on 09-26-201607:20 AM - edited on 11-09-202101:21 AM by usermigration2
Daniel Lopez-Ferrer International Hupo 2016 Systems biology represents a shift in the way biology has been studied in the last century. The ability to identify and quantitate biomolecular components to a high degree of detail on a genomic scale allows us to understand and elucidate global regulatory networks in biological systems. In this work, we first put Orbitrap DDA, Orbitrap DIA, and QTOF DIA technologies head-to-head to evaluate the sensitivity and number of peptides identified and quantified and demonstrate that Orbitrap DDA technology outperforms DIA analyses significantly. DDA acquisition used in conjunction with the label-free quantitation node in PD 2.2 allows for the quantification of 95% of the identified peptides in the study using the MS1 scan to integrate the peptide signals. In addition, over 90% of the quantified peptides have CVs below 15%. Later on, we used label free proteomics in addition to whole genome DNA sequence, whole transcriptome (RNA-seq), the genomic binding locations of 50 transcription factors and 4 histone modification types (ChIP-seq) to define the individual biological components for 5 well-characterized haploid Saccharomyces cerevisiae yeast strains originally isolated from different environments: 2 wine strains, 2 laboratory strains and 1 clinical isolate. Integration of these datasets represents a start to the eventual goal of understanding how an entire biological system operates, and how such systems vary between genetically differing individuals within a species.