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#massspec

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Matrix Science Ltd<p>Sometimes you need a very large sequence database, e.g. search all proteobacteria proteins. Mascot Server has no size limit. Search a database of hundreds of millions of protein sequences without running out of resources.</p><p><a href="https://www.matrixscience.com/blog/big-databases-and-large-peak-lists.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/blog/big-dat</span><span class="invisible">abases-and-large-peak-lists.html</span></a></p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p>
Matrix Science Ltd<p>If your computer breaks down, do you know how to restore Mascot? As long as you regularly back up the right directories and files, it's straightfoward and fully described in the online help:</p><p><a href="https://www.matrixscience.com/help/disaster_recovery.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/help/disaste</span><span class="invisible">r_recovery.html</span></a></p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p>
Matrix Science Ltd<p>Mascot Newsletter, March 2025:</p><p>50% more identifications in Thermo Proteome Discoverer.</p><p>Maternal immune activation imprints translational dysregulation.</p><p>Mascot's ML adapter framework (US HUPO 2025 poster).</p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p><p><a href="https://www.matrixscience.com/nl/202503/newsletter.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/nl/202503/ne</span><span class="invisible">wsletter.html</span></a></p>
Cowboy Cat Ranch<p>Does anyone with a degree in chemistry have any idea what the authors mean with this? HOW did they end up with 5 different functional fractions? <a href="https://mastodon.online/tags/chemistry" class="mention hashtag" rel="tag">#<span>chemistry</span></a> <a href="https://mastodon.online/tags/OC" class="mention hashtag" rel="tag">#<span>OC</span></a> <a href="https://mastodon.online/tags/HPLC" class="mention hashtag" rel="tag">#<span>HPLC</span></a> <a href="https://mastodon.online/tags/MassSpec" class="mention hashtag" rel="tag">#<span>MassSpec</span></a></p>
Julian Bender<p>German mass spectrometry society (DGMS) annual meeting starting this evening in <a href="https://digitalcourage.social/tags/goettingen" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>goettingen</span></a> . Looking forward to three days of science and all things <a href="https://digitalcourage.social/tags/massspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspec</span></a>!</p>
Matrix Science Ltd<p>Mascot Distiller provides DDA LFQ for Bruker, Sciex, Thermo and Waters instruments. Retention time alignment ("match between runs"); ion mobility (Bruker TIMS); fractionation; optimised peak detection; visualisation; and more.</p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p><p><a href="https://www.matrixscience.com/distiller.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/distiller.ht</span><span class="invisible">ml</span></a></p>
Matrix Science Ltd<p>Mascot Newsletter, February 2025:</p><p>Mascot vs FragPipe: semi-tryptic TMTpro.</p><p>Characterization of the noncanonical proteome.</p><p>Mascot Server 3.1 is now available.</p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p><p><a href="https://www.matrixscience.com/nl/202502/newsletter.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/nl/202502/ne</span><span class="invisible">wsletter.html</span></a></p>
Matrix Science Ltd<p>Mascot Distiller can now use machine learning to boost sensitivity of protein quantitation. We processed a Thermo Orbitrap DDA LFQ benchmark data set, where Distiller now quantitates 14% more proteins at 1% FDR.</p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p><p><a href="https://www.matrixscience.com/blog/mascot-distiller-quantitates-more-proteins-with-machine-learning.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/blog/mascot-</span><span class="invisible">distiller-quantitates-more-proteins-with-machine-learning.html</span></a></p>
⏣ Prof. Oliver Jones<p>I am super excited to be an invited speaker at AUS-oMicS 2025 in beautiful Cairns. I'll be talking about my work using mass spectrometry to track pollutants in the environment and assess their effects on biological systems via <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metabolomics</span></a>. <br> <br>The oral abstract submission deadline has been extended until February 14th 2025. Submit yours today and register at <a href="https://www.ausomics.com" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">ausomics.com</span><span class="invisible"></span></a></p><p>See you there!</p><p><a href="https://fosstodon.org/tags/TeamMassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TeamMassSpec</span></a> <a href="https://fosstodon.org/tags/massspectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspectrometry</span></a> <a href="https://fosstodon.org/tags/massspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspec</span></a> <a href="https://fosstodon.org/tags/ozchem" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ozchem</span></a> <a href="https://fosstodon.org/tags/science" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>science</span></a> <a href="https://fosstodon.org/tags/australia" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>australia</span></a></p>
Matrix Science Ltd<p>Do you use Thermo Proteome Discoverer with Mascot Server? Mascot Server 3.1 can now send results refined with machine learning directly to PD.</p><p>PD 3.1: Identify over 20% more proteins.<br>PD 2.4: Identify over 40% more proteins.</p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p><p><a href="https://www.matrixscience.com/blog/using-machine-learning-with-mascot-and-proteome-discoverer.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/blog/using-m</span><span class="invisible">achine-learning-with-mascot-and-proteome-discoverer.html</span></a></p>
