Joerg Doellinger

Check out our preprint @bioRxiv on bacterial biotyping using LC-MS1 with data analysis of < 2 min using a database of > 12000 @uniprot proteomes #microbiology #proteomics biorxiv.org/content/10.110…

Sensitivity for SARS-CoV-2 detection is in the range of LFA rapid tests. The workflow is powered by timsTOF, Evosep and DIA-NN and will enable to identify infected individuals in large sample cohorts in the future. medrxiv.org/content/10.110…

Proteomics goes viral! We present vPro-MS to identify human-pathogenic viruses in patient samples from diaPASEF/DIA data. We developed a peptide library covering the human virome from 20,000 genomes, which enables highly specific detection (>99,9%) using vProID scoring.

@slavov_n Partly marketing,we talk a lot about technical problems and statistics compared to NGS. So customers trust RNAseq more. Isn't it wild to measure RNA and treat it like proteins when analyzing the data (GO)? Shows that even RNAseq considers transcripts less important than proteins.

The cost of both mass spectrometry proteomics & DNA sequencing have decreased, though the question remains: Why is DNA sequencing ubiquitously integrated in modern biomedical research while proteomics remains less ubiquitous? blog.slavovlab.net/2020/05/25/the…

@mjmaccoss @UCDProteomics That's a good point. What standard could be used to analyse this? Best I can think of is a dilution series of the UPS1 (SigmaAldrich) in a yeast matrix? But this doesn't account for the proteoform situation in real samples.

I think it's great it's now easy to download DIA from published manuscripts. But man the more I look at them , the more I feel it's critical people state up front what their Points across their peaks are. I mean an average of 2 isn't even a triangle

@byu_sam It depends on the software, LCMS setup and type of experiment. But for protein quantification using DIA data points per peak can be very low, see biorxiv.org/content/10.110… and pubs.acs.org/doi/10.1021/ac…

#TeamMassSpec In optimizing LC gradients, I've heard recommendations on the number of measurements across an ion's elution in order to get good quantification (like 7 data points at full-width half-max). Are there any pubs about this?

Can DIA take over #proteomics? Recent developments allow deep (> 8000 proteins) and accurate proteome profiling even at 1.5 data points per peak (FWHM) #DIANN #Prosit #µPAC #SPEED biorxiv.org/content/10.110…

Paper In Press: Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction @rki_de mcponline.org/content/early/…