LC-MS quantification algorithms implemented in Proline are based on the prototype software Prosper developed by IPBS. There are a large number of LC-MS map generation tools. However there was no software solution, until Prosper, able to read and compare data generated by different tools. It was thus a tedious work to evaluate the relative performance of the available peak picking solutions. Proline overcomes this problem by implementing the Prosper’s parsers in order to bring a high level of flexibility in the workflows of LC-MS data analysis. Users can use data coming from different peak picking software, and all the rest of the data processing (alignment, normalization, comparison) can be done with Proline‘s integrated tools. Proline also has its own feature detection algorithms.

Figure 1: Overview of the LC-MS quantification workflow. LC-MS maps from different sources can be imported in the LCMSdb. Once loaded, these maps will be treated by several algorithms for data processing and comparison. The result of the analysis can be exported into different file formats.

Analytic workflows have been developed for each quantitative analysis strategies.

• Label-free LC-MS quantitation workflow
• Isotopic labeling LC-MS quantitation workflow