advice for running DIANN for a phosphoproteome with >500 raw files

zy8281263 commented 2 months ago

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

vdemichev commented 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

zy8281263 commented 2 months ago

您好，我已收到您的邮件。我将尽快给您回复。

zy8281263 commented 2 months ago

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.

vdemichev / DiaNN

advice for running DIANN for a phosphoproteome with >500 raw files #1044