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Development of data processing pipeline for multidimensional liquid chromatography coupled to mass spectrometry

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Development of data processing pipeline for multidimensional liquid chromatography coupled to mass spectrometry

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Samenvatting

Biomarker discovery is essential to the pharmaceutical industry for the diagnosis, monitoring and potentially prevention of disease. The Threshold Avoidance Proteomics Pipeline (TAPP) is a tool currently being developed for the discovery of low abundance protein biomarkers, using liquid chromatography coupled with mass spectrometry (1D-LC-MS/MS). The complexity of proteomic samples exhausts the separation power of any single separation technique, which prevents it for distinguishing peptides with similar chemical properties from each other. The use of two liquid chromatography separation phases orthogonal to each other (2D-LC-MS/MS) improves the separation power of the pipeline, but results in data split into fractions. This introduced the need for additional data processing, compared to the 1D-LC-MS/MS algorithm currently used by TAPP. This project aimed to develop a new algorithm using already existing components of TAPP that aligns the fractions in each sample in order to correct for shifts in retention time and links data between the fractions based on proximity. The same fractions of each sample are processed using the one dimensional workflow and combined with the new fraction link information into data format that mimics its predecessor. The additional dimension allows to analyze proteome with larger dynamic concentration range, identifying potential lower abundance biomarkers.

Toon meer
OrganisatieHanze University Groningen
OpleidingAdvanced Sensor Applications
AfdelingHanze Institute of Technology
Jaar2016
TypeMaster
TaalEngels

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