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Mascot Example Slides

Mascot Example Slides. 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. MS2 mixture example.

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Mascot Example Slides

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  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 Serverhttp://www.matrixscience.com/search_form_select.html Class Data Download:http://134.192.153.220/GPLS716Local Web Serverhttp://134.192.153.220/mascotUsername: GPLS716Password: GPLS716

  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.edu Phone number: 8-2031

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