Hi,

I used MaxQuant to perform label-free protein quantification, and enabled the 'match-between-runs' feature. When I ran the output txt files in Proteomics QC (PTXQC) software I can see that MaxQuant did not align the retention times between samples but IDs were being transferred between samples. How can I get MaxQuant to correct the retention times before transferring IDs?

Any help is much appreciated :)

Thanks,

Shannon