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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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No protein identification despite high MS1 and MS2 signal #1133

Open joachims1956 opened 3 months ago

joachims1956 commented 3 months ago

Dear DIANN,

Thanks a lot for developing this amazing software. We implemented it in our single cell workflow. Unfortunately, we got 0 protein identification with our latest mouse single cell experiments despite having a very good MS1 and MS2 signal. As experimental set-up, we acquire the samples using an Evosep (120SPD and 40SPD) and the diagonal-pasef/synchro-pasef method on a TimsTOF instrument. In DIANN (1.9.1) we are using our own murine spectral library and having "--tims-scan" added in the DIANN additional options box. I added below the stats output and the log file (Log level 3) as well. Thanks a lot,

report_diagonal_pasef_JS_first_test_mouse_samples_13082024.log.txt report_diagonal_pasef_JS_first_test_mouse_samples_13082024.pdf

vdemichev commented 3 months ago

Hi,

Can you please upload somewhere one of the runs (just one) and the Mouse_lung_TimsTOF_Ofir_exp_30\report-lib_FIRST_PASS.tsv.speclib? I will then take a look.

Also, how was Mouse_lung_TimsTOF_Ofir_exp_30\report-lib_FIRST_PASS.tsv.speclib obtained?

Best, Vadim

joachims1956 commented 3 months ago

Dear Vadim,

Thanks for your reply. As requested, I shared one of our runs via mail with you. Please let me know if you need further information. Best, Joachim

vdemichev commented 3 months ago

Hi Joachim,

Sorry, I don't seem to have received the email, can you please resend?

Best, Vadim

joachims1956 commented 3 months ago

Hello,

Sorry for the inconveniences. I sent it again (at the Charite mail address).

Best, Joachim