u/bluemooninvestor

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As title. I am in a situation where I have to choose one of these two for procurement without option of trail runs. Hence I need expert opinion.

What would be better got global untargeted metabolomics (Ultimate 3000 + Exploris 120 setup)?

I am a metabolomics noob. Please guide me. Both are 100 Angstrom.

I would be using it to do C13 tracer based work on mmmalian cells (after I gain expertise in basics, of course)

I also have option for ZIC-pHILIC (5 micron) 100mm x 4.6 mm

So my options are

ZIC-pHILIC (5 micron) 100mm x 4.6 mm

ZIC-pHILIC (5 micron) 50mm x 2.1 mm

ZIC-HILIC (3.5 micron) 100mm x 2.1 mm

As title. I am in a situation where I have to choose one of these two for procurement without option of trail runs. Hence I need expert opinion.

What would be better got global untargeted metabolomics (Ultimate 3000 + Exploris 120 setup)?

I am a metabolomics noob. Please guide me. Both are 100 Angstrom.

I would be using it to do C13 tracer based work on mmmalian cells (after I gain expertise in basics, of course)

I also have option for ZIC-pHILIC (5 micron) 100mm x 4.6 mm

So my options are

ZIC-pHILIC (5 micron) 100mm x 4.6 mm

ZIC-pHILIC (5 micron) 50mm x 2.1 mm

ZIC-HILIC (3.5 micron) 100mm x 2.1 mm

Basically I am treating my cells with a drug, which I expect to crosslink certain target proteins. However, it's not a very stable drug so it's side chains and all might degrade, leading to difference in expected and actual mass in the crosslink. Basically even if I expect the crosslinker to be 300 Da, it might even be 260Da, so I am in the dark.

Is there any way to do open-search (Fragpipe like) for crosslinked peptides. I can constrain it with the knowledge that crosslinks will happen between cysteine residues.

Thanks

Hi everyone,

I am doing C13 Glucose based Metabolomics in mammalian cell line samples. I am doing the extraction and all and sending samples for acquisition. I have option to outsource samples to two vendors:

Vendor A has BEH Amide column but charges twice as Vendor B who has BEH HILIC column. Rest equipment is similar.

I know BEH amide is better but is it worth spending twice for BEH amide column over BEH HILIC? How much is the quality difference?

Want to use the data for flux analysis. Untargeted data acquisition.

Hello everyone,

I have been using Pierce Desalting Spin columns for peptide cleanup, and it required 300 uL of 50% ACN to elute.

Now, I have to use the Pierce C18 columns. Despite both of them being small spin columns, the C18 column protocol says that only 20 uL of 70% ACN should be used for elution.

My question is, isn't 20 uL a very small volume? Why is there such a huge difference in elution volume between the two spin columns (Desalting v C18 one)? Lastly, is there any general understanding in the proteomics community to use a larger elution volume with the Pierce C18 spin columns.

The protocol also says one may use 70% ACN with 0.1% TFA, but no idea why that is not the standard elution solution for this setup.

I understand that most hardcore proteomics labs would probably not be using Pierce C18 spin columns, but this is what I am using as a part-time proteomics guy. I don't have any other C18 setup, and I will send the cleaned-samples to a mass-spec facility.

And advice on the Pierce C18 spin columns is greatly appreciated.

Recently I have run into Lip-ms, and there are quite a few high impact papers describing the technique. But there are really few papers who have actually used it for doing science.

I think it is the same for several other techniques like proximity-labelling MS, certain advanced variants of thermal proteome profiling etc.

Why do you think it is like this? If these techniques are so great, why aren't they being used for actual science on a much greater scale? Or is my assumption wrong?

Excited to listen to your views.

For perspective, I am a cancer biologist trying to do omics.

I have submitted a paper to JPR for the first time. It has been three weeks and the status is still "Editorial Review".

Does the manuscript status change to Peer Review or something like that when it's under actual review? Or does it mean it's still with the editor only?