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1
XCMS / Re: mz > 1000
Last post by jjjvanderhooft -
Check the settings of your acquisition method - 1000 is often used as higher end cut-off for the mass window. Also, the tuning influences the number of peaks you will detect above m/z 1000....
2
XCMS / Re: mz > 1000
Last post by Jan Stanstrup -
In my dataset I get features > 1000 with no problems. Are you sure your data contains data above 1000 Da?
If you are sure your data has peaks > 1000 Da your best bet is to post a reproducible example with code and sample data.
3
XCMS / mz > 1000
Last post by hhabra -
It appears that all mz's captured by XCMS are less than 1000, when other methods have found features with greater than 1000.  I'm wondering if it's possible to acquire metabolite features with mz > 1000 using XCMS.

Thanks to whoever can help!
4
Hello, my name is Elisabeth Frankish and I am one of thousands of New Zealanders who are very concerned about our government's use of sodium fluoroacetate as a rodenticide, which is dropped by helicopter into New Zealand native bush including waterways. I'm not a trained scientist but am looking for an appropriate forum in which to ask questions about the metabolic pathway of sodium fluoroacetate and its metabolite fluorocitrate, and the implications of low-dose poisoning especially on the unborn, male fertility and neurotoxicity.
I have done some research and see that there are two other compounds which also metabolise to fluorocitrate, they are:
1. fluorouracil which is a chemotherapy drug, and,
2. fluoroquinolone which is an antibiotic.
Both of these drugs have multiple adverse effects which appear (to me) to be comparable to the adverse effects of sodium fluoroacetate, and I wonder if it is because we're really dealing with the adverse effects of FLUOROCITRATE, rather than the initial compunds. May I ask you all your thoughts?
If so,  would it be possible to borrow the research for fluorouracil and fluoroquinolone  and apply it to sodium fluoracetate? I have asked this question rhetorically on our Facebook page 1080 Eyewitness. https://m.facebook.com/groups/1399949210263741?multi_permalinks=1953946231530700¬if_t=like¬if_id=1502852914481434&ref=m_notif
I attach a diagram showing my question in concept. One of the reasons that our governments continues to drop it is that there is "no evidence" of the impacts, because the research "has not been done".
I am one of many thousands of New Zealanders who I greatly concerned by the implications of this poison and we would all be very grateful for your help, thank you.
Yours sincerely,
Elisabeth Frankish
Member of "1080 Eyewitness."
5
MassBank / Re: RMassBank
Last post by meow -
Hi LN.AW,

sorry for the delay. This functionality is not yet in RMassBank itself, however you can use RMassBank to extract spectra and the OrgMassSpecR functions for comparison (SpectrumSimilarity). We have in-house adapted functions for this but it's not yet all there.
6
Yes, I have it installed on a Windows 64-bits machine!  :)
7
Announcements / Announcement of Opportunity
Last post by stacey.reinke -
Apply to Join the EMN Committee

Deadline: 15th August, 2017

Background
We are inviting 6 early-career researchers to join the Metabolomics Society's Early-career Members Network (EMN) Committee. The mission of the EMN is to recognize the value and importance of our early-career members, to ensure that their views are heard and acted upon, and to ultimately improve their experience in metabolomics science and our community. Current programs and activities offered by the EMN include: workshops and the EMN Reception at the annual Metabolomics conference, the EMN Webinar Series, and the EMN Travel Bursary Program. We are also involved in the Metabolomics Forum and have a Facebook profile to stay connected with the membership. We are looking for creative thinkers to identify challenges faced by early-career researchers in metabolomics and to develop programs to overcome these challenges.

Eligibility
We welcome applications from students conducting higher degrees (Masters, PhDs) in a metabolomics discipline or from those within 5 years of their PhD who are actively engaged in metabolomics science. As an international society we encourage applications from all continents. Successful applicants must be members of the Metabolomics Society (or immediately become members upon joining the task group).

Time Commitment
There is much exciting work to be done and much to achieve! Therefore we anticipate a contribution of up to two hours per week (on average). If the Early-career Members Network organises sessions at conferences or other events, time commitments will increase accordingly. Note also that the existing members of the EMN Committee span many time zones, so some conference calls may occur early or late in the day. No dedicated travel will be required for the EMN Committee discussions. The appointment to the EMN Committee is for one year initially, and may be extended up to two years. It is your responsibility to discuss this commitment with your supervisor(s) prior to applying.

