Single Cell Proteomics

Single-cell proteomics helped discover the earliest symmetry breaking during mammalian development.

https://www.cell.com/cell/fulltext/S0092-8674(25)01255-3

One more week to submit abstracts !
https://single-cell.net/proteomics/scp2025 -and-submit-abstracts

Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Nat Protoc 19, 3750–3776 (2024).
https://www.nature.com/articles/s41596-024-01033-8.

Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with high specificity and sensitivity. To increase its throughput, we developed nano-proteomic sample preparation (nPOP), a method for parallel preparation of thousands of single cells in nanoliter-volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation using the plexDIA MS multiplexing method, which uses non-isobaric mass tags to barcode peptides from different samples for data-independent acquisition, demonstrates accurate quantification of ~3,000–3,700 proteins per human cell. A separate implementation with isobaric mass tags and prioritized data acquisition demonstrates analysis of 1,827 single cells at a rate of >1,000 single cells per day at a depth of 800–1,200 proteins per human cell. The protocol is implemented by using a cell-dispensing and liquid-handling robot—the CellenONE instrument—and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 d to prepare >3,000 single cells. We provide metrics and software (the QuantQC R package) for quality control and data exploration. QuantQC supports the robust scaling of nPOP to higher plex reagents for achieving reliable and scalable single-cell proteomics.

https://doi.org/10.1038/s41596-024-01033-8

This week, we shared results from 2 projects. Each took over 5 years & they were published within an hour. This talk summarizes them.
1. Alternate RNA decoding results in stable and abundant proteins in mammals
2. Proteome asymmetry in mouse and human embryos before fate specification

Uncovering secrets of the proteome: Alternate RNA decoding & Protein asymmetry shaping cell fate This presentation "Uncovering the secrets of the human proteome" was given in May 2024 at the 50th anniversary celebration of the Barnett Institute by Prof. ...