Implementation of Mass Spectrometry of Lipids SPPs

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 Implementation of Lipidomics and Metabolomics SPPs

         Lipidomics and Metabolomics processing is implemented according to previously defined SPPs. Implementation consists of the following major parts:

-Data import

Imported data consists of description of samples used for analysis, lipids identified and their concentrations, or other values (such as corresponding peak intensities and peak areas as well as values for appropriate internal standards) that are required for lipid quantification. If data are imported with already calculated concentrations, data analysis moves to the next steps. Otherwise, quantification values are converted into appropriate concentrations. Specific steps for normalization of lipid values depend on a platform that is generating the data and implemented in a semi-automated fashion. In brief, parameters and functionality of normalization algorithm are chosen with data providers and corresponding algorithms are coded by Zora Biosciences Oy. Using this strategy we can achieve a desired level of flexibility which is absolutely required when data from many different platforms are taken together. Furthermore, different normalization algorithms can be further implemented and their results can be compared on same datasets for choosing an optimal solution.


-Validation of nomenclature used for describing observed lipids in processed samples.

Lipid names and descriptions of samples are checked against a database table with common lipid names selected by LipidomicNet participants. In case of discrepancies between common ontology and lipid names used by data providers they are corrected according to the standards and data providers are notified about these nomenclature conflicts.


-Analysis of quality controls

Depending on a platform used for generating Lipidomic/metabolic data appropriate QC checks are performed. Currently, CV values for each lipid and lipid class are calculated if replicate measurements on same sample sets are present in imported data. Ratios of internal standards are taken into account as one of QC measurements if applicable. This step is implemented in the semi-automated fashion as described above and discussed with data producers prior to data analysis.


-Standardized Output of normalized lipid quantities

Data output is created in a standard way, which includes an Excel like file with lipid names in rows and different samples in columns. A second output file is also generated and represents a list in which each line corresponds to a particular lipid in a particular sample. Such list format is more suitable for direct recording into any relational database and can be used as a data exchange format between bioinformatics partners. Along with lipid concentrations, standard output consists of the following values per sample:


                 - Lipid class concentrations (sum of all concentrations of different lipid species of that class)
                 - Mol.ratios (a percentage of a given lipid concentration to the total lipid class concentration)
                 - Ratio of saturated/monounsaturated/polyunsaturated fatty acid containing lipids in a given class


These calculations are implemented as Oracle based functions and executed when data are retrieved from a database. When needed, more calculations of that type can be included for generating a standard data output of the Lipidomic/Metabolomic processing.

-Statistical analysis of changes in lipid profiles under different conditions (if present in imported dataset)

Output from the previous step is used as an input for statistical analysis of changes in lipid measurements under a given condition. Particular type of statistics applied depends on experimental design and should be implemented individually for each experiment. However, a generalized t-test based statistics is implemented as an Oracle function and performs calculation of paired or independent t-test for each pair-wise combination of experimental conditions. Output of statistical analysis includes significantly changing lipids in different conditions and a corresponding fold change of concentration differences or differences in other measurements calculated in the previous step.

Standard Processing Procedure

Mass Spectrometry of Lipids SPPs

Processing Pipeline

Processing Pipeline for Mass Spectrometry of Lipids SPPs

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