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Insilicos Scientific Posters |
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| The following posters relate to Insilicos' research and scientific direction |
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Bryan J Prazen
The Trans-Proteomic Pipeline (TPP) is an open source
proteomics data analysis pipeline introduced by the
Aebersold group at the Institute for Systems Biology. This
pipeline includes tools for quantitation and statistical
validation of protein identifications from tandem mass
spectrometry experiments. While TPP is extremely useful
and well received, many users struggle with the
application of this data analysis pipeline to Mascot search
results. Most of the pitfalls encountered while applying the
TPP to Mascot data stem from file format converters.
There are multiple data processing paths available for the
analysis of Mascot search results, some of which lead to
more comprehensive protein identifications than other
methods. Recently, Insilicos has issued a version of the
TPP that is known as the Insilicos Trans-Proteomics
Pipeline (IPP). This version of the pipeline allows for
analysis using MS/MS data that went through Mascot
Distiller or DTASuperCharger. Previous versions of the
proteomic pipeline required that MS/MS data from some
instruments be converted to mzXML or mzDATA prior to
searching with Mascot. Presented are results of LC-MS/
MS experiments in which a number of data analysis paths
are explained and compared. Presented at US HUPO, March 2007.
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Bryan J Prazen
The Insilicos Proteomics Pipeline (IPP) includes modules for validation of database search results,
quantitation of isotopically labeled samples and other proteomics functions. IPP is based on the
Trans-Proteomic Pipeline (TPP), a popular open source toolkit for proteomics data processing,
introduced by the Aebersold group at the Institute for Systems Biology (ISB). Presented at HUPO, October 2006.
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Brian S Pratt
The Insilicos Proteomics Pipeline (IPP) is a proprietary software layer around the TPP, which utilizes the core TPP logic while boosting performance dramatically.
Insilicos has thus developed the IPP, a performance enhanced version of the TPP which is significantly faster, more robust, and easier to install and use.
Insilicos continues to be an active contributor to the open source TPP code.
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Bryan Prazen, Erik Nilsson, Brian Pratt, Martin Sadilek, Daniel Martin, John Klimek, Andrew Gemmill, Laura Hohmann, Jennifer Jackson
PeptideProphet was first calibrated using the ThermoFinnigan LCQ mass spectrometer. For this instrument it was shown that PeptideProphet computed probabilities have more correct matches for any given error rate than the conventional filtering criteria. Yet, little is known about how PeptideProphet performs on other instruments. We evaluate the need for instrument specific calibration of PeptideProphet when using two ThermoFinnigan LCQ instruments, a ThermoFinnigan LTQ instrument and an Applied Biosystems API QSTAR Pulsar Instrument.
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Erik J Nilsson, Brian S Pratt, and Bryan J Prazen
Each mass spectrometer manufacturer stores data in a unique file format, some of which are proprietary. Proprietary formats limit the ability to compare results between research groups or even between instruments maintained by the same group. Such formats also discourage the exchange of raw data files and the creation of data repositories. mzXML and mzDATA are two common file formats developed to allow for the exchange of MS data. Presented here is a fast and novel visualization tool for mzXML and mzDATA files, known as InsilicosViewer.
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