How to quantification proteomics data

Question

[LeeLee]

I am new to the proteomics data，I find it difficult to understand the method of protein group quantification. I use maxquant to quantify TMT11 mass spectrometry data. In the proteinGroups file, I found that there are many proteins in the same line. Like below:

Protein IDs sp|Q96PC5|MIA2_HUMAN;sp|Q96RT6|CTGE2_HUMAN;sp|Q8IX95|CTGE3_HUMAN;sp|Q8IX94|CTGE4_HUMAN;sp|Q86UF2|CTGE6_HUMAN;sp|P0CG41|CTGE8_HUMAN;sp|A4FU28|CTGE9_HUMAN;sp|A4D2H0|CTGEF_HUMAN

Majority protein IDs sp|Q96PC5|MIA2_HUMAN;sp|Q96RT6|CTGE2_HUMAN

In RNA-seq, we will discard duplicate mappings. reads, how do we deal with these peptides matched to protein groups in mass spectrometry?,