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Visualisation and Comparison of SYNAPT G2-S LC/MS Data with Progenesis LC/MS
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Waters Corporation

In this technology brief, we present the precise large-scale, label-free analysis of high-density proteomic LC/MS data combined with a qualitative protein strategy that accurately identifies proteins and software that accurately quantifies proteins – both with high reproducibility. The depth to which a complex sample can be interrogated with minimal technical variation is crucial as this characterizes the lowest abundance limit of proteins that can be quantified. This is of equal importance for the software that analyzes LC/MS data since it ultimately defines protein and peptide false quantification rates. ProteinLynx GlobalSERVER™ and Progenesis LC/MS have been integrated, enabling highly accurate, label-free, relative protein quantification.

Large scale LC/MS-based discovery experiments that investigate increasingly complex proteomic samples are conducted to assess variation (either experimental or biological), profile samples, or to quantitatively gauge differences in protein abundance. These factors place a demand on the performance of the analytical LC/MS system, as well as on the bioinformatics software required to analyze the data. Robust peak detection, normalization, and alignment of multiple LC/ MS runs in larger scale studies are required as this will determine the lowest possible amount of proteins that can be resolved. Results from the SYNAPT® G2-S MS for differentially spiked protein standards in a complex cell lysate of Escherichia coli were used to demonstrate the application of Progenesis LC/MS.

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