A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and ap...

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Bibliographic Details
Published in:Journal of proteomics 2019-06, Vol.202, p.103371, Article 103371
Main Authors: Santos, Marlon D.M., Lima, Diogo B., Silva, André R.F., Kurt, Louise U., Clasen, Milan A., Pinto, Antônio F.M., Moresco, James J., Yates, John R., Aquino, Priscila, Barbosa, Valmir C., Fischer, Juliana S.G., Carvalho, Paulo C.
Format: Article
Language:English
Subjects:
Bioinformatics
Differential proteomics
Dimethyl
PatternLab
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Summary:We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.
ISSN:1874-3919
DOI:10.1016/j.jprot.2019.04.021