Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery

The current state of proteomics requires a choice between targeted and global discovery methods. A method, that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins, in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run, using a panel of spike-in standards (SIS), is established and optimized. The absolute quantification (AQ) of SWATH and multiple-reaction monitoring-high resolution (MRM-HR) acquisition methods are compared using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma. SWATH provides equivalent quantification and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data are used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provide similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof-of-concept, the eAQ method is applied to 12 plasma samples from six non-small cell lung cancer (NSCLC) patients and the performance of eAQ values versus peak area quantification is evaluated. There is a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. This eAQ method can provide quantitative data equivalent to AQ or peak area values.