Johannes Rainer<p>Having a great time at the <a href="https://fosstodon.org/tags/EuBIC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EuBIC2025</span></a> developers meeting with our <a href="https://fosstodon.org/tags/SpectriPy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SpectriPy</span></a> hackathon for combined <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>rstats</span></a> :rstats: / <a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python</span></a> :python: <a href="https://fosstodon.org/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a> data analysis. </p><p>Here part of our team on a short hike ⛰️ to get some fresh air for our 🧠</p>
Matrix Science Ltd<p>Mascot Server 3.1 is a patch release that enhances integration with Thermo Proteome Discoverer and fixes a few important bugs introduced in Mascot Server 3.0. You can now import refined results directly from Mascot into PD.</p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p><p><a href="https://www.matrixscience.com/help/mascot_server_3_1_release.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/help/mascot_</span><span class="invisible">server_3_1_release.html</span></a></p>
JIPB<p>In this new <a href="https://mstdn.science/tags/JIPB" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>JIPB</span></a> invited expert review, Sang et al. explore the role of <a href="https://mstdn.science/tags/MassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpectrometry</span></a>-based <a href="https://mstdn.science/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> as powerful analytics tools to further <a href="https://mstdn.science/tags/PlantScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PlantScience</span></a> research.<br><a href="https://doi.org/10.1111/jipb.13841" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.1111/jipb.13841</span><span class="invisible"></span></a> <br>@wileyplantsci<br> <a href="https://mstdn.science/tags/plant" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>plant</span></a> <a href="https://mstdn.science/tags/botany" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>botany</span></a> <a href="https://mstdn.science/tags/massspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspec</span></a></p>
Matrix Science Ltd<p>Mascot Newsletter, January 2025:</p><p>Learn how Mascot uses machine learning.</p><p>Characterising a bacterial microcompartment.</p><p>Mascot protein inference.</p><p><a href="https://www.matrixscience.com/nl/202501/newsletter.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/nl/202501/ne</span><span class="invisible">wsletter.html</span></a></p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p>
Matrix Science Ltd<p>Mascot Server has a lot of functionality and it's sometimes hard to know where to start. The online help now has a table of example data sets shipped with Mascot, including links to the corresponding help topics.</p><p><a href="https://www.matrixscience.com/help.html#EXAMPLES" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/help.html#EX</span><span class="invisible">AMPLES</span></a></p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p>
Matrix Science Ltd<p>If a peptide has two serines and a single phosphate, site assignment may be ambiguous. Mascot helps by calculating a site localisation confidence, where the assignment with more MS/MS evidence gets higher confidence.</p><p><a href="https://www.matrixscience.com/help/site_analysis_help.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/help/site_an</span><span class="invisible">alysis_help.html</span></a></p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p>
Matrix Science Ltd<p>Database searches with semi-specific enzyme traditionally have low sensitivity due to the large search space. Except, Mascot Server 3.0 includes MS²PIP, which boosts sensitivity. We've compared the results to a recent FragPipe publication.</p><p><a href="https://www.matrixscience.com/blog/mascot-vs-fragpipe-uncovering-endogenous-proteolytic-processing.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/blog/mascot-</span><span class="invisible">vs-fragpipe-uncovering-endogenous-proteolytic-processing.html</span></a><br><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/massspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspec</span></a></p>
Matrix Science Ltd<p>Mascot Newsletter, December 2024:</p><p>Predicted fragment intensities with Mascot Server 3.0.</p><p>Self-ligating surface receptor and CD8+ T-cells.</p><p>Saving search results as HTML.</p><p><a href="https://www.matrixscience.com/nl/202412/newsletter.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">matrixscience.com/nl/202412/ne</span><span class="invisible">wsletter.html</span></a><br><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/massspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspec</span></a></p>
Matrix Science Ltd<p>Mascot Daemon is the automation client bundled with Mascot Server. The Quantitation Summary report is an easy way to export protein expression data for complex experiments.</p><p><a href="https://youtu.be/4Ds59gYhL4Q" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">youtu.be/4Ds59gYhL4Q</span><span class="invisible"></span></a></p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/massspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>massspec</span></a></p>
Matrix Science Ltd<p>Check out how Mascot Server 3.0 and MS²PIP work together to boost protein and peptide identifications.</p><p><a href="https://youtu.be/O7LSREqiW8o" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">youtu.be/O7LSREqiW8o</span><span class="invisible"></span></a> </p><p><a href="https://mastodon.social/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.social/tags/MassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MassSpec</span></a></p>
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