Through collaborative development efforts, it is now possible for the ISB’s Trans Proteomic Pipeline (TPP), a set of free, open-source programs developed with support from the National Heart, Lung and Blood Institute that run in series to form a ‘pipeline’, to be launched from GenoLogics Proteus™ lab and data management system for proteomics.
This development was demonstrated by GenoLogics at the US HUPO conference in Boston.
The integration of Proteus and the TPP provide numerous benefits for proteomics researchers, bioinformaticians and managers.
It enables automatic statistical validation of protein search results and calculated quantitation information, improving accuracy and through-put as many more samples can be researched and validated automatically.
Quantitation information tells the amount of a protein/peptide in one sample compared to another sample. Researchers can publish results faster with increased confidence.
Collaboration among researchers is also easier. Researchers can view any spectra on any computer and share mzXML spectra files with colleagues.
There is no need for commercial spectra viewers since various open source mzXML viewers are available for most platforms. Users can also view the result files in the TPP’s own viewer, directly from Proteus.
Bioinformaticians do not have to develop their own interface for the TPP, as it will just work with Proteus. They can data mine the TPP results through the Proteus database, eliminating the need to parse result files or build their own database.
In addition, it is easy for an organization to integrate its own data processing tools into Proteus because of GenoLogics commitment to open data standards and its open integrating platform.
"We are very pleased about our partnership with GenoLogics and their dedicated effort to integrate the Trans Proteomic Pipeline and Proteus," said Dr. Ruedi Aebersold, co-founder of ISB.
"This new development along with GenoLogics’ support network will facilitate installation and broaden the dissemination of new technologies and computational tools for proteomics research to scientists and labs all over the world."
"The ISB has played a ground-breaking role in developing open source tools and furthering the technologies to support systems biology research," said Michael Ball, CEO of GenoLogics.
"The partnership we have with the ISB is very important to us and strongly valued by our customers."
"Collaboration on the integration of the TPP accelerates the dissemination of the ISB open source tools and also expands the use of data management systems, enabling researchers to have more confidence in their results and faster scientific discovery."