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	<title>Matrix Science</title>
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		<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>
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		<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>
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		<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>
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		<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>
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		<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>
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		<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>
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		<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>
		</item>
		<item>
		<title>Replacements for NCBI nr</title>
		<link>https://www.matrixscience.com/blog/replacements-for-ncbi-nr.html</link>
		<comments>https://www.matrixscience.com/blog/replacements-for-ncbi-nr.html#comments</comments>
		<pubDate>Fri, 31 Oct 2025 09:00:37 +0000</pubDate>
		<dc:creator>Ville Koskinen</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[database manager]]></category>
		<category><![CDATA[Fasta]]></category>
		<category><![CDATA[NCBI]]></category>
		<category><![CDATA[sysadmin]]></category>

		<guid isPermaLink="false">/?p=10772.html</guid>
		<description><![CDATA[NCBI nr is the comprehensive database of non-identical protein sequences compiled by the National Center for Biotechnology Information. The database configuration has long been shipped with Mascot Server as the NCBIprot predefined definition. However, it seems the FASTA file has quietly been retired; the last version appears to be the February 2024 file. The last-modified [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/replacements-for-ncbi-nr.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Top-3 Quantitation Summary in Mascot Daemon 3 using DDA-PASEF</title>
		<link>https://www.matrixscience.com/blog/top-3-quantitation-summary-in-mascot-daemon-3-using-dda-pasef.html</link>
		<comments>https://www.matrixscience.com/blog/top-3-quantitation-summary-in-mascot-daemon-3-using-dda-pasef.html#comments</comments>
		<pubDate>Tue, 30 Sep 2025 15:00:38 +0000</pubDate>
		<dc:creator>Patrick Emery</dc:creator>
				<category><![CDATA[Blog]]></category>
		<category><![CDATA[ddaPASEF]]></category>
		<category><![CDATA[Mascot Daemon]]></category>
		<category><![CDATA[Mascot Distiller]]></category>
		<category><![CDATA[quantitation]]></category>
		<category><![CDATA[quantitation summary]]></category>
		<category><![CDATA[timsTOF]]></category>

		<guid isPermaLink="false">/?p=10722.html</guid>
		<description><![CDATA[Mascot Daemon includes a protein level quantitation summary report for both precursor based methods (LFQ, SILAC etc) and MS/MS quantitation (iTRAQ, TMT). The exported format is suitable for importing into statistic packages such as R or Perseus. In Mascot Daemon 3, we added an option to export protein intensity values calculated using the &#8220;Top-3&#8243; method. [...]]]></description>
		<wfw:commentRss>https://www.matrixscience.com/blog/top-3-quantitation-summary-in-mascot-daemon-3-using-dda-pasef.html/feed</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
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		<title>New Mascot distributor in India: BioInnovations</title>
		<link>https://www.matrixscience.com/whats_new/new-mascot-distributor-in-india-bioinnovations.html</link>
		<comments>https://www.matrixscience.com/whats_new/new-mascot-distributor-in-india-bioinnovations.html#comments</comments>
		<pubDate>Thu, 18 Sep 2025 07:49:20 +0000</pubDate>
		<dc:creator>Web Master</dc:creator>
				<category><![CDATA[News]]></category>

		<guid isPermaLink="false">/?p=10702.html</guid>
		<description><![CDATA[We are pleased to announce a new distributor for Matrix Science products! Customers in India and neighbouring countries can now buy Mascot Server through BioInnovations, who provide instruments, software, services and consumables for life sciences and analytical and clinical labs. In addition to India, the distribution agreement covers Bangladesh, Bhutan, Maldives, Nepal and Sri Lanka. [...]]]></description>
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