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PTI Hosts Single-Cell Proteomics Workshop

On May 30 2024, PTI hosted its second annual single-cell proteomics workshop. The workshop gave participants hands-on experience with single-cell sorting, sample preparation, liquid chromatography, mass spectrometry, and proteomics data analysis. PTI hosted 29 researchers from 26 institutions representing 6 countries for the workshop.
Mahlon Collins, PhD
Mahlon Collins, PhDPTI NewsJun 26, 2024
PTI Hosts Single-Cell Proteomics Workshop

The workshop began with an introduction to the nano-ProteOmic Sample Preparation (nPOP) method. nPOP is an automated procedure for isolating single cells and preparing them for mass spectrometry analysis. Sample preparation by nPOP is fully automated, enabling high-throughput analysis of many cells / samples in parallel with high reproducibility. nPOP is implemented on the Scienion cellenONE instrument and workshop participants learned how to operate and troubleshoot sample prep on the cellenONE. Special thanks to Josh Cantlon of Scienion for leading the sample preparation portion of the workshop.

Josh Cantlon (top left) led participants through the single-cell sample preparation portion of the workshop.

Josh Cantlon (top left) led participants through the single-cell sample preparation portion of the workshop.

Preparing samples during the workshop.

Preparing samples during the workshop.

After sample preparation, participants learned how to acquire mass spectrometry data from single cells. Mass spectrometric proteomics of single cells poses unique challenges for data acquisition. Workshop participants learned about library generation, LC separation of single-cell samples, and which controls to include for single-cell proteomic analysis. Special thanks to Christoph Krisp from Bruker for leading the data acquisition session from the workshop.

Christoph Krisp (left) led the mass spectrometry section of the workshop.

Christoph Krisp (left) led the mass spectrometry section of the workshop.

Participants learning about mass spectrometry.

Participants learning about mass spectrometry.

Finally, participants dove into data analysis and interpretation of single cell proteomics data. The data analysis section of the workshop included introductory topics, like basic library searching and assessing labeling efficiency. Participants also had the opportunity to learn about more advanced topics, like pipeline development, identifying trypsin mis-cleavages, and troubleshooting approaches. Special thanks to Andrew Leduc of Northeastern University for leading the data analysis and interpretation section of the workshop.

Andrew Leduc (top right) leads participants during the data analysis section of the workshop.

Andrew Leduc (top right) leads participants during the data analysis section of the workshop.

We look forward to seeing you at PTI for next year's workshop! If you'd like to learn more about the workshop, please visit single-cell.net.

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