Merge pull request #112 from jessegmeyerlab/jessegmeyerlab-patch-10

[ci skip] This build is based on 882d8a9. This commit was created by the following CI build and job: https://github.com/jessegmeyerlab/proteomics-tutorial/commit/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0/checks https://github.com/jessegmeyerlab/proteomics-tutorial/actions/runs/8618250261
jessegmeyerlab · Apr 9, 2024 · 61c9ef4 · 61c9ef4
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diff --git a/manuscript.html b/manuscript.html
@@ -72,8 +72,8 @@
   <meta name="dc.date" content="2024-04-09" />
   <meta name="citation_publication_date" content="2024-04-09" />
   <meta property="article:published_time" content="2024-04-09" />
-  <meta name="dc.modified" content="2024-04-09T15:11:50+00:00" />
-  <meta property="article:modified_time" content="2024-04-09T15:11:50+00:00" />
+  <meta name="dc.modified" content="2024-04-09T15:23:24+00:00" />
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   <meta name="citation_language" content="en-US" />
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@@ -167,9 +167,9 @@
   <meta name="citation_fulltext_html_url" content="https://jessegmeyerlab.github.io/proteomics-tutorial/" />
   <meta name="citation_pdf_url" content="https://jessegmeyerlab.github.io/proteomics-tutorial/manuscript.pdf" />
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+  <link rel="alternate" type="text/html" href="https://jessegmeyerlab.github.io/proteomics-tutorial/v/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0/" />
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@@ -186,9 +186,9 @@ <h1 class="title">Comprehensive Overview of Bottom-Up Proteomics using Mass Spec
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://jessegmeyerlab.github.io/proteomics-tutorial/v/f71427c3fa278a2f63693b9d6663fae1dbf9b465/">permalink</a>)
+(<a href="https://jessegmeyerlab.github.io/proteomics-tutorial/v/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/jessegmeyerlab/proteomics-tutorial/tree/f71427c3fa278a2f63693b9d6663fae1dbf9b465">jessegmeyerlab/proteomics-tutorial@f71427c</a>
+from <a href="https://github.com/jessegmeyerlab/proteomics-tutorial/tree/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0">jessegmeyerlab/proteomics-tutorial@882d8a9</a>
 on April 9, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -973,13 +973,14 @@ <h2 class="page_break_before" id="proteolysis">4. Proteolysis</h2>
 </figure>
 </div>
 <p>Table 2: Common proteases used for proteomics.</p>
-<table>
+<table style="width:100%;">
 <colgroup>
-<col style="width: 16%" />
-<col style="width: 12%" />
-<col style="width: 36%" />
-<col style="width: 16%" />
-<col style="width: 16%" />
+<col style="width: 14%" />
+<col style="width: 11%" />
+<col style="width: 31%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
+<col style="width: 14%" />
 </colgroup>
 <thead>
 <tr class="header">
@@ -988,6 +989,7 @@ <h2 class="page_break_before" id="proteolysis">4. Proteolysis</h2>
 <th style="text-align: center;">class</th>
 <th style="text-align: center;">specificity</th>
 <th style="text-align: center;">optimal pH</th>
+<th style="text-align: center;">notes</th>
 </tr>
 </thead>
 <tbody>
@@ -997,76 +999,87 @@ <h2 class="page_break_before" id="proteolysis">4. Proteolysis</h2>
 <td style="text-align: center;">serine protease</td>
 <td style="text-align: center;">c-term of R/K, not before P</td>
 <td style="text-align: center;">7-9</td>
+<td style="text-align: center;">most common protease</td>
 </tr>
 <tr class="even">
 <td style="text-align: center;">LysC</td>
 <td style="text-align: center;"><em>Lysobacter enzymogenesis</em></td>
 <td style="text-align: center;">serine protease</td>
 <td style="text-align: center;">c-term of K</td>
 <td style="text-align: center;">7-9</td>
+<td style="text-align: center;">high stability</td>
 </tr>
 <tr class="odd">
 <td style="text-align: center;">Alpha-lytic protease</td>
 <td style="text-align: center;"><em>Lysobacter enzymogenesis</em></td>
 <td style="text-align: center;">serine protease</td>
 <td style="text-align: center;">c-term of small side chains</td>
 <td style="text-align: center;">7-9</td>
+<td style="text-align: center;">high stability</td>
 </tr>
 <tr class="even">
 <td style="text-align: center;">GluC</td>
 <td style="text-align: center;"><em>Staphyloccous aureus</em></td>
 <td style="text-align: center;">serine protease</td>
 <td style="text-align: center;">c-term of D/E</td>
 <td style="text-align: center;">4-8</td>
+<td style="text-align: center;">specificity for Glu depends on buffer</td>
 </tr>
 <tr class="odd">
 <td style="text-align: center;">Asp-N</td>
 <td style="text-align: center;"><em>Pseudomonas fragi</em></td>
 <td style="text-align: center;">metalloprotease</td>
 <td style="text-align: center;">n-term of D</td>
 <td style="text-align: center;">4-9</td>
+<td style="text-align: center;">avoid chelators</td>
 </tr>
 <tr class="even">
 <td style="text-align: center;">chymotrypsin</td>
 <td style="text-align: center;">mammal pancreas</td>
 <td style="text-align: center;">serine protease</td>
 <td style="text-align: center;">c-term of larger hydroponics</td>
 <td style="text-align: center;">7-9</td>
+<td style="text-align: center;"></td>
 </tr>
 <tr class="odd">
 <td style="text-align: center;">Arg-C</td>
 <td style="text-align: center;"><em>Clostridium histolyticum</em></td>
 <td style="text-align: center;">cysteine protease</td>
 <td style="text-align: center;">c-term or R</td>
 <td style="text-align: center;">7.2-7.8</td>
+<td style="text-align: center;">avoid oxidation</td>
 </tr>
 <tr class="even">
 <td style="text-align: center;">Ulilysin</td>
