Show threadFatih DemirNov 25, 2025
As a follow-up to this thread: there is now also an editorial emphasizing the value of our resource for the community: https://www.embopress.org/doi/full/10.1038/s44318-025-00633-8
Special emphasis on the non-canonical functions of the human complement system. #SLE #Ntermini #EMBOJournal
Show threadFatih DemirOct 30, 2025
As we started by an unbiased screening in the human plasma, we needed to optimize our already published HUNTER method (https://doi.org/10.1074/mcp.TIR119.001560) for high-throughput and the demands of handling a larger cohort with 143 patient samples (in the end), optimizing timing and efficiency. The improvements were heating it up, making it faster and using a stream-lined approach avoiding multiplex dimethyl labeling to enable "label-free-like" N-terminomics. #Ntermini #SHUNTER 2/n
Fatih DemirNov 24, 2023
Interesting things occur, when using the open search from FragPipe/MSFragger: dimethylated N-termini samples from a HUNTER enrichment show a definitive amount of "deuterated methyl ester" (+17.03448) instead of the expected 34.0631 for the usual dimethylation. Localized mainly (>80 %) to the N-terminus, especially before Ps - is this the ominous expected monomethylation before P upon reductive dimethylation? #TeamMassSpec #Ntermini #proteomics
Fatih DemirJul 25, 2023
Hmm, interesting questions: when doing in-vitro protease digests with recombinant protease, do I exclude self-cleavages of the protease from the putative cleavages as it might be rather an artefact of the excess protease addition? #Proteases #Ntermini
Fatih DemirJan 13, 2023
Anyone else doing plasma proteomics with short nano gradients on an Ultimate3000 (<1h) and FAIMS/Exploris480 combined? I thought we had the golden rule of only 1 CV with shorter gradients lengths, but seems to be not true in terms of peptide-centric working people. #Ntermini #FAIMS #TeamMassSpec
Fatih DemirNov 29, 2022
Another work in progress release of MANTI is out now! MANTI v5.3 (https://sourceforge.net/projects/manti/files/MANTI-v5.3.zip) enables you to analyze DiaNN/MSFragger-generated N-terminomics with the one-stop-shop approach of MANTI! To honor this, MANTI stands now for Mastering Advanced N-Termini Interpretation. It works for simplex data (only dimethyl-labelling currently) with the DIA_SpecLib_Quant workflow in MSFragger - currently, only DIA is supported for MSFragger, but more might be on the way. #MANTIv5.3 #Ntermini #proteomics