#348 Implement isotope-error option in tide-search

[William S Noble]

We need to implement something similar to the isotope_error switch in Comet:

http://comet-ms.sourceforge.net/parameters/parameters_201502/isotope_error.php

[sjoemac]

FWIW, I've implemented "isotope-windows" in sfx that has similar
functionality.

On Wed, Oct 7, 2015 at 5:00 PM, William S Noble wsnoble@users.sf.net
wrote:

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** [issues:#348] Implement isotope-error option in tide-search**

Status: open
Milestone: post v2.0
Created: Wed Oct 07, 2015 10:00 PM UTC by William S Noble
Last Updated: Wed Oct 07, 2015 10:00 PM UTC
Owner: Kaipo

We need to implement something similar to the isotope_error switch in
Comet:

http://comet-ms.sourceforge.net/parameters/parameters_201502/isotope_error.php

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[William S Noble]

This has recently become important to fix, because we are trying to analyze some data that is ~50% derived from peaks other than the monoisotopic one. Sean, do you have a sense for how easily your logic/code from sfx would generalize to tide-search? It would be great if we could get this fix made.

[sjoemac]

In my code, I generate candidates for each window and merge them into one list prior to the scoring. Since tide is sorting the spectra by precursor and using the active peptide queue, I think you would probably have to search each window as it comes up in the active peptide queue and then merge the results to get the top 5 after you have queried all of the windows for a particular scan.