Multi-Omics analysis of human embryonic stem cell neural differentiation

Processing SWATH® Acquisition Data in the cloud with the OneOmics™ Suite

Hunter CL1; Williams KE2,3; Chen H2; Robinson JF2
SCIEX, USA; 2Department of Obstetrics, Gynecology & Reproductive Sciences, UCSF, USA; 3Sandler Moore Mass Spectrometry Core Facility, UCSF, USA


Small project to evaluate RNA and protein level changes (SWATH acquisition), between human embryonic stem cells and the differentiated neural progenitor cells. The cloud based OneOmics™ Project was used for multi-omics analysis.



A quantitative proteomics study was performed and analyzed using the OneOmics Suite of applications. Undifferentiated human embryonic stem cells (hESCs) were compared to their neuronal derivatives, i.e., neuronal progenitor cells (NPCs), to examine common and unique differences at the transcriptional and protein level. hESCs were differentiated into NPCs using a previously developed method1,2, which involves cells growing in suspension and the addition of neural promoting factors. RNA and protein fractions from both cell populations were collected and analyzed. 

Quantitative proteomics was performed using SWATH Acquisition and data were processed using the suite of tools in the OneOmics Suite in the SCIEX Cloud Platfom. Transcriptomic data was analyzed using standard procedures, then both the protein and RNA data was loaded into iPathwayGuide (Adviata) for comparison. For the proteins/genes identified to significantly different between NPCs and hESCs, good correlation in differential expression was observed, especially for the molecules involved in neuronal development-related biological processes (Figure 1). 

Figure 1. Comparing Protein and RNA Expression Changes between hESCs and NPCs. After alignment of the proteins and genes, proteins with significant differential expression were plotted vs the observed RNA expression differences. Green diamonds show the protein set (144) where differential RNA expression was also observed (blue fill indicates proteins (37) involved in a neuronal biological process). Good correlation was observed in terms of the magnitude and direction of differential expression. Orange triangles represent the differentially expressed proteins (197) with no significant RNA expression difference, highlighting the importance of studying both protein and RNA expression.

Key advances of the OneOmics Suite

  • Comprehensive SWATH Acquisition datasets can be generated on proteomics samples for protein expression
  • Improved depth of coverage obtained using Variable Q1 Window Acquisition3
  • Large datasets can be processed quickly in the cloud using the SWATH Acquisition Proteomics Toolkit in SCIEX Cloud
  • Powerful visuals for assessing MS data quality and understanding protein expression differences are automatically generated
  • Ability to compare across or between proteomic and transcriptomic datasets, to identify common and uniquely differentially expressed proteins/RNAs
  • Drill into the biology with powerful tools such as iPathwayGuide (Advaita)