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Exercise 1-5 . Make sequence tags for the spectra below Start with 3 amino acids for sequence tag

Name: Matrikelnumber :. Exercise 1-5 . Make sequence tags for the spectra below Start with 3 amino acids for sequence tag Increase to 4 and 5 amino acids - Note down how many ID’s you get - Note down how the score changes Sequence tag Example: 1223.76 tag(666.43,TQE,1024.58).

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Exercise 1-5 . Make sequence tags for the spectra below Start with 3 amino acids for sequence tag

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  1. Name: Matrikelnumber: Exercise 1-5. Make sequence tags for the spectra below Start with 3 amino acids for sequence tag Increase to 4 and 5 amino acids - Note down how many ID’s you get - Note down how the score changes Sequence tag Example: 1223.76 tag(666.43,TQE,1024.58)

  2. Query syntax and hints Detailed description: http://www.matrixscience.com/help/sq_help.html#TAG Standard example: 1890.2 tag(1004.1, LSADTG, 1548.5) Alternative sequences can be expressed as follows: LSA[DT|M|F]G: LSADTG, LSAMG, LSAFG A tag may run in either direction, but the mass values are ‘glued’ to the ends of the tag. Hence, tag(1004, LSADTG, 1548) is the same as tag(1548, GTDASL, 1004) but different to tag(1548, LSADTG, 1004). The fragment ion mass values m1 and m2 can belong to any ion series (b, y,…) including doubly charged fragments and fragments containing neutral losses (e.g. yn-17). However, m1 and m2 must belong to the same series. Typical error: m2 – m1 ≠ m(‘tag’)

  3. 20130226_1ugA431 # 11169 RT: 52.11 AV: 1 NL: 2.14E4 T: FTMS + c NSI d Full ms2 757.90@hcd30.00 [100.00-1530.00] 1182.63 100 95 90 85 80 75 70 591.82 65 60 55 Relative Abundance 50 45 1085.58 40 857.47 35 201.12 213.09 30 970.56 25 20 742.44 244.16 15 657.34 441.20 314.15 1400.70 10 515.32 5 1313.63 939.48 781.40 1450.98 0 200 400 600 800 1000 1200 1400 m/z 1

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  6. 20130226_1ugA431 # 7726 RT: 37.59 AV: 1 NL: 2.60E4 T: FTMS + c NSI d Full ms2 777.89@hcd30.00 [100.00-1570.00] 777.89 262.14 100 95 242.11 90 85 80 1185.61 1114.58 75 70 65 370.17 441.21 60 524.27 136.08 55 Relative Abundance 50 361.21 45 1031.51 769.38 40 918.43 35 928.50 1313.68 30 1043.54 712.86 637.35 25 155.08 800.41 1296.65 20 935.93 703.85 825.41 512.25 15 386.17 1408.66 593.32 311.14 226.12 853.44 10 549.26 1014.50 478.24 1361.80 5 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 m/z 4

  7. 20130226_1ugA431 # 12592 RT: 59.61 AV: 1 NL: 9.08E3 T: FTMS + c NSI d Full ms2 1122.61@hcd30.00 [100.00-2000.00] 1782.01 100 95 90 85 1484.84 80 75 70 65 60 1284.73 55 334.14 680.44 Relative Abundance 50 45 40 35 235.07 30 1299.74 462.20 25 1397.81 20 1227.71 781.49 1583.91 1765.00 15 946.53 1023.62 1910.07 316.13 351.17 10 1170.69 759.37 1684.96 398.20 660.30 175.12 5 1102.58 1893.05 480.28 873.40 0 200 400 600 800 1000 1200 1400 1600 1800 2000 m/z 5

  8. MS/MS ion search • Lookup the MS/MS information for the scan numbers of the 5 spectra in the MS/MS.txt file • Perform an MS/MS ion search on each of them • Report ID and score • Report how the score changes with -widening the MS and MS/MS tolerance -increasing the number of modifications And explain why Extra: look at error distribution

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