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IPA for pathway analysis

Actually I am doing proteomics. I obtained identified proteins (with their corresponding genes) in a set of experiment based on LC-MS/MS.

Now my question is that if I want to perform pathway analysis, should I use the proteins ID or gene ID using IPA? one problem with both is that I have 1000 proteins identified. each protein has a group (isoforms) should I use all IDs or something else. it is the same for genes as well. sometimes more than two genes are assigned to proteins and their isoform

My last question is that what should i do with those proteins that not any gene is assigned to it?

Thanks

ipa proteomics gene
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written by Learner Learner

IPA is flexible about ID's so you could use either. It will show you how many it is able to map/identify once you import your data in. Since IPA depends on ID's it can map/identify there is not much you can do about those it is unable to find.

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written by GenoMax GenoMax

@genomax2 it is right, but what about the isoforms? should I import all? or better I play with gene names ? do you know maxquant? if I analysis SILAC with maxquant, it mixed up the control and treat ones , do you think an average of intensity is a good choice for it?

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written by Learner Learner

I don't use IPA regularly but I don't recall it being able to analyze data at isoform level. Again you should be able to check on this. I am not familiar with maxquant so someone else will need to help with that one.

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written by GenoMax GenoMax

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