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BlibBuild not reading Thermo raw files

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BlibBuild not reading Thermo raw files lauri.peil  2013-09-20 02:04
 
Hi,

I have run into a problem with generating spectral libraries from .ssl files. I have a self-generated .ssl file according to instructions in https://skyline.gs.washington.edu/labkey/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats and would like to use it in Skyline. However, when I try to build spectral library from that .ssl file, Skyline reports an error:
ERROR: [MSDataFile::readFile()] Unsupported file format..
ERROR: PwizReader could not parse my_raw-file.raw

MSFileReader is installed and Skyline works just fine with Thermo files for other spectral libraries so this can't be the issue.

Furthermore, I tried compiling BiblioSpec fresh and got exactly the same error when using command-line BlibBuild (vendor libraries were included and build process found them, for example msconvert worked fine with .raw files). There seems to be an 'old' v2.0.0 pre-compiled BiblioSpec available (http://proteome.gs.washington.edu/software/bibliospec/documentation/download.html) which requires slightly different .ssl input but otherwise works fine, can find MSFileReader and use it for reading in .raw files.

Looks to me as current BiblioSpec/BlibBuild has a bug somewhere so that it does not link with MSFileReader libraries and therefore can't parse .raw files, unless I have done something completely wrong.

Any ideas?

Thanks a lot,

Lauri
 
 
lauri.peil responded:  2013-09-20 02:13
Forgot to add that this error is seen with both Skyline 1.4 and 2.1.

Lauri
 
Brendan MacLean responded:  2013-09-20 02:17
Hi Lauri,
That is correct. At present, we have disabled reading vendor data files in BlibBuild. You will need to convert to a portable text format (mzML or mzXML) for use with your .ssl file.

Thanks for your post. We will try to make this clearer on the documentation page you reference, and we will also consider whether to enable this case in the future.

--Brendan
 
lauri.peil responded:  2013-09-20 02:23
Hi Brendan,

thanks a lot for your reply, i won't mess with it for much longer then.

just out of curiosity - any particular reason my vendor data files are disabled? converting them to mz(X)ML is one extra step which also requires more disk space... and finally, will there be any differences (in the spectral library) whether i use old BiblioSpec binaries with Thermo support or the one in Skyline, converting raw files to mz(X)ML first?

thanks a lot,

Lauri
 
Brendan MacLean responded:  2013-09-20 02:32
Hi Lauri,
Really? Did was that working at one point? Maybe it just got broken then when I transferred responsibility for building the BlibBuild.exe to the current developer owning BiblioSpec, Kaipo Tamura (prior to the last v1.4 patch release). In theory, it shouldn't be very hard to enable, because for Skyline BlibBuild.exe lives in the same folder with Skyline.exe which already requires all of the vendor reader libraries. It just never occurred to me that it worked, since I knew of no input format that required it to work. So, it was completely untested, and I am a firm believer that untested use cases don't work, or as in this case, don't work for long.

But, if you are sure it used to work, then we will have a quick look at this and see if we can't get back to that for the next v2.1 patch release.

Thanks for your feedback.

--Brendan
 
lauri.peil responded:  2013-09-20 02:43
Brendan,

i don't know if BlibBuild in any of the Skyline versions ever worked or not, i only tried it few days ago, but BlibBuild binary from http://proteome.gs.washington.edu/software/bibliospec/documentation/download.html sure does, provided you have MSFileReader installed. it requires slightly different .ssl input (columns headers and their order have changed somewhat) but other than that it works and produces functional .blib library. might be worthwhile to assign a new version number to the current BiblioSpec and update its documentation, current docs apply to the 'old' version so there is some confusion (i was struggling with it for last few days)...

Lauri
 
Brendan MacLean responded:  2013-09-20 03:02
Okay. We'll have a closer look at how this got broken, and see what it would take to fix it.

Thanks.

--Brendan