Antibody limitations. Detection by antibodies relies on binding to specific regions (epitopes) of the target protein. PTMs such as glycosylation or fragmentation may hinder epitope accessibility. Antibody A recognises non-glycosylated regions and always yields detection independently of sugar removal (left panel). Antibody B recognises epitopes in the vicinity of glycosylated regions. Therefore, recognition is only achieved after deglycosylation. Similarly, if protein fragmentation occurs, only antibody C, which recognises an intact portion, reveals a degradation pattern. Antibody D targets a region affected by fragmentation and can only detect the intact epitope. Consequently, information about degradation is missed. Proteomics interrogates peptides across the whole sequence and allows for consideration of variable modifications at the amino acid level. Different protein forms can therefore be identified and quantified. GAG, glycosaminoglycan; Pan-DG, pan-deglycosylation.