Is BlibSearch still supported?

Is BlibSearch still supported? Chris Ashwood  2021-05-03

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
# Options:
# 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


Nick Shulman responded:  2021-05-03
Yes, I think we can debug BlibSearch.exe.

BlibSearch.exe gets automatically built on our TeamCity automated build server. Here is today's build of all of the components of BiblioSpec:

(click "login as guest" if it asks you to log in)

I am not sure whether any of us remember how to use BlibSearch, but if you send us your files we might be able to figure out what is going wrong.

You can upload your files here:

-- Nick
Chris Ashwood responded:  2021-05-03
Hi Nick,

I am using today's TeamCity build of BlibSearch for the run, same as what you linked (bibliospec-bin-windows-vc141-release-3_0).

Both files are now uploaded.

Thanks for taking a look at this,
Nick Shulman responded:  2021-05-03
Thanks for sending those files.

It appears that BlibSearch.exe is getting confused by the negative charge states in the .blib file. BlibSearch does not know that it's supposed to look at the "negative scan" attribute in the .mzML file in order to know the sign of the charge, and so it thinks that none of the spectra in the mzML have the same charge as what's in the .blib file, so nothing ever matches.

I will ask around and find out if someone can fix this.
-- Nick
Nick Shulman responded:  2021-05-03
I am attaching a .7z archive which contains a build that I made of BlibSearch.exe which has a possible fix for this bug.
You should be able to use the program called "7-zip" to unzip it and run BlibSearch.exe which is in there.

I hope this fixes the problem for you and I will try to get this fix or something similar incorporated into the official builds.
-- Nick
Chris Ashwood responded:  2021-05-03
Hi Nick,

Works great.

Thank you so much for the quick turnaround and the fix!