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Nature Methods features HeLa proteome study from Liu Lab

“We are proteomic scientists and therefore have a long-term research interest in reproducibility and variability analysis,” says Liu. In 2014, they had the idea of using mass spectrometry to profile the proteomic heterogeneity in cell lines with the “same name.” To this end, they used ‘sequential-window acquisition of all theoretical fragments’ mass spectrometry (SWATH-MS), which can efficiently and reproducibly detect thousands of proteins in cell samples. See full text here: https://www.nature.com/articles/s41592-019-0375-1

GenomeWeb features the recent DIA-MS study from Liu Lab

https://www.genomeweb.com/proteomics-protein-research/yale-team-combines-dia-ms-crispr-study-down-syndrome-protein Using two-hour DIA mass spec runs on a Thermo Fisher Scientific Orbitrap Lumos instrument, the researchers were able to reproducibly quantify roughly 6,200 proteins in HeLa cells with CRISPR-deleted HMGN1, confirming deletion of the target gene and identifying 147 proteins with expression levels that changed significantly following knockout of this gene. According to Yansheng Liu, assistant professor of pharmacology at Yale and senior author on the study, the paper offers a proof-of-concept that DIA mass spec can be a rapid and effective method for confirming the outcome of CRIS