Question: how to find up regulated proteins from a label free
gravatar for Nemo
2.3 years ago by
Nemo80 wrote:


I have 4 samples two control (one biological replicate) and two treated(one biological replicate). I have obtained the intensities for them called LFQ.

Do you think deseq2 is a good way to obtained up regulated proteins ? or should I do it as old school method based on Tueky test etc? 

I appreciate any comment 


ADD COMMENTlink modified 2.3 years ago by Laurent Gatto1.0k • written 2.3 years ago by Nemo80
gravatar for Laurent Gatto
2.3 years ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

No, DESeq2 is not appropriate in this case. I would suggest to use limma.

ADD COMMENTlink written 2.3 years ago by Laurent Gatto1.0k

@Laurent Gatto thanks for your message. Is it possible to let me know why? what about other types of proteomics data like SILAC, TMT etc, I guess for them also we cannot use DESeq2, no? is there any paper that used limma for LFQ ? 

one technical question, would you remove those genes that have zero for all samples ? i read or do you keep them? (i personally think they have no value) what about the proteins that are identified but their genes are not ? do you remove those proteins too? to be honest it does not harm to keep them , however, I just ask to get different opinion. 

Once again thanks 



ADD REPLYlink written 2.3 years ago by Nemo80
  • DESeq2 is only relevant for count data, while LFQ produces continuous data. Same for TMT, SILAC (these are ratios), ... all but spectral counting.
  • There is nothing to do with features that have a constant (zero or otherwise) value throughout your samples.
ADD REPLYlink written 2.3 years ago by Laurent Gatto1.0k

@Laurent Gatto Thank you so much for your valuable comment. You are right. so I removed those proteins which did not have gene names and also those proteins which their LFQ intensities were zero for all samples control and treated. however, seems like limma does not really get me somewhere too look at this question I get nothing in my up and down regulated genes

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Nemo80
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