SMART NMR use for metabolomics

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slo...@g.cofc.edu

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Apr 1, 2020, 1:36:01 PM4/1/20
to SMARTNMR
Hi, 

I was wondering if SMART NMR can be used for identifying metabolites. It seems the library is primarily natural products. If it could used for simple identification beyond the natural product discovery component, it would greatly benefit the NMR metabolomics community. I would love to hear if there is any effort towards this. Thank you. 

Amanda

beowu...@gmail.com

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Apr 1, 2020, 3:31:35 PM4/1/20
to SMARTNMR
Thank you for your interest Amanda. Are you talking about human metabolites or primary/secondary metabolites from bacteria/fungus/plants please?

If you are talking about human metabolites, yes, we are currently working towards identifying human disease samples using SMART. If you are referring to primary metabolites of non human species, we are not. But that is an interesting area for us to pursue. I am also glad if you have new ideas that you would like to collaborate with us.

Best,

Chen

Amanda Bayless

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Apr 1, 2020, 3:50:44 PM4/1/20
to beowu...@gmail.com, SMARTNMR
Hi Chen, 

Thank you for your reply. Currently, my interest is primary/secondary metabolites in aquatic organisms. Hyunwoo mentioned that he was working towards an updated version that would include metabolites from the HMDB database. I figured that should include many of the metabolites that I am interested in since I currently use the HMDB database for identification. This is of great interest to me!

Best regards,
Amanda

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Amanda L. Bayless
CofC under contract to NIST
Chemical Sciences Division | NIST

Hollings Marine Laboratory
331 Fort Johnson Rd.
Charleston, SC 29412

beowu...@gmail.com

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Apr 1, 2020, 3:57:33 PM4/1/20
to SMARTNMR
Hi Amanda,

You are welcome. Thanks for sharing your thoughts!

Best,

Chen


On Wednesday, April 1, 2020 at 12:50:44 PM UTC-7, Amanda Bayless wrote:
Hi Chen, 

Thank you for your reply. Currently, my interest is primary/secondary metabolites in aquatic organisms. Hyunwoo mentioned that he was working towards an updated version that would include metabolites from the HMDB database. I figured that should include many of the metabolites that I am interested in since I currently use the HMDB database for identification. This is of great interest to me!

Best regards,
Amanda

On Wed, Apr 1, 2020 at 3:31 PM <beow...@gmail.com> wrote:
Thank you for your interest Amanda. Are you talking about human metabolites or primary/secondary metabolites from bacteria/fungus/plants please?

If you are talking about human metabolites, yes, we are currently working towards identifying human disease samples using SMART. If you are referring to primary metabolites of non human species, we are not. But that is an interesting area for us to pursue. I am also glad if you have new ideas that you would like to collaborate with us.

Best,

Chen

On Wednesday, April 1, 2020 at 10:36:01 AM UTC-7, slo...@g.cofc.edu wrote:
Hi, 

I was wondering if SMART NMR can be used for identifying metabolites. It seems the library is primarily natural products. If it could used for simple identification beyond the natural product discovery component, it would greatly benefit the NMR metabolomics community. I would love to hear if there is any effort towards this. Thank you. 

Amanda

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Raphael Reher

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Apr 1, 2020, 4:00:12 PM4/1/20
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Hi Amanda,

I am pretty sure that most of HMDB db is already implemented in the current version of SMART.
How well you can use it for complex mixtures at this stage is questionable, because primary metabolites often have only few CH correlations.
Additionally, they are often 'building blocks' of secondary metoblites or share at least substructural motifs. That makes it more difficult to detect them as sole entities.
We are working on a way to link the SMART data to MS data, which should make these kind of efforts more feasible.

Best,
Raphael


On Wednesday, April 1, 2020 at 12:50:44 PM UTC-7, Amanda Bayless wrote:
Hi Chen, 

Thank you for your reply. Currently, my interest is primary/secondary metabolites in aquatic organisms. Hyunwoo mentioned that he was working towards an updated version that would include metabolites from the HMDB database. I figured that should include many of the metabolites that I am interested in since I currently use the HMDB database for identification. This is of great interest to me!

Best regards,
Amanda

On Wed, Apr 1, 2020 at 3:31 PM <beowu...@gmail.com> wrote:
Thank you for your interest Amanda. Are you talking about human metabolites or primary/secondary metabolites from bacteria/fungus/plants please?

If you are talking about human metabolites, yes, we are currently working towards identifying human disease samples using SMART. If you are referring to primary metabolites of non human species, we are not. But that is an interesting area for us to pursue. I am also glad if you have new ideas that you would like to collaborate with us.

Best,

Chen

On Wednesday, April 1, 2020 at 10:36:01 AM UTC-7, slo...@g.cofc.edu wrote:
Hi, 

I was wondering if SMART NMR can be used for identifying metabolites. It seems the library is primarily natural products. If it could used for simple identification beyond the natural product discovery component, it would greatly benefit the NMR metabolomics community. I would love to hear if there is any effort towards this. Thank you. 

Amanda

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Amanda Bayless

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Apr 1, 2020, 4:02:56 PM4/1/20
to Raphael Reher, SMARTNMR
Hi Raphael, 

Thanks for the information! This is good to know. 

All the best. 
Amanda

On Wed, Apr 1, 2020 at 4:00 PM 'Raphael Reher' via SMARTNMR <smar...@googlegroups.com> wrote:
Hi Amanda,

I am pretty sure that most of HMDB db is already implemented in the current version of SMART.
How well you can use it for complex mixtures at this stage is questionable, because primary metabolites often have only few CH correlations.
Additionally, they are often 'building blocks' of secondary metoblites or share at least substructural motifs. That makes it more difficult to detect them.
We are working on a way to link the SMART data to MS data, which should make these kind of efforts more feasible.

Best,
Raphael

On Wednesday, April 1, 2020 at 12:50:44 PM UTC-7, Amanda Bayless wrote:
Hi Chen, 

Thank you for your reply. Currently, my interest is primary/secondary metabolites in aquatic organisms. Hyunwoo mentioned that he was working towards an updated version that would include metabolites from the HMDB database. I figured that should include many of the metabolites that I am interested in since I currently use the HMDB database for identification. This is of great interest to me!

Best regards,
Amanda

On Wed, Apr 1, 2020 at 3:31 PM <beowu...@gmail.com> wrote:
Thank you for your interest Amanda. Are you talking about human metabolites or primary/secondary metabolites from bacteria/fungus/plants please?

If you are talking about human metabolites, yes, we are currently working towards identifying human disease samples using SMART. If you are referring to primary metabolites of non human species, we are not. But that is an interesting area for us to pursue. I am also glad if you have new ideas that you would like to collaborate with us.

Best,

Chen

On Wednesday, April 1, 2020 at 10:36:01 AM UTC-7, slo...@g.cofc.edu wrote:
Hi, 

I was wondering if SMART NMR can be used for identifying metabolites. It seems the library is primarily natural products. If it could used for simple identification beyond the natural product discovery component, it would greatly benefit the NMR metabolomics community. I would love to hear if there is any effort towards this. Thank you. 

Amanda

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--
Amanda L. Bayless
CofC under contract to NIST
Chemical Sciences Division | NIST

Hollings Marine Laboratory
331 Fort Johnson Rd.
Charleston, SC 29412

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