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help.php
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help.php
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<!DOCTYPE HTML>
<html>
<head>
<?php
$pageName = "Help";
include("head.php");
include("xiSPEC_scripts.php");
?>
<script type="text/javascript" src="/js/accordion.js"></script>
<script type="text/javascript" src="/js/directURL.js"></script>
</head>
<body>
<!-- Sidebar -->
<?php include("navigation.php");?>
<!-- Main -->
<div id="main">
<div class="container">
<h1 class="page-header accordionHead">
<i class="fa fa-plus-square" aria-hidden="true"></i> xiSPEC Feature support
</h1>
<div class="accordionContent" style="display: none;" id="features">
<ul>
<li><a href="#Hsave_db">Saving a dataset</a></li>
<li><a href="#Hzoom">Zooming</a></li>
<li><a href="#Hmeasure">Measure distances</a></li>
<li><a href="#HmoveLabels">Move labels</a></li>
<li><a href="#HclChange">Change cross-linker position</a></li>
<li><a href="#HmodChange">Change modification position</a></li>
<li><a href="#Hhighlight">Highlight fragments</h5></a></li>
</ul>
</br>
<ul>
<li>
<h5 id="Hsave_db">Saving a dataset <a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/saving.gif" />
<ul style="margin-left:30px;">
<li>After data processing you can view your data as a temporary dataset</li>
<li>To save your dataset simply click on the save icon</li>
<li>Fill out the form and click save</li>
⇨ You will be redirected to your saved dataset!
</ul>
</p>
<br/>
<li>
<h5 id="Hzoom">Zooming <a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/zoom.gif" />
<ul style="margin-left:30px;">
<li>Click and drag the cursor below the x-axis to zoom into a specific area of the spectrum.</li>
<li>Alternatively you can zoom in/out using the mouse wheel.</li>
⇨ xiSPEC updates the annotated spectrum!
</ul>
</p>
<br/>
<li>
<h5 id="Hmeasure">Measure distances<a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/measure.gif" />
<ul style="margin-left:30px;">
<li>Activate measuring mode by checking the 'Measure' option.</li>
<li>Your cursor will change to a crosshair.</li>
<li>Click and drag in the spectrum to measure distances between peaks.</li>
⇨ xiSPEC displays potential amino acid residue hits in the tooltip!
</ul>
</p>
<br/>
<li>
<h5 id="HmoveLabels">Move labels<a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/moveLabels.gif" />
<ul style="margin-left:30px;">
<li>Activate moveable labels by checking the 'Move labels' option.</li>
<li>Click and drag labels to move them around.</li>
⇨ xiSPEC draws dashed lines to the corresponding peaks!
</ul>
</p>
<br/>
<li>
<h5 id="HclChange">Change cross-linker position <a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/changeCL.gif" />
<ul style="margin-left:30px;">
<li>Click on the cross-link line.</li>
<li>Move the mouse over the desired cross-linked amino acids.</li>
<li>Click on the amino acid to confirm the position(s).</li>
⇨ xiSPEC updates the annotated spectrum!
</ul>
</p>
<br/>
<li>
<h5 id="HmodChange">Change modification position <a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/changeMod.gif" />
<ul style="margin-left:30px;">
<li>Click on the modification.</li>
<li>Move the mouse over the desired modified amino acids.</li>
<li>Click on the amino acid to confirm the position.</li>
⇨ xiSPEC updates the annotated spectrum!
