Hardware

Learn more about the technology in your SCIEX systems, get in-depth answers about what goes on inside the technology from the experts.

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MRM method transfer from a SCIEX Triple Quad or QTRAP 6500+ system to the SCIEX 7500 system

MRM method transfer from a SCIEX Triple Quad or QTRAP 6500+ system to the SCIEX 7500 system

General recommendations when beginning method development Objective: The purpose of this document is to provide a quick reference for transferring MRM-based quantification methods from a SCIEX Triple Quad or QTRAP 6500+ system to a SCIEX 7500 system. While the best...

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,...

Adapting a SCIEX high flow source for microflow LC

Troubleshooting low flow LC – Loss of early eluting peptides during trap-elute workflow

Symptom: Early eluting peptides are missing (based on monitoring PepCalMix LC-MS test or observing a change in the shape of the proteome TIC). Test: Use PepCalMix LC-MS test to monitor binding of early eluting peptides. There are a number of very hydrophilic peptides...

CloudTalk – Analytics for proteomics

CloudTalk – Multi-omics – comparing proteomics data with genomics data with OneOmics suite

Now that you have watched the other cloud talks and learned how to use the various different applications for data processing and results review, we show you in this cloud talk how to put it all together and process a multi-omics data set! This CloudTalk (19:14mins)...