Metabolomics Society Interest Groups

Metabolomics Study of Marine Plants

2012-04-05T06:35:11Z

Good day everyone, I've recently joined the group and was wondering whether anyone has done any work on marine plants?
I am interested to find out how similar or different metabolites are when comparing terrestrial, fresh water and marine plants. Furthermore, if there are any additional problems in MS analysis when dealing with marine samples.

Thank you
Hope to get along with everyone and to read some of your works

2 bioinformatics/statistics post-docs available at Imperial College

2012-03-30T12:18:08Z

We are looking for two post-doctoral researchers in the field of bioinformatics/statistics applied to metabolomics and other omics data. Please see the attached adverts for more details or visit http://www3.imperial.ac.uk/employment.

Vacancy for postdoc (6 month position)

2012-03-19T18:10:37Z

This is not strictly a metabolomics position, but is concerned with metabolism of environmentally relevant species:

http://www.jobs.ac.uk/job/AED343/research-associate/

Closing date 16 April.

MATLAB script for STOCSY...???

2012-02-19T13:02:58Z

Hello Everyone,

I am Kashif, working at IBL, Leiden University (The Netherlands), and I need some help. It would be nice if someone kindly provide me the MATLAB script for STOCSY. Please contact me via kashifali.81@gmail.com.

Kashif

MIBBI publication

2012-02-13T22:29:09Z

In case people haven't seen this MIBBI had a publication in Nature Genetics this month...
Toward interoperable bioscience data.

Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.

Nat Genet. 2012 Jan 27;44(2):121-6

Oh and yes I do I have vested interest but I hope this is of interest to people.

UNTARGETED METABOLOMICS: Polling or not pooling samples

2012-02-08T10:14:53Z

Hi to everyone.
I would like to have some feed-back on an issue that has been largely discussed in the field of genomics-proteomics (I coming from that)
UNTARGETED METABOLOMICS: Pooling or not pooling plasma samples when using animal models ? (not when using patients)
In important issue in all omics is the need to reduced technical (MS-MS) and biological variation gaining increased power to detect treatment differences.
In my opinion, when following an untargeted metabolomics approach using animal models, pooling biological samples might be a valid procedure to overcome these limitations.
Because pools represent averages, the dominant differences and similarities between treatment groups might be easier to find (Kendzionski et al., PNAS 2005; Diz et al., Electrophoresios 2009; Karp et al., Proteomics, 2009). The assumption of biological averaging is usually met in animal models where the sources of bias (subject-to-subject variation) are small and can be neglected (Karp et al., Proteomics 2009).
When the initial interest is not on the individual (e.g. making a diagnosis) but rather on the characteristics of the population (e.g. changes in expression patterns in different groups) I usually perform a sample pooling strategy.

Any comment??
thanks so much

data filtering

2012-01-21T09:41:37Z

Hi everybody,
I'm performing large-scale LCMS metabolomic profiling, and I'm looking for a R script that performs quality control-based robust LOESS signal correction to correct for analytical drift within and across analytical batches (such as in Dunn, W. B., Broadhurst, D., Begley, P., Zelena, E., Francis-McIntyre, S., Anderson, N., Brown, M., Knowles, J. D., Halsall, A. et al. (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6: 1060-1083).
I would be extremely pleased if somebody could help,
thanks and see you in washington

jc martin
biomet platform
marseille, france

Metabolomics special issue from 2009

2012-01-04T12:05:31Z

The “environmental metabolomics” special issue of the journal Metabolomics is now nearly three years old. As a result, it’s now possible to use its citation data to compare it to the citation rate of all papers in the journal – which is, of course, basically the same thing as impact factor. Why do this? Well, there isn’t any specific need, of course – but it’s interesting to see if environmental papers are the poor relation of the metabolomics world, given that environmental journals in general have relatively low impact factors compared to biomedical journals.

So, without further introduction, here are the results (all data taken from Thomson Reuters Web of Science, corrections and editorials excluded). The equivalent “impact factor” for the journal based on all papers from 2009 is 4.2. [“Impact factor” = total cites in 2010 + 2011, divided by 2 x the number of papers in 2009.] For papers from the environmental special issue only, it’s 6.4; and for all other papers from 2009, it’s 3.4. Of course, reviews tend to be more highly cited than primary research papers, and so can distort results. With reviews excluded, the “impact factor” for the special issue is 5.1, which still compares very favourably with all other papers (2.9, with reviews excluded).

