GEN-MKT-18-7897-A
Mar 18, 2016 | Blogs, Life Science Research | 0 comments
If you have a TripleTOF® System and you’re using SWATH Acquisition for your quantitative proteomics experiments, you’ve made the right choice. SWATH is a data independent workflow that enables data to be acquired for every detectable analyte in a complex sample. You create a digital map of the sample that can be mined for new information any time new biological insights are hypothesized. It’s all there!
Since the introduction of the workflow at HUPO 2010 in Sydney, Australia, we have been working to further improve the workflow. Optimizations in data acquisition such as smaller and variable Q1 window widths and increased instrument dynamic range have provided increased depth of coverage for your proteomics sample, without compromising reproducibility or data quality.
But what about data processing? Can we improve even further?
The answer is yes! Typically an ion library is used for targeted processing of SWATH data for peptide and protein identification and quantitation. The ion library contains the masses of the peptide ions, sequence-specific fragment ions, relative fragment intensities, and relative retention times, and is easily generated by performing a simple data-dependent acquisition and database search.
In this study, scientists from SCIEX demonstrate that for biological systems that will be studied repeatedly, it is worth taking the extra time to create a deeper ion library as much more information can be extracted from the SWATH acquisition data.
For example, SWATH replicates of a HEK human cell lysate were acquired and processed using three different libraries:
Figure 1. The Impact of Deeper Ion Libraries on Extraction of Quantitative Data from Human Cell Lysate SWATH® Acquisition Data.
As shown in Figure 1, a 118% gain in quantified proteins was observed using a simple ion library (1D HEK) and an extensive ion library (PHL). And the quality and reproducibility of the quantitation are maintained even into the low abundant protein/peptide regime.
A researcher can balance the library generation time with the depth of coverage needed. The three libraries outlined here took increasingly more time to generate. A simple IDA experiment can take only a matter of hours. A 2D fractionation followed by LC-MS/MS on each fraction can be performed in a matter of days. And some groups have invested significantly more time in library generation using multiple cell types and a large degree of fractionation to cover as much of the proteome as possible.
This work also highlights the superior dynamic range of quantitative information that is present in a SWATH Acquisition data file over the traditional data dependent approaches for quantitative proteomics. To read more details of this work, and to see what size
To read more details of this work, and to see what size ion library would make the most sense for your biological system of study, download the full technical note.
It is no secret that (bio)pharmaceutical research and development is complex, both scientific and regulatory processes. Here is an overview of just some of the ways SCIEX is working to support these challenges.
In a recent webinar, available on demand, scientists Luiza Chrojan and Ryan Hylands from Pharmaron, provided insights into the deployment of capillary gel electrophoresis (CGE) within cell and gene therapy. Luiza and Ryan shared purity data on plasmids used for adeno-associated virus (AAV) manufacturing and data on AAV genome integrity, viral protein (VP) purity and VP ratios using the BioPhase 8800 system.
Last year, Technology Networks hosted two webinars that featured groundbreaking research utilizing SWATH DIA (data-independent acquisition) for exposomics and metabolomics. Researchers Dr. Vinicius Verri Hernandes from the University of Vienna and Dr. Cristina Balcells from Imperial College London (ICL) demonstrated how a DIA approach can be successfully implemented in small molecule analysis using the ZenoTOF 7600 system. Their innovative approaches highlight the potential of SWATH DIA to enhance the detection and analysis of chemical exposures and metabolites, paving the way for new insights into environmental health and disease mechanisms.
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