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What is DPD?
Tuesday, 31 October 2006 07:58
The identification and quantification of the protein contents of biological samples plays a crucial role in biological and biomedical research. The DPD (Decision Peptide-Driven) tool implements an application for assisting the user in a specific protocol for protein quantification based on 18O labeled inverse labeling and MALDI-TOF-MS analysis, which compares the results of the direct and inverse experiments and quickly identifies reproducible peptides (i.e. those that have similar direct and inverse ratios) that should be used to subsequent and accurate protein absolute quantification. The interpretation of the mass spectrometry data from direct and inverse labeling experiments is time-consuming and requires a significant amount of time to do all comparisons manually, additionally, amino acid sequence and his isotopic distribution is needed for calculation of labeling ratios.

The developed DPD software takes as input several mass spectra coming from the MALDI-TOF-MS analyses and aids the researcher to (i) compare data from D&I labeling experiments and calculate the corresponding ratios in order to determine those peptides with more reproducible behavior among the sample treatment and (ii) calculate the O16/O18 ratio from a mixture of unknown amount of protein and an internal standard labeled with O18 and consequently determine the unknown amount of protein. DPD was rapidly implemented through the use of our AIBench Java-based application framework

 

Citing DPD

Please cite us in your research works as:
H.M. Santos; M. Reboiro-Jato; D. Glez-Peña; M.S. Diniz; F. Fdez-Riverola; R. Carvalho; C. Lodeiro; J.L. Capelo (2010) Decision peptide-driven: a free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry . Talanta. 82(4):1412-1420. ISSN: 0039-9140

 

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