Reanalysis of Figure 2 data from High-Speed Mass Spectrometers diminish the difference between Data-Dependent and Data-Independent Acquisition Proteomics

Raw data can be downloaded from https://www.ebi.ac.uk/pride/private/ws/archive/v2/file/fdownload/PXD078489/35854891?token=c0c9919b04c1e50d0a380c3c7fbb9d66 wget https://www.ebi.ac.uk/pride/private/ws/archive/v2/file/fdownload/PXD078489/35854891?token=c0c9919b04c1e50d0a380c3c7fbb9d66 -O nDDA.zip unzip nDDA.zip This seems to have 3 replicates of 1, 100 and 1000 nano-grams from “trypsin digested HeLa cell line lysates” collected in DDA and nDIA modes. Authors used Fragpipe which i find amazing for open searches something i should write about 🤞 but my favorite tools for this purpose on our data needs to be checked as well and see if they are good for Astral? Essentially, MaxQuant for DDA and DIA-NN for DIA of course but also added tesorAI, tool that feels like magic! Authors says “FragPipe was chosen for data processing due to its capacity to handle both DDA and DIA” but actually DIA-NN Learned to Search DDA, MaxQuant can DIA for a while and even tesorAI can do both.