pFindStudio
error in pBuild
My mass spec is a Agilent 6550 QTOF. Acquired data is converted to mgf using MSConvertGUI (http://proteowizard.sourceforge.net/index.html), and because pFind does not have an option for "CID QTOF", i choose "CID ITMS" or "CID FTMS".
pFind seems to run ok... but pBuild will throw an error (see attached for both)
Hi,
We have received your mgf and fasta files by e-mail, and have reproduced this error. I think it may be caused by that pFind (and pBuild) was developed based on the raw/wiff data rather than mgf file. After the developers fixed this problem, we will release a new version. Thank you.
We are currently having an identical issue with Bruker QTOF data. Output looks fine but cannot be parsed by pBuild. The pBuild error is identical to that from imwarren.
Hi @imwarren and @lgamon , Thank you for your advice. We have just released the new 3.1.4 version of pFind and change the demonstration of the result from MGF files.
-Hao
Hi, I have the same problem of @imwarren and @lgamon with .mgf files from LC-ESI-MS/MS system Waters, Q-TOF MicroTM Micromass (converted with proteowizard). I used the 3.1.4 version of pFind. I tried the same procedure with files from Thermo instruments (downloaded from PRIDE database in .raw format and then converted in .mgf file with ProteoWizard) but, in this case, the .mgf file correctly work. I think that the problem might be due to Waters .raw files which are wrongly converted to .mgf files. Do you have any suggestions for the analysis of waters files?
Thank you in advance for your support Giosuè
Hi, I have the same problem of @imwarren and @lgamon with .mgf files from LC-ESI-MS/MS system Waters, Q-TOF MicroTM Micromass (converted with proteowizard). I used the 3.1.4 version of pFind. I tried the same procedure with files from Thermo instruments (downloaded from PRIDE database in .raw format and then converted in .mgf file with ProteoWizard) but, in this case, the .mgf file correctly work. I think that the problem might be due to Waters .raw files which are wrongly converted to .mgf files. Do you have any suggestions for the analysis of waters files?
Thank you in advance for your support Giosuè
Hi，
Thanks for your mail. We are now developing the new version that can read the mzML format of MS data. So if you use the new version, you can firstly export .xml files and then specify them in the pFind interface.
Our new version will be released in one or two weeks.
Best Regards,
Hao