Technical repilcates in MSstats

[Amandeep Bhamra]

Dear MSstats team,

 Could someone help me in trying to assign a sample as a technical replicate in a typical LFQ experiment? I have 5 conditions in my experiment each having 3 biological replicates, but for one condition (UTR), I have 2 technical replicates that have come from one biological replicate. I checked in the manual that if I write two samples the annotation.txt file with the same BioReplicate name, MSstats automatically treats them as technical replicates. However, this hasn't been the case. In the dataprocess() command, MSstats tells me that I have 4 MS runs for that particular condition (UTR), 3 biological replicates but only 1 technical replicate. I essentially, want MSstats to register that I have 3 biological replicates for UTR but also 2 technical replicates. Can this be done? I have attached a picture of my annotation.txt file. Could some explain what I am doing wrong, please?

Best wishes,

Amandeep

[thuan...@gmail.com]

Hi Amandeep,

MSstats indeed identified these two technical replicates for biological sample UTR1. When MSstats shows the summary of samples, it calculates the mean technical replicates per condition (total number of MS runs/ total number of biological replicates). In your case, it is 4/3 =1.333 and becomes 1 after rounding  1.333. So this is just how MSstats summarises the annotation information.