1. Temple University MASS SPECTROMETRY SOFTWARE DESIGN Ilyana Mushaeva and Amber Moscato Department of Electrical and Computer Engineering Temple University

2. Temple University: Slide 1 Human Catalase An enzyme (protein that changes the rate of chemical reactions) found in all living organisms. Its function is to decompose Hydrogen Peroxide (bodily toxin) into Water and Oxygen molecules: A protein composed of four peptide chains, over 500 Amino Acids long. Molecular Mass (weight) of 59,800 amu. This is what our data contains. 2 H 2 O 2 → 2 H 2 O + O 2

3. Temple University: Slide 2 Spectrum Breakdown Amino Acids Peptides Proteins Letters Words Sentences Mass Spectrometry is used to determine protein types SpectrometrySpectrometry

4. Temple University: Slide 3 Spectrum Breakdown

5. Temple University: Slide 4 The Software Structure Decode Command Line: sms_cmdl Configuration, Models, Debug, Input Check Command Line Consistency: sms_check Do files exist? Is debug level okay? Load the Models: sms_load Amino Acids, Peptides, and Proteins Recognition: sms_process Open input list and results Loop over file list to process each Exit Program: Print number of files read and processed

6. Temple University: Slide 5 Results After Running Program sp_thresh = 0.9; sp_wait = 1.3 sp_type = 'really good'; f1_amino_acids f2_peptides f3_proteins file1_spectrum1 file2_spectrum2 file3_spectrum3 file4_spectrum4 file5_spectrum5 file6_spectrum6 This is the results file Processing Configuration File... Processing Models File... Processing Results File... More Information Number of files read from input list: 6 Loading cfg_file Loading models_file Reading input_list Reading results_file Debug_level output Number of files read Files processed