</ul>
</p>
<br/>
<li>
<h5 id="Hhighlight">Highlight fragments <a href="#" title="back to top"><i class="fa fa-arrow-up"></i></a></h5>
</li>
<p>
<img src="/images/gifs/highlighting.gif" />
<ul style="margin-left:30px;">
<li>Hover over fragments in any view to highlight the corresponding fragment all views.</li>
<li>Click on a fragment to make the highlight permanent.</li>
<li>Ctrl+Click to add additional fragments to permanent selection.</li>
<li>Click on the spectrum background to reset highlighting.</li>
</ul>
</p>
</ul>
</div>
<h1 class="page-header accordionHead">
<i class="fa fa-plus-square" aria-hidden="true"></i> Peptide identification csv column headings
</h1>
<div class="accordionContent" style="display: none;" id="csv">
<table class="myTable" id="csvTable">
<thead>
<tr><th>column</th><th>required?</th><th>notes</th><th>default</th><th>example</th></tr>
</thead>
<tbody>
<tr><td>PepSeq 1</td><td>Yes</td><td>Peptide sequence for peptide 1 in one letter amino acid code (uppercase) with modifications following the amino acid and consisting of the following characters: a-z:0-9.()\-</td><td>-</td><td>LKECcmCcmEKPLLEK</td></tr>
<tr><td>PepSeq 2</td><td>No**</td><td>Peptide sequence for peptide 2 in one letter amino acid code (uppercase) with modifications following the amino acid and consisting of the following characters: a-z:0-9.()\-</td><td>-</td><td>HPYFYAPELLFFAKR</td></tr>
<tr><td>LinkPos 1</td><td>No**</td><td>Position of cross-linked residue for peptide 1 (1-based)</td><td>-</td><td>2</td></tr>
<tr><td>LinkPos 2</td><td>No**</td><td>Position of cross-linked residue for peptide 2 (1-based)</td><td>-</td><td>14</td></tr>
<tr><td>Protein 1</td><td>Yes</td><td>Identifier for protein 1. Ambiguous results are represented by listing the alternative proteins separated by semi-colons</td><td>-</td><td>HSA</td></tr>
<tr><td>Protein 2</td><td>No**</td><td>Identifier for protein 2. Ambiguous results are represented by listing the alternative proteins separated by semi-colons</td><td>-</td><td>P02768;P13645</td></tr>
<tr><td>Decoy 1</td><td>No</td><td>Set to true if the peptide 1 is matched to a decoy sequence</td><td>FALSE</td><td>TRUE</td></tr>
<tr><td>Decoy 2</td><td>No</td><td>Set to true if the peptide 2 is matched to a decoy sequence</td><td>FALSE</td><td>TRUE</td></tr>
<tr><td> </td><td></td><td></td><td></td><td></td></tr>
<tr><td>Rank</td><td>No*</td><td>Rank of the identification quality as scored by the search engine (1 is the top rank)</td><td>1</td><td>1</td></tr>
<tr><td>Score</td><td>No</td><td>Confidence score for the identification (number)</td><td>0</td><td>10.5641</td></tr>
<tr><td>PassThreshold</td><td>No</td><td>True if the identification has passed a given threshold or been validated as correct</td><td>TRUE</td><td>FALSE</td></tr>
<tr><td> </td><td></td><td></td><td></td><td></td></tr>
<tr><td>Charge</td><td>Yes</td><td>Precursor charge state</td><td>-</td><td>3</td></tr>
<tr><td>CrossLinkerModMass</td><td>No**</td><td>Modification mass of the used cross-linker</td><td>0</td><td>138.06808</td></tr>
<tr><td>ExpMz</td><td>No</td><td>The mass-to-charge value measured in the experiment in Daltons / charge</td><td>-</td><td>985.4341</td></tr>
<tr><td>CalcMz</td><td>No</td><td>The theoretical mass-to-charge value calculated for the peptide in Daltons / charge.</td><td>-</td><td>985.6531</td></tr>
<tr><td>FragmentTolerance</td><td>No</td><td>MS2 tolerance for annotating fragment peaks (in ppm or Da)</td><td>10 ppm</td><td>0.2 Da</td></tr>
<tr><td>IonTypes</td><td>No</td><td>Fragment ion types to be considered separated by semicolon</td><td>peptide;b;y</td><td>peptide;a;b;c;x;y;z</td></tr>
<tr><td> </td><td></td><td></td><td></td><td></td></tr>
<tr><td>ScanId</td><td>Yes</td><td>mzML: 1-based scan number; MGF: 0-based index in file</td><td>-</td><td>2256</td></tr>
<tr><td>PeakListFileName</td><td>Yes</td><td>File name of the associated peak list file that contains the scan</td><td>-</td><td>example_file.mzML</td></tr>
<tr><td> </td><td></td><td></td><td></td><td></td></tr>
<tr><td>meta_xxx</td><td>No</td><td>Up to 3 user defined columns are allowed (using prefix meta_)</td><td>-</td><td></td></tr>
<tr><td>meta_yyy</td><td>No</td><td>Up to 3 user defined columns are allowed (using prefix meta_)</td><td>-</td><td></td></tr>
<tr><td>meta_zzz</td><td>No</td><td>Up to 3 user defined columns are allowed (using prefix meta_)</td><td>-</td><td></td></tr>
</tbody>
</table>
<br/>
<p style="font-size: small;line-height: 1.5em;">
*required if there are multiple alternative explanations for the same spectrum.</br>
