Dr. Maarten Dhaenens
BIG N2N Laboratory for Pharmaceutical Biotechnology, Ghent University
J Schell seminar room
UGent-VIB Research Building FSVM
9052 Zwijnaarde (Gent)
Commercial software tools are sold with a strong emphasis on user-friendliness, i.e. simplicity, giving rise to the impression that proteomics data is well understood. Yet the ion path that peptides travel through a mass spectrometer (an ESI-QTOF in this lecture) immediately provokes thought on just how a computer algorithm can cope with the complexity of the physical reality, which is reflected in the recorded data. Proteomics data still is over 50% of uninterpretable signals, with the other 50% prone to a lot of misinterpretation both at the level of identification and quantification. While many are still struggling to extract increasing amounts of information from the most commonly used “data-directed acquisition” strategy (DDA), mass spectrometry manufacturers have already developed instruments that measure the sample in a “data-independent” manner (DIA), meaning “everything” that elutes from the LC-system is being recorded. No doubt, this will form the basis for a paradigm shift in proteomics data analysis, but sharpening the picture on DDA data will nevertheless remain an essential effort in the time to come.
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