Progenesis Post-Processor

New release 1.0.4-beta version is available from http://progenesis-post-processor.googlecode.com/svn/maven/release/progenesis-post-processor/1.0.4-beta/progenesis-post-processor-1.0.4-beta.zip. More details can be found in release notes.

For those who had used 1.0.2 version for SILAC analysis, please read the announcement first.

General

Progenesis Post-Processor (PPP, version 1.0) was initially conceived to enable results from Progenesis to be converted into mzQuantML for label-free methodologies, and subsequently extended to cover label-based and top3 quantitation.

Progenesis Post-Processor is a Java programming interface to enable the feature-level quantitation performed by Progenesis to be used for some other techniques, such as SILAC. The software searches the table of features to find pairs of features nearby in the RT dimension of the 2D map, separated by the mass shift in the m/z space due to the heavy label being incorporated into lysine or arginine. For example, typical labels incorporate ¹³C and/or ¹⁵N into lysine and arginine to produce known mass shifts of +6Da, +8Da, +10Da, and so on. There are no built-in limits on the mass shift that is permissible, for example overlapping features (say +2Da) are in theory identifiable, so long as Progenesis LC-MS has correctly separated features in the 2D map, although this feature has not yet been comprehensively tested. Minor updates will be made in future releases to capture triple SILAC and labeling on any amino acid.

Top3 quantitation is not natively supported by Progenesis, and as such the Progenesis Post-Processor incorporates a module for top3 quantitation (in fact topX, where X is any integer). The summed (or average) intensity over the top3 can be converted into a value of absolute protein abundance by spiking in one or more proteins of known abundance and scaling protein abundance values accordingly.

Download

The current version of PPP is 1.0 and can be downloaded from here.

Usage

PPP provides a friendly-use interface (see below) with limited parameter settings. It can be executed by double clicking the downloaded jar file.

Contact us

If you have come across any problem or found bugs when using PPP, please don't hesitate to contact us by sending the files (small files only <20M) and describing the problem to Dr Da Qi (D.Qi at liv.ac.uk , replace at with @). Alternatively, open an issue at http://code.google.com/p/progenesis-post-processor/issues/list and it will help us keep tracking, also will allow who peple have the same issue share their comments. You can also use issue list to submit your new feature request for further development. We are open and welcome any feedbacks.

Citation

The PPP paper has been published in OMICS: A Journal of Integrative Biology. If you would like to cite PPP in your paper, please use the following citation:

D. Qi, P. Brownridge, D. Xia, K. Mackay, F. F. Gonzalez-Galarza, J. Kenyani, V. Harman, R. J. Beynon and A. R. Jones. A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS. OMICS: A Journal of Integrative Biology. September 2012, 16(9): 489-495. doi:10.1089/omi.2012.0042.

@article{QI12:OMI, author = {Da Qi and Philip Brownridge and Dong Xia and Katherine Mackay and Faviel F. Gonzalez-Galarza and Jenna Kenyani and Victoria Harman and Robert J. Beynon and Andrew R. Jones}, title = {A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS}, journal = {OMICS A Journal of Integrative Biology}, pages = {489--495}, volume = {16}, number = {9}, year = {2012}, doi = {doi:10.1089/omi.2012.0042}, }