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Figure 1 B) The highest scoring phospho match is enriched for matches from the target database.

Figure 1 B) The highest scoring phospho match is enriched for matches from the target database. 2 nd , 3 rd , 4 th , etc phospho positions are 50/50 target decoy. C and D) create “falsified” data, shift every MS/MS peak by +10 m/z in C and shift precursuor ion mass by 100ppm in D

rhiannon-hensley
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Figure 1 B) The highest scoring phospho match is enriched for matches from the target database.

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  1. Figure 1 B) The highest scoring phospho match is enriched for matches from the target database. 2nd, 3rd, 4th ,etcphospho positions are 50/50 target decoy. C and D) create “falsified” data, shift every MS/MS peak by +10 m/z in C and shift precursuor ion mass by 100ppm in D All in all the target/decoy strategy works as expected for phosphorylation.

  2. Can you guys tell me what this figure means in terms of what was done in the lab?

  3. If you filter on enzyme PPM score you can get matches with a given false discovery rate.

  4. You only have to worry about this when there are to places you can position a PTM.

  5. Ascore algorithm Part 1: determine peak depth Set peak depth i = 6 since This is the smallest peak depth where the score has the biggest gap.

  6. Ascore algorithm Part 2, use a given peak depth Here i = 6 to score site determining Ions. For peak depth 6 the probability of seeing 5 or more site determining peaks matched at random is unlikely

  7. Is this data a good test of the algorithm?

  8. Strip off all phosphorylations in heavy sample Occupancy determining peptide

  9. Do you guys buy this?

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