In Protein quantification by (MaxLFQ) with minimum ratio count of two unique peptides was setup,is the criteria of quantification depends on the presence of these 2 unique peptides in Protein A in sample 1 and 2?is it sum of area under the curve intensities of the two unique peptides?what about if we have Protein A in sample 1 and 2 but in different unique peptides of the same protein in both samples?,is the criteria of quantification depends on the presence of these 2 unique peptides in Protein A in sample 1 and 2?is it sum of area under the curve intensities of the two unique peptides?what about if we have Protein A in sample 1 and 2 but in different unique peptides of the same protein in both samples?
Hi Eric,
If you are viewing the ProteinGroups.txt file, with two unique peptide count as minimum requirement for Protein A and B, the intensities will be intensities of peptides identified in each case, for Protein A and for Protein B. They are not necessarily the same peptides.
Best,
Hediye.
Hi Eric,
I guess, you already know that this is Label Free quantitation, meaning that is based on intensities (peak intensities). As Heyide mention, the minimum criteria for doing Protein quantitation is 2 peptides, and usually these are the same peptides in both samples. At the protein level the quantitation is done using the sum of intensities from the identified peptides.
I hope that this is clear, all the best in your research
Martin
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