2.1.Stand alone: how to run a probabilistic based scoring function to compare two given spectra data sets

The stand-alone tool can be started by running a command prompt in a folder that contains scoring_pipeline-X.Y.Z.jar (X.Y.Z shows the current version number). On the command prompt, the following line needs to be executed:

java -cp scoring_pipeline-1.0.jar main.ScorePipeline

Parameters must be introduced in MS2Similarity.properties. Parameters are explained here