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tvpham / iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
BSD 3-Clause "New" or "Revised" License
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Protein quant for SILAC data #11

Open Benjamin-Raymond opened 1 year ago

Benjamin-Raymond commented 1 year ago

Hi Thang,

I have some SILAC data that I have searched using DIA-NN and was recommended to process using the iq package. I was told that in order to have protein quantities from this dataset, I would need to calculate them based on the Precursor.Translated tab from the report.tsv using MaxLFQ in iq. Based on the description under "Processing a DIA-NN output", I can't seem to figure out how to do this. I can extract the column, but I don't believe it is being used in the calculation. Would you be able to help with this at all?

Thanks in advance!

Ben

tvpham commented 1 year ago

Hi Ben,

I can look into SILAC data. But it might take quite some time.

Perhaps it is better to look at the R code (https://cran.r-project.org/web/packages/iq/vignettes/iq-fast.html) and the published paper, and process your data accordingly. The code in "Processing a DIA-NN output" is a one-line command to make it easier for end-users with label-free data.

Thang

HYTang69 commented 5 months ago

I wonder if anyone has any update on how to use iq to process SILAC data searched with DIA-NN. Thanks.

Benjamin-Raymond commented 4 months ago

Hi there, I have a bit of a long-winded bit of code in R that seems to work nicely for analysing SILAC data. I am happy to share this with you, if you'd like?

HYTang69 commented 4 months ago

Yes! That would be great! Can you email it to me at hy_tang@hotmail.com? Greatly appreciate this.