Use of the Nanomics Proteonano™ platform for deep proteomic analysis of mouse blood samples
To develop a high throughput and reliable workflow that incorporates Proteonano™ Ultraplex Proteomics Platform based sample processing and high resolution mass spectrometry technology to enable deep proteomic analysis of mouse blood samples.
Proteonano™ Ultraplex Proteomics Platform
Number of Protein Identifications and Dynamic Range in Mouse Blood Samples
Using this sample processing, data acquisition, and data analysis pipeline identified 3791 protein groups from mouse serum samples, 5406 protein groups from mouse plasma samples, and 6585 protein groups from mouse whole blood samples. Sample processing by the Proteonano™ Mouse Plasma Proteome Enrich Kit provided about two-fold increase in protein groups detected for each of the sample type relative to samples processed without using the kit, thus significantly increasing proteomic detection depth.
When mouse proteins identified in the study were mapped to the reported plasma concentrations of their protein counterpart in human plasma protein project (HPPP), their concentration span nine orders of magnitude, indicating efficient detection of low abundance proteins.
Comparison of Protein Group Identified in Mouse Blood Samples Between Proteonano™ and Olink Target
While higher multiplexity Olinks panels are marketed, they are less commonly used than Olink’ s 48 and 96 panel kits. When the 6931 protein groups identified in mouse blood samples were compared with Olink Mouse Target 48&96 panels, it was found that the mouse plasma samples processed by all three platforms could detect Q08048 (Hepatocyte growth factor) and P18340 (C-X-C motif chemokine 9). Proteonano™ and Olink_Mouse_48 shared detection of 5 proteins, while Proteonano™ and Olink_Mouse_96 shared detection of 29 proteins (Table 2).
By supplementing the protein information missed by the Olink Target Mouse Panel, researchers can enhance their systematic understanding of the protein composition in mouse blood, which facilitates the revelation of potential biological mechanisms and the discovery of new biomarkers ( Figure 4)
