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A list of common neutral losses

Dear colleagues,

I have been looking for a comprehensive list of neutral losses commonly seen in MS/MS spectra but haven't been able to find one. Instead, I've started to compile a list on my own with some additional information, such as the functional groups to which the neutral loss may be related and how the moieties may be further fragmented. You can access and use the list in Excel format using the OneDrive link below and expand it freely. Also, any good source for additional information is most welcome.

Neutral_losses

Sincerely,
Ville Koistinen

Re: A list of common neutral losses

Reply #1
Hi Ville.

There are a couple of good resources. The best is the supplementary material from:
Keller BO, Sui J, Young AB, Whittal RM. Anal Chim Acta. 2008;627(1):71–81.

There is also the book "Pretsch, Buļhlmann & Badertscher. Structure Determination of Organic Compounds: Tables of Spectral Data." with more fragments. Your might have access online through your library.

Then there is the list I compiled for CAMERA annotation: https://github.com/stanstrup/chemhelper/tree/master/inst/extdata (beware that the mz difference is to the monoisotopic +/- H peak in that list)

I have some additions to the Keller list. Perhaps I can put that on github and we can expand from that. Or perhaps google docs etc might be easier. What do you think? I know Keller wouldn't mind (I wrote with him recently) and as far as I know the publisher, Elsevier in this case, doesn't have copyright on the data itself (can someone confirm this?).
Blog: stanstrup.github.io

Re: A list of common neutral losses

Reply #2
Thank you @Jan Stanstrup for the useful information. Yes I think we could work on compiling all this data. To me it does not matter which file sharing method is used.

Re: A list of common neutral losses

Reply #3
I echo @Jan Stanstrup in his resources. Depending on your definition of 'common', you could deduce some 'common' losses from the Precursor-Product Frequency tables here: http://metabolomics.jp/wiki/Index:MassBank [derived from MassBank spectra].

FYI: In your table you do not differentiate between pos and neg mode; though some neutral losses might appear preferentially in one mode. Also, the column with the losses is called 'mass fragments', whereas I think you mean 'neutral losses'....(perhaps just copy paste from other table as there are some other columns present not relevant for the losses)

I think the 'raw data' is not owned by a journal, but processed data might be. Worth knowing a bit more about, but slightly off topic here I think?  ;)

Hope this helps!

Re: A list of common neutral losses

Reply #4
Thank you @jjjvanderhooft for your comments and advice. Indeed the moiety being cleaved off will often ionize in one mode only, in which case it will be seen as a neutral loss in one mode and as a peak (with possible fragments) in the other. This should be taken into account but so far I haven't had enough data to classify the information based on that.


Re: A list of common neutral losses

Reply #6
I suggest uploading the Excel to Figshare.

Re: A list of common neutral losses

Reply #7
I have created a github and added the Keller list as separate tsv files: https://github.com/stanstrup/common_mz
I have opened issues from some of the other possible sources that were mentioned here: https://github.com/stanstrup/common_mz/issues

It would be cool if we could collaborate on this.
One thing I have been thinking about is how to handle fragments of contaminants. For example can you think of a nice way to add all known masses originating from a specific PEG?
If you think it should be organized differently please speak up.
Blog: stanstrup.github.io

Re: A list of common neutral losses

Reply #8
Hi Jan,

That could grow to a very useful respository! :) Thanks for creating those - hope we will be able to add more in the nearby future....

Are those tables available as csv as well?

Cheers Justin

Re: A list of common neutral losses

Reply #9
The tsv files? I think you can treat them as csv for all practical purposes. Just that opening csv in excel seems to be system dependant (expecting different separators depending on the locale). With tsv it is explicit what to expect.
Blog: stanstrup.github.io

Re: A list of common neutral losses

Reply #10
I see - okay - never really used tsv format before.... :-)

Re: A list of common neutral losses

Reply #11
I have created a github and added the Keller list as separate tsv files: https://github.com/stanstrup/common_mz
I have opened issues from some of the other possible sources that were mentioned here: https://github.com/stanstrup/common_mz/issues
It would be cool if we could collaborate on this.
One thing I have been thinking about is how to handle fragments of contaminants. For example can you think of a nice way to add all known masses originating from a specific PEG?
If you think it should be organized differently please speak up.

Great idea, have you seen MaConDa?
http://www.maconda.bham.ac.uk/
Quote
MaConDa is a comprehensive and manually annotated database that provides a useful and unique resource for the MS community. The information contained in MaConDa is based on published literature and data provided by several colleagues and instrument manufacturers. MaConDa currently contains ca. 200 contaminant records detected across several MS platforms. The majority of records include theoretical as well as experimental MS data. In a few cases experimental data was included without definite identification.


Re: A list of common neutral losses

Reply #12
I did see MaConDa. Unfortunately it doesn't seem like there is a submission form (apart from a message to the devs)...
Blog: stanstrup.github.io

Re: A list of common neutral losses

Reply #13
will try to contact Ralf.W for this...

Re: A list of common neutral losses

Reply #14
Jan, Reza, others, more than happy to discuss this in more detail.

Would be great to extend / update MaConDa and develop some new features (API - partly done already, etc). Let's not reinvent the wheel.

Jan, see your GitHub as well.