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compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
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Unspecific Digestion and Amanda settings_SearchGUI.xml #254

Closed sheep71 closed 4 years ago

sheep71 commented 4 years ago

When searching with unspecific digestion (Search Settings - Identification settings - Spectrum Matching - Digestion) and MS AMANDA, in the corresponding settings_SearchGUI.xml (/resources/MS Amanda/windows) the value for missed_cleavages is erroneously set to 50 leading to the following error:

From the Log: Reading settings file... Allowed values for missed cleavages parameter are between 0 and 5 Error reading settings file ...

hbarsnes commented 4 years ago

You are correct, the maximum number of missed cleavages is indeed set to 50 for MS Amanda when using unspecific digestion. The reason being that it is not clear what the correct value ought to be in this case. Hence we set it to a sufficiently large number, given that setting it to a value between 0 and 5 did not seem to make a lot of sense as this would greatly influence the length of the resulting peptides as all cleavage sites would be allowed and thus potentially considered as missed?

We were however not aware that setting the value to 50 would result in an error in the MS Amanda settings. Do you happen to know what the correct option should be? If so, we'd of course be very happy to change our default values. If not, perhaps you can contact the MS Amanda developers directly via https://groups.google.com/forum/#!forum/msamanda? Hopefully they can provide us with the correct settings for unspecific digestion.

sheep71 commented 4 years ago

Thanks for the prompt reply. You can leave the setting at the default value (e.g. 2) since the parameter is neglected during search (but not for settings checking, hence the error) when using unspecific digestions, i.e. all possible peptides within the given mass and length constraints are considered.

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On 13. Oct 2020, at 16:08, Harald Barsnes notifications@github.com wrote:

 You are correct, the maximum number of missed cleavages is indeed set to 50 for MS Amanda when using unspecific digestion. The reason being that it is not clear what the correct value ought to be in this case. Hence we set it to a sufficiently large number, given that setting it to a value between 0 and 5 did not seem to make a lot of sense as this would greatly influence the length of the resulting peptides as all cleavage sites would be allowed and thus potentially considered as missed?

We were however not aware that setting the value to 50 would result in an error in the MS Amanda settings. Do you happen to know what the correct option should be? If so, we'd of course be very happy to change our default values. If not, perhaps you can contact the MS Amanda developers directly via https://groups.google.com/forum/#!forum/msamanda? Hopefully they can provide us with the correct settings for unspecific digestion.

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hbarsnes commented 4 years ago

Thanks for the tip! I've now fixed the problem and released a new version of SearchGUI. If the unspecific searches still do not work as wanted, please let me know and I'll reopen the issue.