a single, user-friendly, informatic framework, that is simple to use
and fully customizable, for the enabling of LC-MS-based quantitative
proteomic workflows of any size, able to guide the user seamlessly from
MS data generation, through data processing, visualization, and
statistical analysis steps, to the identification of differentially
abundant or expressed candidate features for prioritized targeted
identification by subsequent MS/MS.
A goal of Corra was to enable the integration of
multiple and disparate LC-MS data analysis tools, and integrate them,
seamlessly, with common statistical packages to allow for better comparison
between differently-processed datasets, via the addition of statistical measures
of confidence and error rates. The integration of tools was achieve via AMPL
(Annotated Putative peptide Markup Language) and the various parsers, and in the current build of Corra, we have implemented
SpecArray and SuperHirn. Current distributed Corra contains APML adapted open source of SpecArray and SuperHirn.
Corra and its biological application is published in the BMC
Bioinformatics 2008 9:542 and be accessible by http://www.biomedcentral.com/1471-2105/9/542
Corra and APML download site:
You can download source codes and documentation by http://sourceforge.net/projects/corra
You can download
ftp://ftp.systemsbiology.org/Corra/example_mzXML.tgz file contains 6 mzXML files (1.3 GBtye) acquired from ThermoFinnigan
LTQ Orbitrap data from yeast wild type and gene knockout dataset, which
is described in the above paper.
Corra tutorial guides:
Corra v3.0 tutorial guide can be downloaded by CorraUserGuide-Tutorial.pdf
Corra-ATAQS developer code base and discussion group
Please join as project member for future development and biomedical research collaborators and please join for discussion.
SRM based hypothesis-driven computational tool
As a complementary to Corra tools, we recently developed and published hypothesis-driven computational tool called ATAQS.
Mi-Youn Brusniak, Ph.D.
Thank you for
interested in using Corra for your biological data application or enhancing
current software or algorithm research.
We are looking
forward to hearing from you and future collaboration as a community based code
* Copyright (c) 2008 Institute for Systems Biology
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* Contact info:
* Mi-Youn K. Brusniak
* Insitute for Systems Biology
* 1441 North 34th St.
* Seattle, WA 98103 USA