 <td style="text-align: center;"><em>Methanosarcina acetivorans</em></td>
 <td style="text-align: center;">metalloprotease</td>
 <td style="text-align: center;">N-term of R/K</td>
 <td style="text-align: center;">6-9</td>
+<td style="text-align: center;">stable to 55℃</td>
 </tr>
 <tr class="odd">
 <td style="text-align: center;">Lys-N</td>
 <td style="text-align: center;"><em>Grifola frondosa</em></td>
 <td style="text-align: center;">metalloprotease</td>
 <td style="text-align: center;">N-term or K</td>
 <td style="text-align: center;">7-9</td>
+<td style="text-align: center;">stable to 70℃</td>
 </tr>
 <tr class="even">
 <td style="text-align: center;">Pepsin A</td>
 <td style="text-align: center;">mammal pancreas</td>
 <td style="text-align: center;">aspartic acid protease</td>
 <td style="text-align: center;">broad including W, F, Y, L</td>
 <td style="text-align: center;">1-4</td>
+<td style="text-align: center;">common for HDX</td>
 </tr>
 <tr class="odd">
 <td style="text-align: center;">Proteinase K</td>
 <td style="text-align: center;"><em>Tritirachium album</em></td>
 <td style="text-align: center;">serine protease</td>
 <td style="text-align: center;">broadest</td>
 <td style="text-align: center;">4-12</td>
+<td style="text-align: center;">common for limited proteolysis</td>
 </tr>
 </tbody>
 </table>
@@ -1407,7 +1420,7 @@ <h4 id="solid-phase-extraction-spe">Solid phase extraction (SPE)</h4>
 After washing the bound peptides, they can be eluted by switching the liquid phase to something hydrophobic, which allows the peptides to partition more into the liquid phase and elute from the solid phase.</p>
 <div id="fig:SPE" class="fignos">
 <figure>
-<img src="images/SPE_v04.png" style="width:100.0%" data-tag="5" alt="Figure 5: Solid phase extraction (SPE). SPE is a sample preparation technique that uses a solid adsorbent contained most commonly in a cartridge device to selectively adsorb certain molecules from solution. The first step is the conditioning of the cartridge which involves wetting the adsorbent to solvate its functional groups and filling the void spaces with solvent thereby removing any air in the column. This is necessary to produce a suitable environment for adsorption and thus ensure reproducible interaction with the analytes. After conditioning, the sample is loaded in the cartridge. This can be performed with the aid of positive or negative pressure to ensure a constant flow rate. In this step molecules bind the adsorbent and interferences pass through. Next, the column is washed with the mobile phase to eliminate the contaminants while ensuring the analyte remains bound. Finally, peptides are eluted in an appropriate buffer solution with polarity or charge that competes with interaction with the solid phase." />
+<img src="images/SPE_v05.png" style="width:100.0%" data-tag="5" alt="Figure 5: Solid phase extraction (SPE). SPE is a sample preparation technique that uses a solid adsorbent contained most commonly in a cartridge device to selectively adsorb certain molecules from solution. The first step is the conditioning of the cartridge which involves wetting the adsorbent to solvate its functional groups and filling the void spaces with solvent thereby removing any air in the column. This is necessary to produce a suitable environment for adsorption and thus ensure reproducible interaction with the analytes. After conditioning, the sample is loaded in the cartridge. This can be performed with the aid of positive or negative pressure to ensure a constant flow rate. In this step molecules bind the adsorbent and interferences pass through. Next, the column is washed with the mobile phase to eliminate the contaminants while ensuring the analyte remains bound. Finally, peptides are eluted in an appropriate buffer solution with polarity or charge that competes with interaction with the solid phase." />
 <figcaption aria-hidden="true"><span>Figure 5:</span> <strong>Solid phase extraction (SPE).</strong>
 SPE is a sample preparation technique that uses a solid adsorbent contained most commonly in a cartridge device to selectively adsorb certain molecules from solution.
 The first step is the conditioning of the cartridge which involves wetting the adsorbent to solvate its functional groups and filling the void spaces with solvent thereby removing any air in the column.
@@ -5742,7 +5755,7 @@ <h2 class="page_break_before" id="references">References</h2>
 <div class="csl-left-margin">765. </div><div class="csl-right-inline"><strong>Proteomics in Non-model Organisms: A New Analytical Frontier.</strong> <div class="csl-block">Michelle Heck, Benjamin A Neely</div> <em>Journal of proteome research</em> (2020-08-20) <a href="https://www.ncbi.nlm.nih.gov/pubmed/32786681">https://www.ncbi.nlm.nih.gov/pubmed/32786681</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1021/acs.jproteome.0c00448">10.1021/acs.jproteome.0c00448</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32786681">32786681</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7874939">PMC7874939</a></div></div>
 </div>
 <div id="ref-69obv795" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">766. </div><div class="csl-right-inline"><a href="https://ensembl.org">https://ensembl.org</a></div>
+<div class="csl-left-margin">766. </div><div class="csl-right-inline"><strong>Ensembl genome browser 111</strong> <a href="https://useast.ensembl.org/index.html">https://useast.ensembl.org/index.html</a></div>
 </div>
 <div id="ref-1EGyqGdLr" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">767. </div><div class="csl-right-inline"><strong>Ensembl Genomes</strong> <a href="http://ensemblgenomes.org/">http://ensemblgenomes.org/</a></div>

