tag:blogger.com,1999:blog-17504313303541581542024-03-13T21:43:00.608+01:00findX software & updatesfindX sofware & updateshttp://www.blogger.com/profile/11551560832494417936noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-1750431330354158154.post-42604311062928649062012-06-24T10:13:00.001+02:002012-06-24T10:20:39.688+02:00Two working versions of findX<br />
<span style="font-family: Georgia, 'Times New Roman', serif;"><b>These latest findX versions</b> </span><span style="font-family: Georgia, 'Times New Roman', serif;">(FINDX_BS3g_7ppm.py & FINDX_BS3g_20ppm.py) for use with the BS3 cross-linker can be found</span><span style="font-family: Georgia, 'Times New Roman', serif;"> <a href="https://docs.google.com/uc?id=0B-gNVIu5jBm9RkYycFpMZEhhaEk">here</a></span><span style="font-family: Georgia, 'Times New Roman', serif;"> (7ppm) and <a href="https://docs.google.com/uc?id=0B-gNVIu5jBm9WlZMRmJWVDRDMVE" target="_blank">here</a> (20 ppm)</span><span style="font-family: Georgia, 'Times New Roman', serif;">.</span><br />
<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">If you're new to findX please view the <a href="https://docs.google.com/uc?id=0B-gNVIu5jBm9NzZmNWNlZjQtZDY5ZS00MmY0LWEwNGEtNGFiZWFlZThlNmU2" target="_blank">manual</a>. In order to run findX you must have <a href="http://www.python.org/getit/releases/2.7.2/" target="_blank">Python version 2.7.2</a> installed on your machine.</span><br />
<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><br /></span><br />
<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">In this version of findX I have:</span><br />
<span style="font-family: Georgia, 'Times New Roman', serif;"><br /></span><br />
<ul>
<li><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Fixed some bugs in MSMS mode.</span></li>
<li><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Introduced the possibility to run findX with isotope mixes other than 50%.</span></li>
<li><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Added a filter based on peak intensities.</span></li>
<li><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Improved the sensitivity for H12/D12 doublet verification.</span></li>
<ul>
<li><span style="font-family: Georgia, 'Times New Roman', serif;">Either a stringent 7 ppm cut-off for doublet verification, or a more loose 20 ppm cut-off.</span></li>
</ul>
</ul>
<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Please note that the distiller compatibility is still not full functional. Also, peak list files need to be prepared for findX being able to read them properly.</span><br />
<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><br /></span><br />
<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Please cite: Söderberg <i>et al.</i> (2012)</span><span style="font-family: Georgia, 'Times New Roman', serif;"> Detection of crosslinks within and between proteins by LC-MALDI-TOFTOF and the software FINDX to reduce the MSMS-data to acquire for validation (<a href="http://www.blogger.com/goog_1481990198">DOI: </a><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038927">10.1371/journal.pone.0038927</a>) if you use findX.</span>findX sofware & updateshttp://www.blogger.com/profile/11551560832494417936noreply@blogger.com0tag:blogger.com,1999:blog-1750431330354158154.post-13386237236163950402011-08-04T11:59:00.001+02:002011-08-04T14:23:24.570+02:00FINDX_BS3e.py<div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><b>The latest findX software</b> (FINDX_BS3e.py) for use with the BS3 cross-linker can be found <span class="Apple-style-span"><a href="https://docs.google.com/uc?id=0B-gNVIu5jBm9YjM1ZTI4MWMtYTYxNy00NmYzLTk3MWMtZTU1Nzc4Njk4MDdl">here</a></span></span><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">.</span></div><div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">If you're new to findX please view the <a href="https://docs.google.com/uc?id=0B-gNVIu5jBm9NzZmNWNlZjQtZDY5ZS00MmY0LWEwNGEtNGFiZWFlZThlNmU2">manual</a>. In order to run findX you must have <a href="http://www.python.org/getit/releases/2.7.2/">Python version 2.7.2</a> installed on your machine.</span></div><div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><span class="Apple-style-span" style="background-color: #f1c232;"><br />
</span></span></div><div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">In this version of findX I have:</span></div><div style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"></div><ul><li><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Added support for </span><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><a href="http://www.matrixscience.com/distiller.html">Mascot Distiller</a></span><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"> output. Basically if you use Mascot Distiller to extract and process data from your MALDI mass spectrometer, and output it to .txt (comprehensive) or .mgf (mascot generic file) files then findX can now read the relevant information (peak masses and intensities).</span></li>
<li><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Added better control of the merging process in MS mode. You can now set a dedicated tolerance level for merging masses and a dedicated tolerance level for matching masses.</span></li>
</ul><div><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><br />
</span></div><div><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><i>Please direct any questions or bugs either in the comment section below, or to <a href="mailto:findxlink@gmail.com">findxlink@gmail.com</a>. </i></span><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"><i>To make it easier to find the problem p</i></span><i><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">aste any error message received. And if you email then attach data files</span><span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;"> in use e.g. sequence file(s), peak lists (zipped) and FINDX_settings.txt.</span></i></div>findX sofware & updateshttp://www.blogger.com/profile/11551560832494417936noreply@blogger.com0tag:blogger.com,1999:blog-1750431330354158154.post-86318921740497396412011-07-14T16:39:00.003+02:002011-08-04T11:58:32.253+02:00findX blog premiere<span class="Apple-style-span" style="font-family: Georgia, 'Times New Roman', serif;">Here is where you will find up to date versions of the findX software used to annotate masses found with MALDI mass spectrometry.</span>findX sofware & updateshttp://www.blogger.com/profile/11551560832494417936noreply@blogger.com0