Open zy8281263 opened 2 months ago
Hi Yuan,
We now provide a very detailed guidance on how to use DIA-NN 1.9 for phospho https://github.com/vdemichev/DiaNN?tab=readme-ov-file#ptms-and-peptidoforms . For now, only Windows version is available, Linux coming soon.
Best, Vadim
您好,我已收到您的邮件。我将尽快给您回复。
Thanks for your advice, Vadim! Now, we used the DIA-NN 1.8 for phospho test on linux, the used command is here: --lib "" \ --threads 30 \ --verbose 1 \ --out /data/projects/brain/protein_ptm/first_batch_81/human_brain_phospho_20240516/diann_analysis/result/20240516_humanBrain_Phospho_report.tsv \ --qvalue 0.01 \ --matrices \ --out-lib /data/projects/brain/protein_ptm/first_batch_81/human_brain_phospho_20240516/diann_analysis/result/20240516_humanBrain_Phospho_report-lib.tsv \ --gen-spec-lib \ --predictor \ --fasta /data/shared_data/uniprotkb/02human_uniprotkb_proteome_UP000005640_2023_09_28.fasta \ --fasta-search \ --min-fr-mz 200 \ --max-fr-mz 1800 \ --met-excision --cut K,R \ --missed-cleavages 1 \ --min-pep-len 7 --max-pep-len 30 \ --min-pr-mz 300 --max-pr-mz 1800 \ --min-pr-charge 1 --max-pr-charge 4 \ --unimod4 --var-mods 3 --var-mod UniMod:35,15.994915,M --var-mod UniMod:21,79.966331,STY --monitor-mod UniMod:21 --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal
We are not sure if the parameter selection and settings are appropriate.
Hello, we want to run DIANN for phosphorylation detection on over 500 raw files simultaneously (together as input files, had already used mscovert ), our linux has 88 available cpu cores and 1T ram, could you please give me some advice to increase the run-success rate and save the time? Thank you a lot!
Yuan