectrometry</a></li>
+    <li><a href="https://www.khanacademy.org/science/ap-chemistry-beta/x2eef969c74e0d802:atomic-structure-and-properties/x2eef969c74e0d802:mass-spectrometry-of-elements/v/mass-spectrometry">Kahn Academy Video on Mass Spectrometry</a></li>
+    <li><a href="https://masspec.scripps.edu/learn/ms/">Scripps Center for Metabolimics</a>.  A more thorough discussion of current techniques.</li>
+    <li><a href="https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Spectroscopy/Mass_Spectrometry">LibreTexts Chemistry Chapter</a>.  Another pretty thorough discussion.</li>
+    <li><a href="https://www.youtube.com/watch?v=wx4F6kGy1Fs">Simple overview of proteomics from Lars Juhl Jensen</a></li>
+    <li><a href="https://www.youtube.com/watch?v=ZgwNWRul98o">More detailed presentation of proteomics from Lennart Martens</a></li>
+    <li><a href="https://www.youtube.com/watch?v=2BDYcoVB45U&t=1s">EMBL-EBI Training presentation on proteomics</a></li>
+  </ul>
+</section>
+
+
+<section>
+	<h1>Questions?</h1>
 </section>
 
 
diff --git a/presentations/modules/proteomics/peptide-identification.png b/presentations/modules/proteomics/peptide-identification.png
diff --git a/presentations/modules/proteomics/pipeline.jpg b/presentations/modules/proteomics/pipeline.jpg
diff --git a/presentations/modules/proteomics/ptm-spectra.png b/presentations/modules/proteomics/ptm-spectra.png
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