1. IIC Information Flow Interesting ions? Priority list of interesting ions Empty priority list? QA/QC? Peptide identification Protein identification External Databases query Y N Y N N Step 1 Step 2 Step 3 sample N Y

2. IIC Architecture

3. Intelligent Instrument Control Algorithms design –Design of the MS simulator, Task 1: Hazem –Spectra Deconvolution (Data filters and noise removal) Task 2: Mohamed Eltabakh –Protein/peptide identification Task3: Mingwu –Other simple algorithms, e.g., priority list, –IIC design and architecture (API, … ) Dr. Ahmed –Integrated Access to external databases ( protDB to support identification and other BioDBs to support correlation with other information, for example interactive proteins, related metabolites, etc.) Experimental Simulation –In silico generation of spectrum, Task 1: Hazem –Algorithms implementation (simulation)

4. Intelligent Instrument Control Integration with the instrument –Data collection (API) –Control of the instrument (API) –Actual implementation (algorithms) –Database design: Data representation (streams, database) Optimized storage of massive data –Raw data –Analyzed data Experimental settings Dr. –Selection of a biology system, e.g., yeast –Two types of experiments Target analysis Global analysis

5. Intelligent Instrument Control Prediction of upcoming peaks ( need more data to build math model ) Online data mining

6. Integrated Access to External Bio-databases Context: Informatics tools –Glycosylated peptide identification –Non-glycosylated peptide identification Goal: Enabling uniform access to different protein databases

7. Integrated Access to External Bio-databases Tasks –Database description and organization, and Schema mediation –Query Processing –Data correlation E.g., Sequence alignment Non-overlapping schemas Contradictory information –Web service enabled access Settings: Target databases selection (focus)