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Topic: Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL (Read 3186 times) previous topic - next topic

Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL

Hey Hiroshi,

I planned to import Sciex data from DDA experiments in order to build an own, user- and device-specific MS/MS spectral library for  annotation in MSDIAL.

In this context, I would like to ask you what MSDIAL compatible data format is suggested for this purpose?
Are there variable options, how to extract the MS2 spectra from the raw files? Following this, should the assigned MSMS spectra left as they are or would it be better to eliminate the noise within the spectra before, und if so, how can this be done reliably?

Many thanks for your advice in advance!

Best regards
Falco

 

Re: Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL

Reply #1 –
Hi,

Taking a stab at it from my past experience. Here can be the helpful steps:


[a] Sciex's WIFF/WIFF2 files can be converted using ProteoWizard's MS convert
: http://proteowizard.sourceforge.net/tools.shtml where you can convert Sciex file into "mzML format that are centroided data". See attached pic on "MSconvert".

Once this individual mzML files with spectra for reference standards are available to you, you can run them on MSDIAL and export out individual spectra from each file as a NIST .msp format file, as shown in the attached pic: "Exporting Spectra"!

[c] Once you have exported all the reference MS/MS spectra as .MSP files you can simply add them up in a .text file or following instructions here: https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-8txhwpn

I followed the same workflow as above [a-c], but for a different instrument from Thermo and GC-MS : https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00774

Hope it helps!

Thanks,
Biswa

Re: Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL

Reply #2 –
Thanks Biswa!!
Using the following MSP libraries should be good to start for making your own library.
http://prime.psc.riken.jp/compms/msdial/main.html#MSP

Use notepad++ etc for editting.
Thanks,

Hiroshi

Re: Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL

Reply #3 –
Hi FalcoB,
Maybe you can take a look at this paper (Tada, I., Tsugawa, H., Meister, I., Zhang, P., Shu, R., Katsumi, R., Wheelock, C.E., Arita, M., Chaleckis, R., 2019. Creating a reliable mass spectral–retention time library for all ion fragmentation-based metabolomics. Metabolites 9. https://doi.org/10.3390/metabo9110251).

In my experience, I used target analysis (prepare a target list that contains all injected standard for MS-DIAL) without considering retention time. Then MS-DIAL will annotate all features with the matched mass, and I exported these features into a folder. Then you can import these features to MS-FIDNER and export them to *.msp in MS-FINDER. If you have all metadata prepared in the target list then they will be included in the *.msp file. Of course, you can also edit them in MS-FINDER. You can do this in a batch way, for example 10 standard as a batch. But just be careful not to put standards with the sample formula into a same batch because you will not able to distinguish which is which.

Best,
Sukis