Ashoka Polpitiya, D.Sc.
Senior Research Scientist
Fundamental & Computational Sciences Directorate
Pacific Northwest National Laboratory, WA.

High throughput proteomics using mass spectrometry


Mass spectrometry (MS) has become an indispensable technique for proteomics studies whose goal is to identify and quantify proteins from complex mixtures. Protein level study of cellular functions is fundamental to the emerging field of Systems Biology and also in biomarker discovery. MS based proteomics relies on the availability of the genome sequence databases, and many technological advances (ionization and chromatography techniques) have greatly contributed to its rapid popularity.

At Pacific Northwest National Laboratory, we have developed a technique called Accurate Mass and Time Tags (AMT Tags) method to study proteomics in a high-throughput fashion. We draw upon the disciplines of chemistry, biology, computer science, and mathematics to greatly enhance the throughput, sensitivity, and accuracy of our methods. We have built a pipeline architecture which comprises a set of tools that can capture the measurements from mass spectrometers and analyze them in a pseudo automated fashion.

During this talk, I will describe how we utilize this pipeline in identifying and quantifying proteins, highlighting the computational challenges. Topics include, peptide identifications using tandem MS/MS, deisotoping MS features, feature matching and alignment, and downstream analysis.