Improvements in LFQ for reproducible quantification of proteomic experiments: how DDA outperforms DIA

[Orbitrap_SciLib]

Ignacio Ortea1, Romain Huguet2, David Horn2, Andreas FR Huhmer2, and Daniel Lopez-Ferrer2

While Data Independent Acquisition (DIA) has been receiving a lot of attention lately within the proteomics community, Data Dependent Acquisition (DDA) remains the gold standard for label-free quantitation (LFQ) proteomics. DIA analyses can test whether or not a specific peptide is in a sample above a certain threshold; however, DDA methods outperform DIA when it comes to the number of peptide identifications and quantitative inter-experimental reproducibility, especially in conjugation with advanced label free quantitation software. In this work we compare HRAM quadrupole-Orbitrap™ DDA, AND HRAM quadrupole-Orbitrap DIA methods head-to-head to evaluate the sensitivity and number of peptides identified and quantified ,and demonstrate that HRAM quadrupole-Orbitrap DDA technology outperforms DIA analyses significantly in proteome coverage and quantitative reproducibility.


1 IMIBIC, Cordoba, Spain 2 Thermo Fisher Scientific, San Jose, USA