Extending Progenesis to embrace SILAC and Hi3

Qi, D., Brownridge, P., Xia, D., Mackay, K., Gonzalez-Galarza, F.F., Kenyani, J., Harman, V., Beynon, R.J. & Jones, A.R. (2012) A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS OMICS JIB, 2012, 16(10), (in press)

Numerous software packages exist providing support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many support only a subset of experimental methods or instrument types, meaning that laboratories often have to use multiple software packages. The Progenesis LC-MS software from Nonlinear Dynamics is a software solution for label-free quantitation. However, many laboratories using Progenesis also wish to employ stable isotope based methods, which are not natively supported in Progenesis. We have developed a Java programming interface that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods. We have developed post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labelling data and top3 pseudo-absolute quantitation. We have also created export to the new data standard, mzQuantML, produced by the Proteomics Standards Initiative to facilitate the development and standardisation process. The software is provided to users with a simple graphical interface for accessing the different features. The underlying programming interface may also be used by other Java developers to develop other routines for analysing data produced by Progenesis.