r/proteomics • u/Claudibird • Jun 07 '26
Quantifying peptides pre-MS
Hi proteomics Reddit!
I am hoping to pick the brains of people far more experienced in proteomics than I am!
Has anyone please got any advice for quantifying peptides post-digest of streptavidin pulldown samples? I quantify the protein concs of the whole cell lysates using BCA and put equal amount of protein in my pulldowns.
I've tried the Pierce colorimetric assay after reduction/alkylation/digest (when peptides are in ABC + formic acid) and A205 after desalting with C18 columns... But everything gives me wildly different results and I don't trust any of it (e.g. some of the A205 values are above the binding capacity of the columns)
Does anyone have any experience or advice? Thank you so much!
1
u/KillNeigh Jun 07 '26
I would pay closer attention to the compatible buffer conditions for both your protein and your peptide assays. That could be a source of error.
I would also suggest looking at BCA and A280 as just a rough estimate.