Supplementary Figure 8: Logistics of data handling and effect of different database search strategies
From: Building ProteomeTools based on a complete synthetic human proteome
(a) Schematic representation of the data handling pipeline governed by the internal pipeline/database used for the ProteomeTools project. After pool design and peptide synthesis, an initial survey acquisition run followed by an automatic MaxQuant search was used to identify the desired full length peptides. The results were imported into the internal database which then automatically prepared the acquisition methods for the HCD, IT and ETD acquisition runs (see Supplementary Information for details). These subsequent acquisitions were again automatically searched and imported into the database for quality control and data organization. (b) Comparison of database searches for peptide identification. Upper panel: Analysis of 20 pools from the “proteotypic” set in separate searches or searched together (combined). It is evident that shorter peptide identifications are lost when combining peptide pools for database searching. Lower panel: Analysis of 96 pools from the “proteotypic” set, searched either with tryptic or unspecific digestion of the database. It is evident that searching without tryptic specificity results in lower peptide identifications. We note that both these are issues of current database search algorithms that need addressing.
