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Messages - Reza Salek

16
Compound identification / Re: Metabolomics and clinical practice
As a new Biomarker, yet to materialise. However, there are many new proposed ones. But it needs to pass the test of time and reproducibility. I would be also interested if anyone else came across one with good potentials. 
18
Galaxy / Re: How to implement a 'commerical' MS data processing software in Galaxy ?
You need to check if the commercial tools licensing would allow you to do it, even if you plan to run it locally.
You can generate a "tool config file" or "wrapper" and share that if you wish (without the commercial tool).
There are many tutorial and wikis on this and larger community to ask questions. @Ralf Weber  know quite a lot more.
Best Wishes,
Reza
23
Compound identification / Re: A list of common neutral losses
Quote from: Jan Stanstrup – on
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.

24
Publication Committee / Re: New Metabolomics Society Journal - Your Input Needed!
Quote from: egonw – on
Quote from: billwikoff – on
The question of a new journal does not exist in a vacuum and this question of how the Metabolomics journal was handled is absolutely relevant.

This forum topic raises a lot of questions with me too. The reasons why the current journal is no longer suitable, sound like the key things the new journal must improve.
Just a clarification the Metabolomics Journal is a great journal to publish and I would personally continue to do so, the only thing that has change is the relationship with the society, see above email.
25
Publication Committee / Re: New Metabolomics Society Journal - Your Input Needed!
Dear @billwikoff and @egonw, I do agree with both for you on transparency and engagement with community, hence one the reasons forum was updated to engage better with you. While I seek a more official and transparent reply to your questions, I'm sharing an email send around to members on 25 November 2015. 
Reza

The email send to the community

Quote
"After ten years of close affiliation between the Metabolomics Society and Springer’s journal Metabolomics, the relationship comes to an end on 31st December 2015. The Society was instrumental in making Metabolomics a leading journal in the field and many members have served on the Editorial Board along with Editor in Chief Prof Roy Goodacre. Roy is to be commended for his central role in establishing and growing the journal. He will continue to serve as Editor in Chief as Springer continues to publish Metabolomics.  Springer’s Metabolomics will therefore no longer be the “Official Journal of the Metabolomics Society”. Many members access Metabolomics through their institutional subscription, and for them nothing will change. Those Members using their Society membership to access Metabolomics are advised that they will need to find an alternative mechanism to do so after 31st December 2015.

The Society will be pursuing other avenues for Society-related scholarly publications that will serve the interests of the whole Metabolomics Society. The Publications Committee looks forward to any suggestions or comments at publications[at]metabolomicssociety.org.

Ute Roessner, President
Dan Bearden, Treasurer
Tim Ebbels, Secretary

On behalf of the Board of Directors "




29
Data Standards / Data Standards -Task Group Announcement
The remit of this Task Group is to leverage upon the past, current and future activities of MSI (http://www.metabolomics-msi.org) and HUPO-PSI (http://www.psidev.info) communities on data standards. Our activities complements the work conducted within the Metabolite Identification, and data Quality Task Groups. We aim to (1) coordinate and promote interaction and integration between MSI and HUPO-PSI communities; (2) share and discuss infrastructure and bioinformatics activities and strategies in promotion, annotation and reporting of metabolomics data. This will be achieved through announcing tools, targeted publications, news groups, MetaboNews, dissemination of information through this forum, and your input <!-- s:) -->:)<!-- s:) --> .

Please visit http://metabolomicssociety.org/board/scientific-task-groups/data-standards-task-group to learn more.

And please join this active community and post your thoughts, question and ideas in this forum.
30
Other / Re: Automatic detecion of problems during analysis
Depending on which problems you are after to prevent (samples or QC/QA) and what is your instrument make-model and data type. Have a look at:
http://www.ncbi.nlm.nih.gov/pubmed/23088386
SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments.
Again there are others  particularly if QC/QA is the target, which also can give feeling for sample quality or potential issues. They are mostly for proteomics data sets but should equally work for metabolomics data from similar instrument. 

Your idea for XCMC equally should work in a pipeline and with a mean of visualising and interrogating the results.

Reza