In parallel acquired tandem mass spectra were subjected to homology-based database searching.
Modern UPLC QTOF instruments can acquire tandem mass spectra with very high scan speeds up to 100 Hz.
The acquired tandem mass spectra and retention time information on kinase-derived peptides with desthiobiotin labeling were then processed using Skyline for the MRM library construction.
For the duration of the LC-MS/MS experiment, the mass spectrometer coupled to the liquid chromatography system constantly acquires tandem mass spectra from eluting peptides.
The limitations of these strategies arise directly from the semirandom sampling methods used to acquire tandem mass spectra (MS/MS spectra) for peptides in complex proteome digests.
An unexpected finding [ 5] was a number of somatically acquired tandem duplications, a kind of structural change that has rarely been detected until recently but is interesting because it can lead to gene fusion [ 9].
For example, isomerization of aspartic acid or epimerization of any chiral residue within a peptide do not lead to mass shifts but can be identified by examination of independently acquired tandem mass spectra or by combination with another technique.
Nevertheless, these mixtures are typically still far too complex to allow the mass spectrometer to acquire tandem mass spectra for all peptides in a single LC-MS/MS experiment.
Skyline facilitates the generation and refinement of proteomic peptide lists from protein sequences or database entries, both by utilizing online MS/MS spectral repositories and by supporting the generation of custom-built libraries based upon sets of locally acquired tandem spectral data.
Further analysis of the chromosomal locations and phyletic patterns of the FBG domains suggest that they have been acquired by tandem duplication and shuffling.
