Classification of the identified proteins into eight functional classes.

Virtual 2D gel of proteins identified in the spliceosome preparation. The coordinates are the theoretical molecular mass and isoelectric point for each protein. The gray circles represent factors identified in this study, and the black circles represent proteins identified in this and our previous study (Neubauer et al. 1998). The box indicates the coordinate space spanned by our previous investigation using 2D gel electrophoresis.

Protein abundance index (PAI) for the identified proteins. Plot of PAI index, which is defined as the number of identified peptides divided by the number of calculated, observable peptides, plotted for the identified proteins in seven different classes. The individual spots represent the PAI for each protein in the category. The bar shaded in gray extents to the average value of the PAI for each category. The white bar encompasses 95% of the proteins in each category.

On-line LC MS/MS mass spectrometric analysis of the spliceosome. (A1) Sum of the ion intensity measured by mass spectrometry at any point in the chromatogram for the mass range m/z = 350–550 (total ion chromatogram[TIC]), (B1) m/z = 550–750, and (C1) m/z = 750–1400. (Insets) Current for an ion of specific mass (m/z window 0.2) eluting around the marked time in the chromatogram. (A2,B2,C2) Mass spectra obtained at the marked time in the corresponding upper panels. Several peptides coelute. (Insets) Zoom of the peak marked with an asterisk. (A3,B3,C3) Fragmentation spectra of the peak marked with an asterisk in the corresponding mass spectra above. The insets show that there was high resolution and the ability to determine the charge state by the differences between isotopic peaks. Open circles mark the peaks corresponding to predicted fragments for the peptide sequence retrieved by the database search. The insets show that there was high-quality data for the fragments, which aided the database search and validation. (D) The proteins identified by the peptides shown in A–C are also independently identified by a large number of other peptide fragmentation spectra, leading to substantial sequence coverage of 32%–57% for these three proteins.