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	<title>Proteomics 2.0</title>
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	<link>http://proteomics2.com</link>
	<description>A community for the new generation of proteomics, hosted by Sage-N Research, Inc.</description>
	<pubDate>Tue, 24 Aug 2010 00:42:32 +0000</pubDate>
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			<item>
		<title>Changing nature of software in Proteomics (or why you can&#8217;t buy great software for SILAC)</title>
		<link>http://proteomics2.com/?p=158</link>
		<comments>http://proteomics2.com/?p=158#comments</comments>
		<pubDate>Fri, 28 May 2010 12:05:00 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[Views]]></category>

		<category><![CDATA[ETD]]></category>

		<category><![CDATA[proteomics]]></category>

		<category><![CDATA[SILAC]]></category>

		<category><![CDATA[Sorcerer]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=158</guid>
		<description><![CDATA[by David.Chiang@SageNResearch.com
Proteomics technology is now a robust discovery tool, at least in capable hands with the right tools, for characterizing post-translational modifications such as phosphorylation, right alongside gene expression and cellular imaging for tumor and stem cell research.
However, the complexity, scale, and criticality of the data from a modern mass spectrometer such as an Orbitrap [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=158</wfw:commentRss>
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		<item>
		<title>&#8220;Translational Proteomics 2.0&#8243; User Meeting before ASMS</title>
		<link>http://proteomics2.com/?p=157</link>
		<comments>http://proteomics2.com/?p=157#comments</comments>
		<pubDate>Wed, 19 May 2010 18:28:29 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[News]]></category>

		<category><![CDATA[John Yates]]></category>

		<category><![CDATA[Sorcerer]]></category>

		<category><![CDATA[Steve Gygi]]></category>

		<category><![CDATA[translational proteomics]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=157</guid>
		<description><![CDATA[The meeting is open to in-warranty Sorcerer customers and by invitation only. Pre-registration is required. A light buffet and refreshments are being provided, and there will be a drawing for customer door prizes. We will have the brand-new, ultra-cool Apple iPad as our door prize! (But make sure you come on time for the best [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=157</wfw:commentRss>
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		<item>
		<title>Introducing SEQUEST 3G - A New Translational Proteomics Standard</title>
		<link>http://proteomics2.com/?p=153</link>
		<comments>http://proteomics2.com/?p=153#comments</comments>
		<pubDate>Mon, 10 May 2010 20:54:28 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[News]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=153</guid>
		<description><![CDATA[

What exactly is SEQUEST 3G? What can it do for me?
SEQUEST 3G is the latest, next-generation SEQUEST standard specifically developed and optimized for translational proteomic applications involving phosphorylation and other post-translational modifications (PTMs). Defined by Sage-N Research in close collaboration with Dr. John R. Yates, III of the Scripps Research Institute, SEQUEST 3G defines a [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=153</wfw:commentRss>
		</item>
		<item>
		<title>Which SORCERER is right for you?</title>
		<link>http://proteomics2.com/?p=154</link>
		<comments>http://proteomics2.com/?p=154#comments</comments>
		<pubDate>Mon, 10 May 2010 20:51:05 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[Views]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=154</guid>
		<description><![CDATA[As you may know, Sage-N Research offers three SORCERER platforms —  the SORCERER Enterprise,  the SORCERER 2, and  the SORCERER Lab.
The SORCERER Enterprise
The SORCERER Enterprise is a customizable and secure  throughput and biorepository system for aggregate analysis. Provided as a  scalable Blade server with integrated life-science optimized storage,  the [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=154</wfw:commentRss>
		</item>
		<item>
		<title>The Truth About Probability Scores</title>
		<link>http://proteomics2.com/?p=152</link>
		<comments>http://proteomics2.com/?p=152#comments</comments>
		<pubDate>Mon, 10 May 2010 19:59:48 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[tips and hints]]></category>

		<category><![CDATA[binomial score]]></category>

		<category><![CDATA[Probability Score]]></category>

		<category><![CDATA[proteomics]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=152</guid>
		<description><![CDATA[&#8220;All models are wrong, but some are useful.&#8221; George E. P. Box
The Truth About Probability Scores
What is Probability Scoring?
Probability Scoring is a popular method of ranking possible peptide sequences that best fits an observed tandem mass spectrum. This can be computed as the primary score in a search engine (e.g. Mascot), or as a second [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=152</wfw:commentRss>
		</item>
		<item>
		<title>What Probability Scoring algorithm does the SORCERER offer?</title>
		<link>http://proteomics2.com/?p=155</link>
		<comments>http://proteomics2.com/?p=155#comments</comments>
		<pubDate>Mon, 10 May 2010 19:30:26 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[Views]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=155</guid>
		<description><![CDATA[Starting with v4.0 software, the Sage-N Research SORCERER platform will  provide the 2-stage scoring (i.e. different from 2-stage searching)  architecture that generally mimics the current Gygi Lab workflow, which  does a first-stage SEQUEST (i.e. SEQUEST 3G starting with v4.0) followed  by our open-source MUSE scripting version of the Gygi Lab&#8217;s &#8220;Bino [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=155</wfw:commentRss>
		</item>
		<item>
		<title>New workflow for XCalibur 2.1 RAW files (Velos) is released to beta</title>
		<link>http://proteomics2.com/?p=148</link>
		<comments>http://proteomics2.com/?p=148#comments</comments>
		<pubDate>Tue, 02 Mar 2010 02:24:23 +0000</pubDate>
		<dc:creator>james</dc:creator>
		