**required for cross-linked peptides.
</p>
</div>
<h1 class="page-header accordionHead">
<i class="fa fa-plus-square" aria-hidden="true"></i> Input data format for manual data input & re-annotation requests
</h1>
<div class="accordionContent" style="display: none;" id="syntax">
<ul>
<li><h5>Peptide Sequence</h5></li>
<table class="myTable" style="max-width: 700px;">
<thead>
<tr>
<th>What?</th>
<th>How?</th>
<th>Example(s)</th>
</tr>
</thead>
<tr>
<td>amino acid residues</td>
<td>uppercase one letter code</td>
<td>ARNDCEQGHILKMFPSTWYV</td>
</tr>
<tr>
<td style="vertical-align:middle;">modifications</td>
<td style="line-height:1.2em;">anything not uppercase<br />(following the residue)</td>
<td style="vertical-align:middle;">Mox | Kbs3nh2 | K(+16)</td>
</tr>
<tr>
<td>peptide delimiter</td>
<td>;</td>
<td rowspan="2" style="vertical-align: middle">K#LM;DAHK#SEVR</td>
</tr>
<tr>
<td>cross-linked residue</td>
<td>#</td>
</tr>
</table>
</p>
<br/>
<li><h5>Peaklist</h5></li>
<p>The peak list format accepted by xiSPEC is simple and easily extracted from most MS formats. Each line contains a pair of numbers: the first is a m/z value and the second is the corresponding intensity. The two numbers should be separated by either spaces or tabs.</p>
<p>
Example:
<br/>104.31995 1077.574
<br/>110.07077 1154.813
<br/>116.98479 1330.395
<br/>120.08031 6500.032
</p>
</ul>
</div>
<h1 class="page-header accordionHead">
<i class="fa fa-plus-square" aria-hidden="true"></i> mzIdentML support
</h1>
<div class="accordionContent" style="display: none;" id="mzIdSupport">
<table class="myTable" id="mzidSupportTable">
HUPO PSI provide <a href="http://www.psidev.info/tools-implementing-mzidentml">a list of tools that support mzIdentML</a>.
<br/>
We tested output from the following tools and confirmed that they successfully worked in xiSPEC. <a href="mailto:[email protected]" title="Contact us">Contact us</a> if you noticed a tool missing from the list and we will add it.
<ul>
<li>
<a href="http://www.matrixscience.com/">Mascot (Matrix Science)</a>
</li>
<li>
<a href="http://www.proteomesoftware.com/products/scaffold/">Scaffold</a>
</li>
<li>
<a href="http://compomics.github.io/projects/peptide-shaker.html">PeptideShaker</a>
</li>
<li>
<a href="https://www.thermofisher.com/order/catalog/product/OPTON-30795">Proteome Discoverer</a>
</li>
<!-- <li>
<a href="https://github.com/Rappsilber-Laboratory/xiFDR">xiFDR</a>
</li> -->
</ul>
</table>
</div>
</div> <!-- CONTAINER -->
</div> <!-- MAIN -->
</body>
</html>