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Unlocking Big Tissue Biobanks: Analyzing the Proteome Using SWATH® Acquisition and Spectronaut Analysis


Dear  Subscriber,


The preservation of tissue biopsies is a critical step to enable a variety of biochemical analysis, leading to a better understanding of the molecular features responsible for a given disease state. Simple fixation using formalin and subsequent embedding in paraffin (FFPE) allowed researchers to build up large libraries and biobanks for more than a century. These samples are very often well described by classical pathological methods and hold great potential to gain deeper insights into the underlying mechanisms of disease. The key to this great resource combines a reproducible sample preparation, robust LC-MS platform, and high analytical depth in combination with high throughput of the whole workflow, including data analysis.


In our joint App Note with SCIEX, we demonstrate how the SWATH® Acquisition on a TripleTOF® 6600 system, using micro-flow chromatography, facilitated a quantitative protein profiling of 105 colon cancer samples. The whole dataset was analyzed in only 5 days with a high analytical depth of ~4,500 proteins. Spectronaut provided fast data processing for protein quantification, and advanced results processing including various statistical and gene ontology analyses. Based on the proteome profiles, we were able to identify three different cancer subtypes. One of them was characterized by a high expression level of HNF4α, potentially caused by an amplification of the HNF4α gene.


To learn more about how high throughput proteomics can be utilized to pave the way to a better understanding of health and disease, please follow this link:

Should you be present at the SCIEX LC-MS/MS Symposium tomorrow, please make sure to stop by Biognosys’ table. Our experts will be happy to explain to you how Spectronaut could support your high-throughput research with great analytical depth. To request a free 30-day trial, please click the button below:


- The Biognosys Team


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