What Are the New Visualization Features in the OneOmics Suite for DIA-NN Software Output Files?

For research use only. Not for use in diagnostic procedures.

Answer

The DIA Results app, new software feature in the cloud-based OneOmics™ suite for processing DIA-NN software output, helps visualize proteomics data and interpret the protein characterization results in the Analytics and Browser sections. DIA-NN is a widely used proteomics processing platform whose output is a simple text file in TSV file format that contains a list of all of proteins, peptides, transitions numbers and their extracted quantitative values and measurements.

The OneOmics suite has the ability to process these complex DIA-NN data sets in a meaningful way by converting the TSV data in the DIA Results app found in the OneOmics suite (https://community.sciex.com/2022/09/22/new-features-in-oneomics-suite/). The DIA Results app then interprets and visualizes the protein quantification results.

Here are the important steps for data processing TSV data in the DIA Results app in the OneOmics suite:

1. Upload the DIA-NN output file (TSV file) from your desktop.
2. Launch the DIA Results app. 
3. Process and transfer the data set.
4. Assign the metadata.
5. Launch the Assembler.
6. Visualize the data in the Analytics and Browser sections of the OneOmics suite.

After conversion, TSV data visualized in the Analytics and Browser section of the OneOmics suite (see below) can be used to answer biological questions.


Similar to the previous version of OneOmics, each tile in the Analytics section can be selected to obtain more information, as shown below for area variance metrics:



Each graph can be download by selecting the purple arrow.

Here are some examples of how the data is visualized in the the Browser section of the DIA Results app:


Users have access to sample grouping, normalization, and ontology information; protein fold changes are shown in the bottom section and are represented in a volcano plot. Selecting the question mark symbol in the upper right hand corner of each tile describes each feature in more detail.

Selecting the protein fold changes tile will list each fold change for a protein response in table format (see below). Here, a blue cell represents down-regulation of protein expression; an orange cell represents an up-regulated response. The steps used to process data in the DIA Results app support both spectral library-based and library-free data.