Life Science Research

Life science research is the study of living organisms, including human beings, animals and plants, covering subjects in biology, biotechnology, bioinformatics, target discovery and the Omics. Chat with your peers about how to get the most out of your proteomics, metabolomics and lipidomics studies.

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Adding the PepCalMix to your SWATH acquisition ion Library as a Retention Time Calibration Protein

How does the scoring and FDR analysis work for SWATH acquisition data processing? For proteomics

Similar extraction processes are used in both the SWATH acquisition microapp in PeakView software on the desktop and the Extractor app in OneOmics suite. After the fragment ions have been selected for each peptide, the extracted ion chromatograms are generated and the...

Adding the PepCalMix to your SWATH acquisition ion Library as a Retention Time Calibration Protein

How are peptides and transitions selected for use in quantification, when importing from a ProteinPilot software group file – using SWATH acquisition microapp or Extractor in OneOmics suite?

Similar selection processes are used in both the SWATH acquisition microapp in PeakView software on the desktop and the Extractor app in OneOmics suite. During the protein grouping process in ProteinPilot software, there is an extensive analysis that is done on the...

Adding the PepCalMix to your SWATH acquisition ion Library as a Retention Time Calibration Protein

What software do I need to process my SWATH acquisition data using the desktop or cloud solutions?

Desktop solution: If you are processing your SWATH acquisition data using the SCIEX pipeline, there are a 3 software packages that work together seamlessly for processing.  First, you would process your IDA data using ProteinPilot software to create an ion library. ...

Adding the PepCalMix to your SWATH acquisition ion Library as a Retention Time Calibration Protein

What is the best way to build spectral ion libraries for use in processing of proteomics SWATH acquisition data?

The information needed for targeted data extraction in our current SWATH acquisition workflow is relatively simple.  You need the parent ion m/z; you need the m/z and relative intensities of the major fragment ions that are produced during MS/MS; and you need to know...

Adding the PepCalMix to your SWATH acquisition ion Library as a Retention Time Calibration Protein

What is variable window SWATH acquisition and why does it improve results quality?

To continue to improve the quality of the SWATH acquisition data that one can achieve in complex matrices, we are working on ways that we can decrease the size of the Q1 window, while still maintaining full mass range coverage and optimal cycle times.  One great way...

Adding the PepCalMix to your SWATH acquisition ion Library as a Retention Time Calibration Protein

What is SWATH acquisition and what are the critical acquisition attributes?

In data-independent acquisition strategies like SWATH acquisition, an expanded mass isolation window is stepped across a mass range covering the mass-to-charge (m/z) distribution of peptides and a full scan MS/MS spectrum is collected at each step. Post-acquisition,...