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Uploading data for use in OneOmics suite

There are two options for data storage when working with the OneOmics suite. You can store your data either within the SCIEX Cloud platform in the Data Store, or you can store data in BaseSpace (Illumina) and link your BaseSpace account with the SCIEX Cloud platform. CloudConnect for PeakView software 2.2 is used to upload […]

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December 14, 2021

Visualizing SWATH acquisition results in CloudConnect

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 that you can view your raw XIC data for the quantified proteins […]

December 13, 2021

Getting access to demo data and other files for learning the OneOmics suite

In order to help you get proficient in using the OneOmics suite workflows, we have provided some demo datasets along with numerous other valuable files and supporting information to help you get started. Once you get access to your SCIEX Cloud account and can view your SCIEX Data Store, you will notice that there is […]

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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 sets of XICs generated make up the peptide groups that are scored for […]

September 28, 2021

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 proteins and peptides that are identified. These results are annotated according to what […]

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.  Ion libraries only need to be created once, and are loaded into the SWATH […]

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, high resolution ion chromatograms are extracted for specific fragment ions of the peptides of interest, and these are […]

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How to download and use SVG files from OneOmics suite

Results workspaces in the OneOmics suite contain a variety of figures, all available for download as SVG (scalable vector graphic) files. To download your figures, select the orange arrow icon located in the upper right-hand corner of each plot. Download will immediately begin on your computer and an SVG file will be available for use. […]

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September 24, 2021

How to share your results with collaborators

As multi-omics research is often highly collaborative, tools for rapidly sharing important results files are needed to drive scientific progress. The SCIEX Data Store in the OneOmics suite enables you to not only organize your uploaded multi-omics data files into studies for further processing, but also to share your studies easily and securely with your […]

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CloudTalk – Analytics for proteomics

This CloudTalk video (6:34min) describes the use of the Analytics app in OneOmics suite for evaluating the quality of your SWATH acquisition data.   RUO-MKT-18-6582-A

September 20, 2021

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