|parse rules MS Amanda||kguehrs||2021-01-05|
Hi Skyline team,
First of all: Happy New year with good health and ongoing success in all things of your personal and professional life.
I have tried to generate a spectral libraries from DDA runs with MS Amanda integrated in the newest Skyline version. In my first approach, I have used a limited but refined (adapted to UniProt headers) database. MS Amanda performed well and created a library as expected. In my second approach, I used the same DDA files but a larger but not refined in-house generated database. MS Amanda did all the searches and created the mzID files but failed to create the library due the failure to parse the database entries. The database was generated in our institute and has a header format that is obviously not recognized by MS Amanda in its default state of integration into Skyline. Unfortunately, the standalone version of MS Amanda is not very handy for generating results of multiple searches and I actually have no idea how to change parse rules in MS Amanda.
I there any documentation about the parse rules MS Amanda applies and which type of database headers are supported. This would be helpful to adapt the databases if necessary. The other way would be to have a possibility to adapt/change the parse rules when using MS Amanda in Skyline to generate libraries.