The Skyline team has developed a nice pipeline for evaluation of LC-MS/MS performance over time for MS systems in the research lab environment. To help you use this solution, we have set up two Skyline Documents that you can use for continuous system monitoring....
When you think about calibration of a mass spectrometer, there are actually two aspects to consider. There is the accuracy of the calibration (that it is correct when calibration is performed) and the stability or precision of the mass calibration (that it remains...
When using the Auto-Calibration option in Extractor, a set of retention time calibration peptides will be determined automatically from the library and used for RT calibration. To determine how the fit looks for the calibration on each datafile, follow these steps....
CloudConnect in PeakView software 2.2 enables both the upload of data files to the OneOmics suite as well as the download of SWATH acquisition results files for viewing. This post will describe how to download and visualize the results from Extractor processing, so...
Here, we provide a quick reference for the source/gas settings to use at various flow rates with Turbo V, IonDrive Turbo V and OptiFlow Pro ion sources that come with the various SCIEX mass spectrometers. While performing a full source/gas optimization can provide the...
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...
The most important consideration in adding a new RT calibration protein to your library is making sure you are getting the retention time for both into the same retention time or chromatographic frame. Below is a list of steps that walks you through how to do this....
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...
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...
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. ...
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...
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...