Data independent acquisition has seen increased adoption over the last few years because of its many important attributes. It combines the quality of quantitation of targeted proteomics with the high degree of multiplexing of discovery proteomics to provide a powerful tool for quantitative proteomics. Today we'll introduce the new TripleTOF ® 6600 system with SWATH TM 2.0 acquisition. The power of this combined solution will have a big impact on quantitative biology and usher in the next wave

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... proteomics. Quantitative MS-based approaches are emerging as a core technology in the biomedical and clinical fields for addressing health-related queries in systems biology. In several 'omics disciplines (proteomics included), MRM/MS with stable isotope-labeled standards (SIS) is the preferred technique for quantifying and screening putative analytes (proteins in this context) in biological samples. For its application in protein biomarker verification/validation studies and its ultimate acceptance in the clinic, the technique must be standardized to facilitate precise and accurate quantitation, within and between laboratories. To that end, we have developed a series of kits for assessing method/platform performance as well as for screening candidate protein biomarkers in undepleted and non-enriched human plasma samples. The kits collectively utilize a MRM with SIS peptide approach and require regression analysis of standard curves to obtain assay metrics and endogenous concentrations of the proteins in the QC and biomarker assessment kits. This presentation will highlight the development, implementation, and application of these kits (using the Agilent 1290 Infinity UPLC and 6490 triple quadrupole LC/MS systems), along with the use of our recently developed software tool -Qualis-SIS -to help expedite curve generation and results interpretation in quantitative proteomic studies. http://dx. In shotgun proteomics it is desirable to identify and quantify a large number of individual peptides from complex samples, such as tryptic digests of human plasma samples or whole cell lysates in the shortest possible time. Complexity and concentration range, however, pose a great challenge to the MS instrumentation in terms of sensitivity, resolution and dynamic range. Several hardware modifications of a bench-top UHR-QTOF instrument were carried out addressing these particular performance aspects. For higher sensitivity at fast acquisition speed, ion extraction from the collision cell into the orthogonal acceleration of the TOF-analyzer was improved by using a novel collision cell design. Increased resolution without changing the effective flight path could be achieved with a modified reflectron. In addition, a faster detector (reduced width of individual ion signals) led to further improvements in resolving power. 2212-9685/$ -see front matter