diff --git a/mzrecal.go b/mzrecal.go index 76f099f..9862558 100644 --- a/mzrecal.go +++ b/mzrecal.go @@ -1280,7 +1280,7 @@ peaks are considered for computing the recalibration. <1 means all peaks.`) 2.0, `max mz error (ppm) for accepting a calibrant for calibration`) par.scoreFilter = flag.String("scorefilter", - "MS:1002466(0.99:)MS:1002257(0.0:1e-2)MS:1001330(0.0:1e-2)MS:1001159(0.0:1e-2)", + "MS:1002257(0.0:1e-2)MS:1001330(0.0:1e-2)MS:1001159(0.0:1e-2)MS:1002466(0.99:)", `filter for PSM scores to accept. Format: ([]:[])... When multiple score names/CV terms are specified, the first one on the list @@ -1290,7 +1290,8 @@ and post-search scoring software: MS:1002257 (Comet:expectation value) MS:1001330 (X!Tandem:expectation value) MS:1001159 (SEQUEST:expectation value) - MS:1002466 (PeptideShaker PSM score)`) + MS:1002466 (PeptideShaker PSM score) + `) par.charge = flag.String("charge", "1:5", `charge range of calibrants, or the string "ident". If set to "ident",