		<category><![CDATA[Application notes]]></category>

		<category><![CDATA[Interesting]]></category>

		<category><![CDATA[News]]></category>

		<category><![CDATA[tips and hints]]></category>

		<category><![CDATA[XCalibur RAW Velos msconvert ReAdW]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=148</guid>
		<description><![CDATA[We have developed an new flow for processing Thermo RAW files that works both with the most recent XCalibur V2.1, as well as with earlier versions. This flow has been giving good results in internal testing, and we are now releasing it for beta testing to any interested, actively supported Sorcerer customer.
Thermo LTQ Velos users [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=148</wfw:commentRss>
		</item>
		<item>
		<title>Video: &#8220;Peptide ID with Target-Decoy Searching&#8221; by Prof. Josh Elias (Stanford)</title>
		<link>http://proteomics2.com/?p=146</link>
		<comments>http://proteomics2.com/?p=146#comments</comments>
		<pubDate>Sat, 09 Jan 2010 03:26:35 +0000</pubDate>
		<dc:creator>techteam</dc:creator>
		
		<category><![CDATA[Download]]></category>

		<category><![CDATA[Interesting]]></category>

		<category><![CDATA[Webcasts]]></category>

		<category><![CDATA[tips and hints]]></category>

		<category><![CDATA[Decoy]]></category>

		<category><![CDATA[FDR]]></category>

		<category><![CDATA[mass spec]]></category>

		<category><![CDATA[proteomics]]></category>

		<category><![CDATA[SEQUEST]]></category>

		<category><![CDATA[Sorcerer]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=146</guid>
		<description><![CDATA[
Prof. Josh Elias (left) of Stanford University receives a thank-you gift from David Chiang after his talk.
Ever wondered about target-decoy searching?  Want to gain a better understanding and realistic expectation of this effective tool? SageNResearch’s video “Addressing Peptide Identification Signal-to-noise With Target-Decoy Searching”, given by Professor Josh Elias of Stanford University at our “Translational [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=146</wfw:commentRss>
		</item>
		<item>
		<title>Video: &#8220;Peptide ID and Protein Inference..&#8221; by Prof. Alexey Nesvizhskii (U. Michigan)</title>
		<link>http://proteomics2.com/?p=144</link>
		<comments>http://proteomics2.com/?p=144#comments</comments>
		<pubDate>Wed, 16 Sep 2009 19:23:58 +0000</pubDate>
		<dc:creator>techteam</dc:creator>
		
		<category><![CDATA[Download]]></category>

		<category><![CDATA[Interesting]]></category>

		<category><![CDATA[News]]></category>

		<category><![CDATA[Webcasts]]></category>

		<category><![CDATA[tips and hints]]></category>

		<category><![CDATA[Alexey Nesvizhskii]]></category>

		<category><![CDATA[PeptideProphet]]></category>

		<category><![CDATA[protein ID]]></category>

		<category><![CDATA[ProteinProphet]]></category>

		<category><![CDATA[proteomics]]></category>

		<category><![CDATA[Sorcerer]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=144</guid>
		<description><![CDATA[
Prof. Alexey Nesvizhskii (left) of University of Michigan receives a thank-you gift from David Chiang after his talk.
If you really want to understand how peptide and protein identification is done, this video talk is a must-see!
Professor Alexey Nesvizhskii of the University of Michigan is one of the co-inventors (with Dr. Andy Keller) of the popular [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=144</wfw:commentRss>
		</item>
		<item>
		<title>Secret Insights to Translational Proteomics Success</title>
		<link>http://proteomics2.com/?p=142</link>
		<comments>http://proteomics2.com/?p=142#comments</comments>
		<pubDate>Wed, 02 Sep 2009 22:18:48 +0000</pubDate>
		<dc:creator>david</dc:creator>
		
		<category><![CDATA[Interesting]]></category>

		<category><![CDATA[mass spec]]></category>

		<category><![CDATA[protein ID]]></category>

		<category><![CDATA[proteomics]]></category>

		<category><![CDATA[SEQUEST]]></category>

		<category><![CDATA[Sorcerer]]></category>

		<category><![CDATA[translational medicine]]></category>

		<category><![CDATA[translational proteomics]]></category>

		<guid isPermaLink="false">http://proteomics2.com/?p=142</guid>
		<description><![CDATA[by David.Chiang@SageNResearch.com
Proteomics mass spectrometry is finally sensitive and specific enough for robust translational medicine (at least in capable hands), and holds tremendous promise to revolutionize biology and medicine. For some, it holds the key to incredible research power for decades to come.
However, there is a chasm that continues to grow between the productive and unproductive [...]]]></description>
		<wfw:commentRss>http://proteomics2.com/?feed=rss2&amp;p=142</wfw:commentRss>
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