Now you can analyse labelled samples and perform absolute quantification with Progenesis LC-MS

This post refers to Progenesis LC-MS, which has since been superseded by Progenesis QI for proteomics. All of the information described, however, remains relevant. A fuller description of the new product can be found here.


The Nonlinear Support Team

A new publication and software toolkit from the Protein Function Group at the University of Liverpool has just made Progenesis LC-MS even more attractive for quantitative proteomics. The toolkit, free to download and use, allows you to:

  • Analyse SILAC data or other mass-shift labelled peptides measured at the MS1 level
  • Perform absolute quantification using Top3, or Top‘X’, peptides
  • Export peptide or protein level results in the mzQuantML PSI standard

logo-with-textThe Progenesis Post-Processor (PPP) provides a simple piece of software to use alongside your copy of Progenesis LC-MS. TIP: To run the PPP you need to make sure you have installed Java.

All that the group who developed the toolkit ask is, if you use it, cite the following reference.  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 and top3 quantification using Progenesis LC-MS. OMICS: A Journal of Integrative Biology, 16(10), 2012(in press).



How the Progenesis Post-Processor looks for analysing results of labelled experiments

How do I use it?

The publication gives examples of analysis including an S. cerevisiae SILAC test sample, absolute quantification using Sigma48 UPS proteins of varying concentrations 0.25-20 fmol/uL  spiked into a yeast culture and exporting data as standardised mzQuantML output.

I have gone through the process of downloading and trying the Progenesis Post-Processor and even as a non-bioinformatician I found it is easy with Java already installed and Progenesis LC-MS downloaded. Just save the PPP to a suitable location, double-click the icon and it opens ready to use in the following way:

  1. Use the guided workflow of Progenesis LC-MS to generate results and in the Review Proteins view export the peptide measurements as a .csv file. The mzQuantML conversion can use an exported .csv file of peptide or protein measurements.
  2. Open the Progenesis Post-Processor and select the data processing you want from one of the three separate task tabs, applying any parameters you need.
  3. You are promoted to save the processed results as a .csv for review or to easily incorporate them into any downstream bioinformatics workflow.

The PPP, as of 15th August, is a v1.0 Beta. So if you come across any issues or have any feature requests you can post them here to help in developing future versions.

Try it yourself

Over the last year the message at meetings we have attended has been that label-free quantitation is rapidly growing in its use for proteomics research. We chose to support solving the challenges of label-free relative quantitation from the start with Progenesis LC-MS. This meant, until now, anyone using labelling approaches could not benefit from our software. With the availability of the toolkit you can see the benefits it offers whatever approach you use, including:

  • Platform independent analysis of data from a range of sources Label-free
  • Labelled and absolute quantification from one easy to use workflow
  • Support for standard proteomics data formats, including export of the new mzQuantML

Get in touch or download a free trial copy of Progenesis LC-MS to start using the workflow and see the results from your own data.