Dear Skyline team,
I hope you are all well. I am trying out the BlibSearch tool from Bibliospec and am getting no matches to spectra. The mzml being searched is one of the files which was used to make the blib file so there should certainly be matches.
I believe this error below (from the program run in verbose) may reveal the reason why I am getting no matches to spectra. The blib itself works fine in Skyline, just not with BlibSearch:
At line:1 char:1
+ .\BlibSearch.exe -w 5 .\Redacted2.mzML .\Redacted. ...
+ CategoryInfo : NotSpecified: (Using library(s) .\Redacted1.blib .:String) , RemoteException
+ FullyQualifiedErrorId : NativeCommandError
DEBUG: Creating reader for library .\Redacted.blib.
DEBUG: Highest lib spec ID is 501.
DEBUG: Creating PwizReader.
An exerpt of the console output in verbose can be found below, the final line is always scoring 0 matches:
DEBUG: PwizReader looking for index 17416.
DEBUG: Searching spectrum 17417
DEBUG: Adding spectrum 274, precursor 739.27.
DEBUG: Adding spectrum 275, precursor 739.27.
DEBUG: Adding spectrum 276, precursor 739.27.
DEBUG: Adding spectrum 277, precursor 739.27.
DEBUG: Found 4 spec between 738.37 and 748.37.
DEBUG: Scoring 4 matches.
DEBUG: Scoring 0 matches.
The actual output (.tmp file) looks like this:
# Date: Mon May 3 21:20:05 2021
# query file: Redacted2.mzML
# Library file list:
# libID1 Redacted.blib
# clear-precursor = true
# topPeaksForSearch = 100
# mz-window = 5
# low-charge = 1
# high-charge = 5
# report-matches = 5
Query LibId LibSpec rank dotp query-mz query-z lib-mz lib-z copies candidates sequence TIC-raw bp-mz-raw bp-raw lbp-mz-raw num-peaks matched-ions