What should we conclude from this? Not much, I would suggest! Firstly, we are not making direct comparisons (for instance, the special issue papers were published in the first issue of 2009 and so have had longer to be cited; and there are several other reasons why it’s not so simple to compare between sub-fields – listing these will be left as an exercise for the reader). Secondly, we have only a small sample set: 12 papers in the special issue, and only 42 papers in Metabolomics in total in 2009. But I do suggest that it possibly shows a healthy interest in environmental metabolomics, which may be encouraging to those working in the field.

databases for metadata - what systems do people use?

2011-12-02T05:01:19Z

Hi all

I'd like to pick up on something Susanna and Adam wrote about - databases.

We're at a crunch point in my lab and need to put a system in place to manage our data from info about source organism to where the NMR or MS data files are. There are commercial LIMS systems available but I'd be interested in hearing more about what everyone else is using.

Our lab also includes proteomics and any solution we put in place would need to be compatible (at least at the interfaces) with our colleagues in genomics (who are in the process of changing their LIMS). We are looking at between 3000-10,000 samples per project and any LIMS will be managed on the department's cluster (unix).

isa tools seems to be something a few people have talked about. I'm not a data base expert but I've tried to have a look at some of the documentation on this. Is it an relational database that is customisable? Is this working well for people? Could we get it to recognise and/or produce bar codes? The ontology and experimental descriptors look good and certainly seems like it would work for our systems biol work.

What are other people using?

cheers
Simone

Welcome to the Data Analysis Interest Group forum

2011-11-24T11:33:59Z

Thank you for visiting this group! This is THE place on the web to discuss data analysis issues relevant for metabolomics. Do you need to find a suitable program for data preprocessing? Are you struggling to find the most suitable data analysis method to answer your experimental question? Any other question regarding number-crunching your metabolomics data?
On the other hand: maybe you invented or found a data analysis method that you think will bring many metabolomics researchers further! In all cases: Do not hesitate to post!

Human Metabolome Database Integrated with PubChem (finally!)

2011-11-16T22:47:55Z

Just an announcement that the HMDB (version 2.5) is now available in PubChem and will be synched with it on a regular basis. If you have any input on ways we can make the data easier to access and integrate, let me know!

To see all deposited structures: PubChem HMDB Structures.

Assessment of nutritional status

2011-11-14T00:20:36Z

Can members tell me what has been done to develop markers for determining an individual's nutrition status using a non -invasive biological fluid such as urine? We want to use this approach to determine if people on certain diets have been adhering to those diets or indeed if the diet thay are on is having the required effect.

Job posting for a mass spectrometrist at Cambridge, UK

2011-11-12T21:08:10Z

A post for a mass spec post doc with an interest in obesity and type II diabetes at Cambridge University.

http://www.admin.cam.ac.uk/offices/hr/j … i?job=9492

If you are interested please reply through the website or drop me a line.

Vacancy for postdoc in molecular ecotoxicology/metabolomics

2011-11-11T21:27:09Z

New 3-year postdoc available to conduct integrated metabolomics and transcriptomics studies in ecotoxicology.

See: http://www.biosciences-labs.bham.ac.uk/ … ancies.htm

Welcome!

2011-11-10T19:49:10Z

Hi Folks,

Welcome to the Medical/Pharmaceutical Interest Group!

I am an active member of the metabolomics society and I would encourage other folks conducting metabolomics research in the medical or pharmaceutical development field to join the society and participate in this user group. In particular I think like-minded scientists would be interested in how users in biomedical fields are employing the technology. Questions of particular interest are:

a) Are your main interests clinical or preclinical?
b) What platforms do you use and on what types of samples?
c) What endpoints are you employing metabolomics for (e.g. biomarkers, mechanisms, safety assessment, etc)?
d) What is the focus of your research (e.g. oncology, metabolic diseases, safety assessment of pharmaceuticals, etc)?

Hopefully, the forum will grow with time and serve as a clearing house for new hot papers of biomedical interest.

To provide a little background about me...

I work at Bristol-Myers Squibb in Princeton, NJ USA. We use metabolomics across the spectrum of pharmaceutical development from early preclinical efforts in animal models through clinical trials and manufacturing (fermentation analysis). We utilize NMR, LCMS and GCMS for our analyses tending to breakdown the analysis using NMR for urine and LCMS and GCMS for serum (not an absolute). We divide the work in that fashion mainly for pragmatic reasons (workload division). Our workload (at least at the moment) is probably about 40% preclinical safety assessment, 40% clinical, and 20% other things (e.g. preclinical efficacy, manufacturing, etc). Being in the pharmaceutical community, our focus is wherever new drug targets bring us, but I have found that recently it is heavily in the area of metabolic syndrome, diabetes, etc. Of course safety assessment can take you into all kinds of interesting directions completely separated from the therapeutic target. That is our group in a nutshell (no jokes please...). Hope to hear from some more of you soon.

Don Robertson