Dear all, Does anybody know how to predict MS/MS spectrum of a given chemical that is not present in Pubchem by MS-FINDER? I am working with oligomers which could be any combination of monomers, e.g. diethylene glycol (DEG), phthalic acid (PA), triethylene glycol (TEG). However, many of them are not present in Pubchem, for example, cyclic TPA-EG-TPA-DEG. I am thinking if MS-FINDER can work like a MS/MS fragmentator that allows input of a given structure and give us the in-silico MS/MS spectrum?
Thanks a lot for testing. I understand now it was because of the abf converter I used (an old version probably). Downloading the latest abf converter, it works fine now.
" a. When dealing with Waters MSE data, in my experience, it is better to remove function 3 files (_FUNC003.DAT, _FUNC003.IDX, AND _FUNC003.STS, they are for the lockmass) from the *.raw file before converting into *.abf file for MSIDAL processing. Otherwise, the deconvoluted MS/MS spectra might weird.
According to my understanding, the function storing lock mass data is not stored in abf. If you see such an issue, we have to ask the developers of abf converter. Please send me an example .raw file of Waters if you face on such an issue."
I recently encountered this problem again. i think i find a good example now.
I upload two screenshots here. after removing the function 3 from the raw file, the deconvoluted MS/MS is much better.
I found that some GC-MS peaks do not align correctly. For example, benzaldehyde and 1.2.4-trimethylbenzene have quite difference spectra according to the NIST library, however they are aligned as one peak and only 1.2.4-trimethylbenzene is reported even though I have set 80% spectrum similarity for the alignment (please see the attachment). Does anybody know what is wrong here?
To export from UNIFI you must open a port on the server and connect MSConvert to it via network. For this you have this "Browse network resource" field in the upper part of the window.
thanks a lot for your help. I know how to connect MSconvert and UNIFI. The problem is which filter should I use? As peak picking filter using vendor format does not support UNIFI. I have tried to use peak picking applying CWT setting. it can be converted to*.ibf file and processed by MS-DIAL. The accuracy of the mass, retention time as well as drift time are perfect, but the deconvoluted MS2 spectra seem weird. I attach the spectra of a standard from UNIFI and MSDIAL below to show the difference. it seems something wrong with the MS-DIAL MS2 deconvolution. As MS-DIAL works perfectly for MSe data, i suppose the problem could be the converted *.mzML file.
by the way, does anybody know how go get the coefficient for calculating Waters ccs values? As the ccs values obtained in MS-DIAL were far from correct. I suppose it is because I didn't set these values when processing with MS-DIAL.
Unfortunately, MSconvert does not support to convert raw files from UNIFI as I attached. it specifies that it does not support UNIFI when applying peak picking filter.
Dear Hiroshi, Our UNIFI is capable to export *.mzML and *.mzXML using MSconverter. I have tried *.mzXML before, but it didn't work. I will try *.mzML and let you know how it will be going.
