I am working on evaluating cancerous niches using secretome media and will further with 2D-gel. Do we have any others methods to evaluate secretome other than 2D-gel or LCMS?
Beside, is there any best suggestion to study cancer niche?
There are commercial cytokine detection assays to detect several cytokines in your extracellular media. But most of them target known ones and limited number of cytokines. If you are dealing with more global than that including novel cytokines, I don't know better or cheaper methods other than 2D and LC-MS/MS methods.
LC MS technique no doubt help you to separate the peptide components in your secretome in terms of mass accuracy, resolution and speed. Methods which couple LC directly to the mass spectrometer are rapidly replacing gel-based methods because they provide a drastic speed advantage... So, this method would be great for your secretome analysis....But, it would be more sensible if you can perform your analysis with good quantification of your proteins among your different samples...so for it you can label your different secretome samples with different isotopes and then do Mass spectrometry, this will give you quantification data for your identified proteins that are present in your secretome...simply known as ITRAQ technique.
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