Protein Identification and Quantification

Mass spectrometers have many different modes of data acquisition. The two most important for proteomics are Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA). 

Data Dependent Acquisition is used to sequence and identify individual peptides and with them proteins. Its advantage is that the sequence data is the most reliable. Its disadvantage lies in the relative lack of reproducibility on the peptide level.

Data Independent Acquisition is used to reliably quantify peptides which are known to be in the sample. Its advantage is its high reproducibility on the peptide level. Its disadvantage is a smaller sensitivity in peptide detection on trapping instruments compared with DDA and, when used to retrieve novel sequences, its comparably smaller reliability of the retrieved sequences. 

There are two different programmes used to identify and quantify proteins based on its mode - for DDA data: MaxQuant and for DIA data: DIA-NN.