diff --git a/docs/module_docs/id_lipid_annotation/MSMS-Parameters.png b/docs/module_docs/id_lipid_annotation/MSMS-Parameters.png new file mode 100644 index 00000000..de12510d Binary files /dev/null and b/docs/module_docs/id_lipid_annotation/MSMS-Parameters.png differ diff --git a/docs/module_docs/id_lipid_annotation/MSMS-parameters.png b/docs/module_docs/id_lipid_annotation/MSMS-parameters.png deleted file mode 100644 index f493ef8a..00000000 Binary files a/docs/module_docs/id_lipid_annotation/MSMS-parameters.png and /dev/null differ diff --git a/docs/module_docs/id_lipid_annotation/lipid-annotation.md b/docs/module_docs/id_lipid_annotation/lipid-annotation.md index 9a9e0082..f1b43a79 100644 --- a/docs/module_docs/id_lipid_annotation/lipid-annotation.md +++ b/docs/module_docs/id_lipid_annotation/lipid-annotation.md @@ -31,7 +31,7 @@ This rule-based annotation approach follows Lipidomics Standards Initiative guid This parameter lists all pre-configured lipid classes in MZmine. Each selected lipid class will be added to the search scope. #### Side chain parameters -![matched-signals](side-chain-parameters.png) +![side-chains](side-chain-parameters.png) Set the allowed min and max for chain length (number of carbons) and double bond equivalents (DBE) in a lipid chain. The number of chains is defined in the lipid class. 12 to 26 carbons and 0 to 6 DBEs is recommended as a starting point. @@ -48,7 +48,7 @@ Set the allowed min and max for chain length (number of carbons) and double bond Enter m/z tolerance for exact mass matching on MS1 level. Lipids outside the m/z tolerance will not be matched. #### Search for lipid class-specific fragments in MS/MS spectra -![side-chains](side-chain-parameters.png) +![msms-parameters](MSMS-Parameters.png) Activate this parameter to highly increase lipid annotation confidence. @@ -57,7 +57,7 @@ Activate this parameter to highly increase lipid annotation confidence. Mass detection on MS2 level needs to be performed first. Set a mz tolerance for matching signals in MS2 spectra. -Set a Minimum MS/MS score to accept a lipid annotation. The score is the explained intensity [%] of all signals in MS/MS spectrum. Matches below the set score will be removed, except the optional parameter Keep unconfirmed annotations is selected. +Set a Minimum Explained intensity to accept a lipid annotation. Matches below the set value will be removed, except the optional parameter Keep unconfirmed annotations is selected. Unconfirmed annotations will be marked with a comment in the feature list. #### Search for custom lipid class