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	<title>Matrix Science</title>
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		<title>Automation of report creation for Mascot Distiller: MSstats report</title>
		<link>https://www.matrixscience.com/blog/automation-of-report-creation-for-mascot-distiller-msstats-report.html</link>
		<comments>https://www.matrixscience.com/blog/automation-of-report-creation-for-mascot-distiller-msstats-report.html#comments</comments>
		<pubDate>Tue, 23 Jun 2026 09:50:38 +0000</pubDate>
		<dc:creator>Richard Jacob</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[AI]]></category>
		<category><![CDATA[Mascot Distiller]]></category>
		<category><![CDATA[reports]]></category>
		<category><![CDATA[statistics]]></category>

		<guid isPermaLink="false">/?p=11110.html</guid>
		<description><![CDATA[In April&#8217;s blog post, we introduced the mascot-parser skill and developed an example QC plot. In this follow-up post, we introduce a Mascot Distiller skill and develop a new report that saves an MSstats formatted file from Distiller results. Mascot Distiller has a range of reports that cover a lot of common use cases. It [...]]]></description>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>ASMS 2026 poster PDFs now available</title>
		<link>https://www.matrixscience.com/whats_new/asms-2026-poster-pdfs-now-available.html</link>
		<comments>https://www.matrixscience.com/whats_new/asms-2026-poster-pdfs-now-available.html#comments</comments>
		<pubDate>Wed, 17 Jun 2026 08:06:12 +0000</pubDate>
		<dc:creator>Web Master</dc:creator>
				<category><![CDATA[News]]></category>

		<guid isPermaLink="false">/?p=11123.html</guid>
		<description><![CDATA[It was a pleasure to meet many of you at ASMS 2026 in San Diego, CA this June. We presented three posters featuring Mascot DIA using real data. PDF copies of the posters are now available.]]></description>
		<wfw:commentRss>https://www.matrixscience.com/whats_new/asms-2026-poster-pdfs-now-available.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Automate data processing and reporting with coding assistants</title>
		<link>https://www.matrixscience.com/blog/automate-data-processing-and-reporting-with-coding-assistants.html</link>
		<comments>https://www.matrixscience.com/blog/automate-data-processing-and-reporting-with-coding-assistants.html#comments</comments>
		<pubDate>Tue, 28 Apr 2026 15:10:14 +0000</pubDate>
		<dc:creator>Richard Jacob</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[AI]]></category>
		<category><![CDATA[automation]]></category>
		<category><![CDATA[Mascot Daemon]]></category>
		<category><![CDATA[QC]]></category>
		<category><![CDATA[reports]]></category>

		<guid isPermaLink="false">/?p=10997.html</guid>
		<description><![CDATA[With the advent of large language model (LLM) coding assistants developing software and novel reports has never been easier. We now provide a coding skill for LLMs that allows the coding assistant to interact with Mascot Server, automate tasks and generate custom reports. Although LLMs are well known to hallucinate, the coding skill combined with good planning of the [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/automate-data-processing-and-reporting-with-coding-assistants.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Mitigations against uncontrolled web crawlers and bots</title>
		<link>https://www.matrixscience.com/whats_new/mitigations-against-uncontrolled-web-crawlers-and-bots.html</link>
		<comments>https://www.matrixscience.com/whats_new/mitigations-against-uncontrolled-web-crawlers-and-bots.html#comments</comments>
		<pubDate>Fri, 27 Mar 2026 09:30:54 +0000</pubDate>
		<dc:creator>Web Master</dc:creator>
				<category><![CDATA[News]]></category>

		<guid isPermaLink="false">/?p=10974.html</guid>
		<description><![CDATA[The server running matrixscience.com is being overwhelmed by millions of HTTP requests from distributed botnets, which amounts to a distributed denial of service (DDoS) attack. Due to the high load, matrixscience.com has been periodically unavailable this week as the server does not have enough hardware resources. We are now forced to restrict access to certain [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/whats_new/mitigations-against-uncontrolled-web-crawlers-and-bots.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Processing Thunder-DDA-PASEF data with Mascot Distiller</title>
		<link>https://www.matrixscience.com/blog/processing-thunder-dda-pasef-data-with-mascot-distiller.html</link>
		<comments>https://www.matrixscience.com/blog/processing-thunder-dda-pasef-data-with-mascot-distiller.html#comments</comments>
		<pubDate>Mon, 23 Mar 2026 10:47:27 +0000</pubDate>
		<dc:creator>Patrick Emery</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[hla]]></category>
		<category><![CDATA[machine learning]]></category>
		<category><![CDATA[Mascot Distiller]]></category>
		<category><![CDATA[MS2PIP]]></category>
		<category><![CDATA[peak picking]]></category>
		<category><![CDATA[timsTOF]]></category>

