Tag Archives: SEQUEST

How to use SORCERER to search ETD ms/ms spectra

Electron transfer dissociation (ETD) is a promising dissociation technology for analyzing labile post-translational modifications (PTMs) such as phosphorylation. Unlike CID, ETD generates positively charged c and z* (z-radical) ions instead of b and y ions. There are two caveats in … Continue reading

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Video: “Peptide ID with Target-Decoy Searching” by Prof. Josh Elias (Stanford)

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 … Continue reading

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Secret Insights to Translational Proteomics Success

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 … Continue reading

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Announcing Sorcerer PE v4.0 with Enhanced ETD and Quantitation

Our R&D team is busy working on the next major version of the Sorcerer-PE software, and expects to release it to then-in-warranty customers in the next few weeks.  Early previews and beta tests of some of the components will be … Continue reading

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New Target-Decoy capabilities with DTASelect and Muse

We’ve developed a new Muse workflow for target-decoy analysis and false discovery rate estimation, based on our integration of DTASelect from the Yates lab. DTASelect can now use target-decoy FASTA files that are installed on Sorcerer to support its statistical … Continue reading

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Experts agree: use semi-enzymatic search for best sensitivity and specificity

Three of the world’s leading experts on MS-MS protein identification came together recently at Sage-N Research’s annual user group meeting, and presented methods and results for the techniques and tools with which they are associated: Jimmy Eng, co-inventor of Sequest … Continue reading

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Video: “SEQUEST and TPP Tips” by Jimmy Eng (U. Washington)

Jimmy Eng (left) of University of Washington receives a thank-you gift from David Chiang after his talk. During our Translational Proteomics 2.0 Meeting, we were privileged to have Jimmy Eng (University of Washington) give us his uncommon insights into using … Continue reading

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Secrets to successful workflows for advanced ‘Proteomics 2.0′ analyses

Common PC proteomic software is designed primarily to be easy to use with low throughput and small datasets up to a few 1000 spectra. PC programs like Mascot or other software generally work fine at this scale. However, high-throughput and … Continue reading

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Summarize SEQUEST outputs in CSV for Excel with ‘sorcout.mu’

The MUSE script ‘sorcout.mu’ can be used to summarize the top peptide scores from SORCERER-SEQUEST into a CSV format for importing into Excel. This is useful to performing non-standard analyses (i.e. separate from PeptideProphet or Scaffold), or for further manipulation … Continue reading

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Sequence-based search for N-linked glycopeptides

N-linked protein glycosylation is a common post-translational modification (PTMs) in many cellular processes. Atwood et al (RCMS 2005) describe a tandem mass spec-based methodology to analyze N-linked glycopeptides. Enriched glycopeptides are treated with peptide N-glycosidase F, which removes the carbohydrate … Continue reading

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Download John Yates talk on Quantitative Mass Spec

Dr. John Yates from the Scripps Research Institute gave the talk “Driving Biological Discovery using Quantitative Mass Spectrometry” at the 2008 Proteomics 2.0 Meeting hosted by Sage-N Research.   The audio MP3 file is available by download here (click to … Continue reading

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SORCERER: Evolution of the SEQUEST Architecture

by David.Chiang@SageNResearch.com Orbitraps and other fast ion trap mass spectrometers (e.g. FT, LTQ) are popular instruments for discovery proteomics research. The SEQUEST cross-correlation score is almost tailor-made for the spectral characteristics of ion trap data, whose information-rich spectra are challenging due to multiply-charged … Continue reading

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SORCERER Takes Over From SEQUEST Cluster

Discovery proteomics research, such as for biomarker discovery, requires advanced “Proteomics 2.0″ analyses for PTMs like phosphorylation, ETD, and quantitation in addition to high-throughput. With the transfer of the high-throughput SEQUEST Cluster business, the choice for high-throughput data analysis is … Continue reading

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Use the 80/20 Rule to Guarantee Research Success

If you have attended a conference lately, such as the ASMS in Denver, you would have found a bewildering array of exciting new products and ideas for your advanced proteomic mass spectrometry research.  More than ever, there is a need to remain … Continue reading

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Why Many Proteomic “Probabilities” Aren’t

Probability scores make search engine results easier to interpret. However, it is important to understand what they mean in order to avoid assigning more significance to the data than there is. We continue to find researchers who mistakenly believe that … Continue reading

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