Michael Steidel @michaelsteidel.bsky.social · 07/12/2025I agree MaxLFQ isn’t meant for absolute quantification. But that still doesn’t explain the complete lack of correlation with UPS2. From my experience, iBAQ and MaxLFQ usually correlate well (R² ~0.78, non related example dataset shown), suggesting they track the same MS1 signal. 110
Michael Steidel @michaelsteidel.bsky.social · 07/10/2025Surprised that u go so low. With EvoSep 24 min method we can load lots more on our Ultra2 until reaching saturation especially with ICC2.0 100
Michael Steidel @michaelsteidel.bsky.social · 01/10/2025On a separate note: I was surprised to find that none of the non-canonical SwissProt isoforms are included in the official human reference proteome (UP000005640). Anyone know what’s going on here? 🤔 #proteomics #bioinformatics @pwilmarth.bsky.social il 220
Michael Steidel @michaelsteidel.bsky.social · 30/09/2025Hey #TeamMassSpec, Many non-human proteomics studies still search against taxon-filtered FASTAs. ❌ Redundant sequences ❌ Inflated search space ✅ Reference proteomes cut redundancy, improve annotation, and make results comparable. 👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot 292
Michael Steidel @michaelsteidel.bsky.social · 25/09/2025Thanks @pwilmarth.bsky.social - also included the less-redundant "one protein per gene" db here ...Has anybody assessed potential benefits of the reduced search space on sensitivity? 220
Michael Steidel @michaelsteidel.bsky.social · 25/09/2025Hey #TeamMassSpec, When you run proteomics on non-human species (mouse, rat, macaque, etc.) — which protein FASTA do you prefer? Taxonomy-filtered UniProt (all entries) Reference proteome (SwissProt+TrEMBL) Ensembl/GENCODE Something else? 140
Michael Steidel @michaelsteidel.bsky.social · 19/07/2025Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run. www.biorxiv.org/content/10.1... 050
Michael Steidel @michaelsteidel.bsky.social · 27/06/2025Sciex in the game. Pretty impressed by ScanningSWATH data on the new ZenoTOF 8600. #TeamMassSpec 1112
Michael Steidel @michaelsteidel.bsky.social · 24/06/2025..diaPASEF down to 1 ng Hela looks ok (using E.Coli entrapment) 110
Michael Steidel @michaelsteidel.bsky.social · 18/03/2025Slice-PASEF: Almost as beautiful as gazing into the starry sky at night 140
Michael Steidel @michaelsteidel.bsky.social · 11/03/2025Ion mobility stability over time is a helpful metric which we always generate to control for weather-related, or ITI-contamination driven drift effects.. 160
Michael Steidel @michaelsteidel.bsky.social · 05/03/2025For those interested: Have found the segmentation feature in timsControl. Simply right click in the 'chromatogram' pannel, and select 'Insert New Segment'. 251
Michael Steidel @michaelsteidel.bsky.social · 14/02/2025Popularity of current DIA data analysis tools (vendor-independent, based on citations of initial publication) Updated for 2024: 1209
Michael Steidel @michaelsteidel.bsky.social · 30/01/2024Inerestingly, this picture changes when using fulltext search where algorithms based on Sequest (as implemented in ProteomeDiscover) dominate... 000
Michael Steidel @michaelsteidel.bsky.social · 30/01/2024Trying to estimate popularity of search engines. (Something widespread I missed out?) Based on citations/year of initial publication it seems as MSFragger would take over soon... 100