		<guid isPermaLink="false">/?p=10952.html</guid>
		<description><![CDATA[Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets in vaccine and immunotherapy development. They are also challenging to identify in standard mass-spec based proteomics; they are typically short, present at low abundance, and are not generated by a specific protease, requiring that search without enzyme specificity is conducted &#8211; dramatically increasing [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/processing-thunder-dda-pasef-data-with-mascot-distiller.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Change of address for UK office</title>
		<link>https://www.matrixscience.com/whats_new/change-of-address-for-uk-office.html</link>
		<comments>https://www.matrixscience.com/whats_new/change-of-address-for-uk-office.html#comments</comments>
		<pubDate>Sun, 01 Mar 2026 09:00:33 +0000</pubDate>
		<dc:creator>Web Master</dc:creator>
				<category><![CDATA[News]]></category>

		<guid isPermaLink="false">/?p=10937.html</guid>
		<description><![CDATA[The physical office of Matrix Science Ltd has moved one block up the road. The new address is: Matrix Science Ltd 83 Baker Street London, W1U 6AG United Kingdom Matrix Science Ltd has been based in London, UK since 1998; the old address was 64 Baker Street. There is no other change to our contact [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/whats_new/change-of-address-for-uk-office.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Identifying Mycobacteria with custom spectral libraries</title>
		<link>https://www.matrixscience.com/blog/identifying-mycobacteria-with-custom-spectral-libraries.html</link>
		<comments>https://www.matrixscience.com/blog/identifying-mycobacteria-with-custom-spectral-libraries.html#comments</comments>
		<pubDate>Thu, 26 Feb 2026 14:24:56 +0000</pubDate>
		<dc:creator>Richard Jacob</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[metaproteomics]]></category>
		<category><![CDATA[spectral library]]></category>

		<guid isPermaLink="false">/?p=10854.html</guid>
		<description><![CDATA[Mass spectrometry can be used for rapid identification of difficult to culture or slow growing bacteria so that the patient can receive prompt treatment. The quickest identification method is searching the MS/MS spectra against a species-specific spectral library (SL). Here, we detail the steps to build a custom Mycobacteria spectral library and using it with [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/identifying-mycobacteria-with-custom-spectral-libraries.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Converting BLIB spectral libraries to MSP (and back again) for use with Mascot Server</title>
		<link>https://www.matrixscience.com/blog/converting-blib-spectral-libraries-to-msp-and-back-again-for-use-with-mascot-server.html</link>
		<comments>https://www.matrixscience.com/blog/converting-blib-spectral-libraries-to-msp-and-back-again-for-use-with-mascot-server.html#comments</comments>
		<pubDate>Wed, 04 Feb 2026 06:49:30 +0000</pubDate>
		<dc:creator>Richard Jacob</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[metaproteomics]]></category>
		<category><![CDATA[spectral library]]></category>

		<guid isPermaLink="false">/?p=10865.html</guid>
		<description><![CDATA[Mascot Server can create and search NIST MSP formatted spectral libraries. However, BiblioSpec, which is part of the Skyline software, creates spectral libraries in the BLIB format which cannot be used. We have developed a script that can convert BLIB to MSP files or vice versa, MSP to BLIB files. The conversion script allows Mascot [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/converting-blib-spectral-libraries-to-msp-and-back-again-for-use-with-mascot-server.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Strange software failures? Check your disk space</title>
		<link>https://www.matrixscience.com/blog/strange-software-failures-check-your-disk-space.html</link>
		<comments>https://www.matrixscience.com/blog/strange-software-failures-check-your-disk-space.html#comments</comments>
		<pubDate>Tue, 30 Dec 2025 11:43:02 +0000</pubDate>
		<dc:creator>Ville Koskinen</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[database manager]]></category>
		<category><![CDATA[Mascot Daemon]]></category>
		<category><![CDATA[Mascot Distiller]]></category>
		<category><![CDATA[MGF]]></category>
		<category><![CDATA[sysadmin]]></category>

		<guid isPermaLink="false">/?p=10828.html</guid>
		<description><![CDATA[From time to time, a piece of software that has been working reliably suddenly doesn&#8217;t. The most common reason for Mascot Server to fail is running out of disk space, which can cause all kinds of weird faults. Proteomics software is more prone to it than others due to the large size of input data [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/strange-software-failures-check-your-disk-space.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Peak list arcana: Area vs. signal to noise</title>
		<link>https://www.matrixscience.com/blog/peak-list-arcana-area-vs-signal-to-noise.html</link>
		<comments>https://www.matrixscience.com/blog/peak-list-arcana-area-vs-signal-to-noise.html#comments</comments>
		<pubDate>Wed, 26 Nov 2025 09:00:20 +0000</pubDate>
		<dc:creator>Patrick Emery</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[Mascot Distiller]]></category>
		<category><![CDATA[peak picking]]></category>
		<category><![CDATA[site analysis]]></category>

		<guid isPermaLink="false">/?p=10788.html</guid>
		<description><![CDATA[A recent paper from Hijazi et al. [1] raised some interesting points about how a peaklists file can differ from the appearance of the underlying raw file, and specifically raised some differences with the peaklists generated by Mascot Distiller if you output the signal to noise (S/N) as fragment ion intensity instead of the default, [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/peak-list-arcana-area-vs-signal-to-noise.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
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