diff --git a/manuscript.md b/manuscript.md
@@ -41,8 +41,8 @@ header-includes: |
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   <meta name="citation_publication_date" content="2024-04-09" />
   <meta property="article:published_time" content="2024-04-09" />
-  <meta name="dc.modified" content="2024-04-09T15:11:50+00:00" />
-  <meta property="article:modified_time" content="2024-04-09T15:11:50+00:00" />
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@@ -136,9 +136,9 @@ header-includes: |
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+  <link rel="alternate" type="text/html" href="https://jessegmeyerlab.github.io/proteomics-tutorial/v/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0/" />
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 <small><em>
 This manuscript
-([permalink](https://jessegmeyerlab.github.io/proteomics-tutorial/v/f71427c3fa278a2f63693b9d6663fae1dbf9b465/))
+([permalink](https://jessegmeyerlab.github.io/proteomics-tutorial/v/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0/))
 was automatically generated
-from [jessegmeyerlab/proteomics-tutorial@f71427c](https://github.com/jessegmeyerlab/proteomics-tutorial/tree/f71427c3fa278a2f63693b9d6663fae1dbf9b465)
+from [jessegmeyerlab/proteomics-tutorial@882d8a9](https://github.com/jessegmeyerlab/proteomics-tutorial/tree/882d8a9eaaab75de6b2e55f77e9359bd59fe3bd0)
 on April 9, 2024.
 </em></small>
 
@@ -999,7 +999,7 @@ Therefore, this will allow more protein isoforms and post-translational modifica
 Table 2: Common proteases used for proteomics. 
 
 |  Protease |  source | class | specificity | optimal pH |  notes |
-|:-----------:|:--------:|:--------------------------:|:-----------:|:-----------:|
+|:-----------:|:--------:|:--------------------------:|:-----------:|:-----------:|:-----------:|
 | Trypsin    | mammal pancreas | serine protease | c-term of R/K, not before P    | 7-9  | most common protease |
 | LysC	     | _Lysobacter enzymogenesis_ | serine protease | c-term of K    | 7-9 | high stability | 
 | Alpha-lytic protease | _Lysobacter enzymogenesis_ | serine protease | c-term of small side chains | 7-9 | high stability | 
@@ -1413,7 +1413,7 @@ This can be performed with the aid of positive or negative pressure to ensure a
 In this step molecules bind the adsorbent and interferences pass through. 
 Next, the column is washed with the mobile phase to eliminate the contaminants while ensuring the analyte remains bound. 
 Finally, peptides are eluted in an appropriate buffer solution with polarity or charge that competes with interaction with the solid phase. 
-](images/SPE_v04.png){#fig:SPE tag="5" width="100%"}
+](images/SPE_v05.png){#fig:SPE tag="5" width="100%"}
 
 #### Specific Types of peptide purification
 There are many additional peptide purification methods that are commonly used in proteomics currently. 

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
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