Application Procedure
Please send the following, in one document (.docx or .pdf), to the EMN committee (info.emn@metabolomicssociety.org).

One-page CV with relevant experience in developing and leading networking activities (e.g., student rep for other societies) plus your research experience in metabolomics (e.g., presentations, publications, etc.). If you are currently a member, please provide your membership number to us as well.

Up to 300 words on why you fit the role and up to an additional 300 words (one page in total) on what ideas you are passionate about developing as part of the Early-career Members Network. Applications will then be reviewed by members of the existing EMN committee members, and successful candidates will be notified by the end of September 2017 to start in October 2017.
8
Hi,

Can it also be installed in a 64-bit Windows 10 machine? Thanks!
9
Model Organism Metabolomes / Re: Metabolomics in C. elegans
Last post by michael.witting -
Hi all.

for people interested in C. elegans metabolomics:
We have started the WormJam "initative", which will curate metabolites, metabolic pathways etc present in the worm and collect everything in a consesus metabolic model. If you are interested in joining have a look into our google group:

https://groups.google.com/forum/#!forum/wormjam

Best regards,

Michael
10
Dear all,

from the 9.11. ot 10.11.2017 we will host a workshop at the Helmholtz Zentrum München to work on the consensus metabolic model for the nematode C. elegans. This workshop will include mainly hands-on group work on curating pathways, edit wrong annotations and add new ones.
This workshop could be interesting for all metabolomics scientist working with C. elegans.

More information and the registration page can be found here:

https://www.helmholtz-muenchen.de/genie-workshop-2018/index.html

Best regards,

Michael

GENiE Workshop:
Extending the consensus representation of C. elegans metabolism

Topic

C. elegans has recently been advanced as a premier model organism for the study of metabolism, with the publication of two whole-genome metabolic models. Using those models together with transcriptomics, metabolomics and proteomics data allows the relationship between gene expression, nutrition, metabolism, and phenotype to be explored in-depth in data-driven systems-level in silico simulations. In a GENiE workshop held April 19-20 2017 at the Babraham Institute, Cambridge, UK, the relationships between the two existing metabolic models have been explored with the objective of generating a consensus model that builds on the strengths of each separate model. This consensus model will be directly usable by a wide range of C. elegans researchers. However, the two published models are still incomplete, and certain important pathways and areas of metabolism are currently under-annotated, e.g. lipid metabolism and many metabolites that are specific to nematodes. During the April 2017 workshop, specific such areas of incompleteness have been discussed together with the community in order to prioritize "key" missing annotation pathways of importance for current GENiE community objectives in C. elegans metabolic research. A number of such pathways will be selected for this follow-up "annotation jamboree" workshop.

One of the strengths of our first workshop and that we intend to also bring to the second workshop, was that it brings together GENIE members with the larger C. elegans community as well as with a wider community of computer scientists with expertise in Metabolic Reconstruction and with experts in Metabolomics from a wide variety of fields. Therefore our workshops will bring a wide range of new skills and knowledge to the worm community.

Goals

The aim of the second workshop is to fill such gaps and annotate missing pathways. It will thus constitute a natural follow-on from the success of the first workshop. Scientists using metabolomics to study C. elegans metabolism will be asked to participate in this workshop to add their knowledge on newly identified molecules. This workshop will be more hands-on and practical compared to the first one. We will only have a few tutorials and a keynote talk on important aspects of metabolic pathway curation and/or C. elegans metabolism. Different pathways and gaps will be annotated in group work.

Specific overall goals of the workshop are:

    Gap filling of metabolic pathways
    Curation of new pathways, especially secondary metabolism and lipid metabolism
    Annotation of new enzymes
    Planning of validation experiments
    Bring new cutting edge methods and technology to Worm Recon 2.
    Expose C. elegans researchers to gold standards in metabolomics and Flux balance analysis practices.
    Align European standards with WormBase and the wider Metabolic reconstruction community.
    Gear towards a publication of a merged open source model, available to the C. elegans community at large.

This workshop is open to all researchers with an interest in C. elegans metabolomics and is not limited to GENiE consortium members. There are a limited number of places available, please register using the link on the left.