Processing Pipeline for Mass Spectrometry of Lipids SPPs

From LipidomicsWiki

A variety of methods and platforms for lipid quantification results in a high complexity of a system for data analysis. Given this complexity and a time frame of LipidomicNet project we chose to develop the system in a semi-automated fashion. This implies coding of certain common software components in a general way so it does not depend on MS methods or lipids identified. Such components include valuators of lipid names, calculations of CV values of lipid concentrations in replicate measurements, database output functions, calculation of lipid class concentrations, mol.ratios, ratios of saturated vs unsaturated fatty acids and basic t-test based statistics.

These common general software parts are then combined programmatically in one semi-automated framework together with custom codes designed to perform specific calculations for a specific experiment or method used for producing Lipidomic/Metabolomic datasets.

This type of implementation is beneficial for efficient analysis of heterogeneous data and avoids problems associated with programming of a general “one software fits all” type of system, which is a tedious and very time consuming process. Furthermore, it allows for combining multiple software packages especially suited for a particular task (for example Oracle for data handling, Java for coding custom components and communication between components and R for statistic).

Under semi-automated scenario for data processing, data files can be sent electronically directly to Zora Bioscience Oy or via LipidomicNet Wiki. These data will be reviewed by Zora specialist and data providers will be contacted for agreeing on data processing steps specific to their platforms and experiments. A processing code will be then assembled from existing or, if needed, newly created parts and data outputs will be sent back to data providers or published on LipidomicNet Wiki.

Standard Processing Procedures

Mass Spectrometry of Lipids SPPs Standard Processing Procedure Main Page

Implementation

Implementation of Mass Spectrometry of Lipids SPPs