Abstract
A mass spectrometry analysis of the yeast proteome shows that complex mixture analysis is not limited by sensitivity but by a combination of dynamic range and by effective sequencing speed.
Highlights
Mass spectrometry has become a powerful tool for the analysis of large numbers of proteins in complex samples, enabling much of proteomics
The gel was cut into 20 slices, proteins were in-gel digested with trypsin and the resulting peptides extracted from each gel slice were analyzed by automated reversed-phase nanoscale liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS)
The peptides were electrosprayed into the source of a linear ion trap-Fourier transform mass spectrometer (LTQ-FT) [20]. This hybrid instrument consists of a linear ion trap (LTQ) capable of very fast and sensitive peptide sequencing combined with an ion cyclotron resonance trap (ICR)
Summary
Mass spectrometry has become a powerful tool for the analysis of large numbers of proteins in complex samples, enabling much of proteomics. Despite spectacular advances in mass spectrometric technology, no cellular or microorganismal proteome has been completely sequenced. This has not hindered successful application of proteomics, as most biologically relevant studies have focused on functionally relevant 'subproteomes'. Our laboratory has been interested in protein constituents of organelles such as the nucleolus and mitochondria [4,5,6]. These proteomes have complexities of about a 1,000 proteins and are largely within reach of current technology. If proteomics is to be used in diagnostic applications by in-depth analysis of body fluids, even higher performance would be desirable [10]
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