1. Mascot Example Slides

2. MS/MS Database Search Example Data: BSAonespectra.mgf (one spectra) Database: bovine Fixed modifications: Carboxymethyl(C + 58.01) Varied modifications: Oxidatation(M) Peptide Mass Tolerance : 0.1 Da Fragment Mass Tolerance: 0.1 Da

3. MS2 mixture example Data: mixture10spectra.mgf Database: yeast Fixed modifications : Carbamidomethyl (C+57.02) Variable modifications : Oxidation (M) Peptide Mass Tolerance : 0.1 Da Fragment Mass Tolerance: 0.1 Da

4. MS1 PMF(peptide mass fingerprinting) Search Example Data: testms1.txt, 210 MS1 peaks Database: bovine Fixed modifications : Carboxymethyl (C) Variable modifications : Oxidation (M) Peptide Tolerance: 0.1 Da Monoisotopic mass Mass Value: Mr

5. Quantification Search Example Data: 18O_BSA_100fmol_1to5_01_071018.RAW.mgf Database: bovine Fixed modifications : Carbamidomethyl (C) Peptide Tolerance: 8 Da (required for O18 labeling) Fragment Tolerance: 0.2 Da Quantification Method: 18O corrected multiplex

6. Public Web Server http://www.matrixscience.com/search_for m_select.html Class Data Download: http://134.192.153.220/GPLS716 Local Web Server http://134.192.153.220/mascot Username: GPLS716 Password: GPLS716 http://134.192.153.220/mascot

7. Homework 1. Phosphorylation protein identifications: Data:BIG3021307.RAW.mgf Recommend parameters: Database: human. Variable Modification: Phospho(ST) Fixed modification: Carboamidomethyl(C). 2. O18 quantification analysis: Data: 18O_BSA_500fmol_1to5_071013.RAW.mgf. Questions: Contact Yunhu Wan, email: ywan@som.umaryland.eduywan@som.umaryland.edu Phone number: 8-2031