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Automatically optimizing parameters #486

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acesnik opened this issue Feb 6, 2018 · 2 comments
Open

Automatically optimizing parameters #486

acesnik opened this issue Feb 6, 2018 · 2 comments
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@acesnik
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acesnik commented Feb 6, 2018

We could build functionality to automatically optimize parameters. Lollipop is instantiated, so it can be run with several different parameters, and the results could be compared.
@leahvschaffer
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leahvschaffer commented Feb 8, 2018 •
edited by acesnik
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We could start with testing the ones I normally change:

  • # PTM's allowed in theoretical database
  • Variable oxidized methionine
  • Min. top-down C-score
  • Component mass tolerance
  • Agg exp mass tolerance
  • Min required observations
  • Peak width base EE and ET
  • And maybe export a table of results with # id'd and FDR's so you could decide which you want.

@acesnik
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acesnik commented Feb 8, 2018 •
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Sounds great! Sean is doing lots of manual optimization. Let's ask him for input, too.

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@acesnik @leahvschaffer