Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition.

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition. Mol Cell Proteomics. 2019 Dec 30;: Authors: Huang T, Bruderer R, Muntel J, Xuan Y, Vitek O, Reiter L Abstract In bottom-up, label-free discovery proteomics, biological samples are acquired in a data dependent (DDA) or data independent (DIA) manner, with peptide signals recorded in an intact (MS1) and fragmented (MS2) form. While DDA has only the MS1 space for quantification, DIA contains both MS1 and MS2 at high quantitative quality. DIA profiles of complex biological matrices such as tissues or cells can contain quantitative interferences, and the interferences at the MS1 and the MS2 signals are often independent. When comparing biological conditions, the interferences can compromise the detection of differential peptide or protein abundance, and lead to false positive or false negative conclusions.We hypothesized that the combined use of MS1 and MS2 quantitative signals for detecting differential abundance could improve our ability to detect differentially abundant proteins. Therefore, we developed a statistical procedure incorporating both MS1 and MS2 quantitative information of DIA. We benchmarked the performance of the MS1-MS2-combined method to the individual use of MS1 or MS2 in DIA using four previously published controlled mixtures, as well as in two previously unpublished controlled mixtures. In the...
Source: Molecular and Cellular Proteomics : MCP - Category: Molecular Biology Authors: Tags: Mol Cell Proteomics Source Type: research