1. Inclusion List Builder Plug-In

2. 22 Inclusion List Builder Goal: Create an easy to use lab tool for iterative construction of inclusion lists from MS level 1 and level 2 data to replace existing approaches that involve excessive manual intervention.

3. 33 (Iterative) Workflow LC- MS LC- MS LC- MS LC- MS/ MS LC- MS/ MS LC- MS/ MS LC- MS/ MS pick, filter, align import master table inclusion lists filter, extract, export feed, run search map, update mzXML SpecArray/Superhirn output pepXML

4. 44 Implementation in Prequips plug-in, i.e. uses Prequips infrastructure, e.g.: –data providers for mzXML and pepXML –employs Prequips meta information concept, a general method to quickly integrate new data types (here: master table) inclusion lists are sets of master table features –filters used to select sets of features –further filtering possible after creation of inclusion list –filters associated with inclusion list correspond to a log or history interactive, tabular views to represent master table and inclusion lists before export inclusion list is segmented export produces log file

5. 55 Important Developments time correction (linear) –reference time in master table –predicted time in exported inclusion list –corrected time (adjusts peptide t r to reference time) peptide mapping options –time and mass tolerance defined by user –time correction function defined by user –manual selection possible in case of multiple assignments –results to tab-delimited file user interface –more settings for segmentation and mapping algorithms –comprehensive inclusion list feature view –variable font size for tables

6. 66 Example: Master Table filters master table view feature details

7. 77 Example: Inclusion List segment info inclusion list overview (for a given master table) exported inclusion list log file inclusion list view

8. 88 Example: Peptide Mapping master table with mapping information all mappings selected (and best) mapping