No Output is Generated

[Maithy15]

Hi Vadim,

I am trying to use the new version for PTM analysis. I can see the quant files but no output (none of report.tsv files) is generated. Especially if click MBR ON it gives output but without MBR there is no output.

Another question regarding the contaminants, is it enough to include contaminants while generating the library or should the box be checked for analysis as well?

Thanks for your help, Maithy

[vdemichev]

Hi Maithy,

How does the log look like?

About contaminants, yes, need to be selected at both lib generation and analysis steps.

Best, Vadim

[Maithy15]

Not a single file is written, including the log.

[vdemichev]

Yes, but if you use the 'Save log' button?

[Maithy15]

Thanks for the prompt response. I will upload the log from the current run as soon as it ends.

[Maithy15]

Hi Vadim,

Here is the log file. Thanks for the help.

Cheers, Maithy 06_15_2024 10_51_28.txt

[vdemichev]

How much RAM is in the system?

[Maithy15]

256 GB

[vdemichev]

OK, many thanks for the log, I will take a look.

[vdemichev]

Would you please be able to share the .quant files in "D:\Maithy\240608_Lena_Phos\" as well as D:\Maithy\240608_Lena_Phos\FASTA\From_Uniprot\LysN\Phospho_LFQ_Mouse_LysN.predicted.speclib and D:\Maithy\240608_Lena_Phos\FASTA\From_Uniprot\uniprotkb_mus_musculus_AND_reviewed_tru_2024_06_15.fasta?

[Maithy15]

May I email you? Could you please give me your email ID?

[vdemichev]

Yes, thank you! Please email to: Email: my first name dot my last name at gmail dot com

[vdemichev]

Hi Maithy,

OK, I looked at the log and was successfully able to reproduce the error using similar analysis settings. Basically, what happens is that the 'Contaminants' function does not work properly if, at the same time, (i) a predicted library is used, (ii) MBR is disabled. So the fix in your case is to enable MBR, even if you do not need the MBR results, i.e. if the purpose of the analysis is solely to generate a DIA-based spectral library. You can enable 'Use .quant files', i.e. the reanalysis will be fast.

Many thanks for reporting this. A fix will be added to the 1.9.1 release update, also supporting such a scenario.

Best, Vadim

[Maithy15]

Hi Vadim,

Thank you so much for figuring the problem out. I have one more qiestion. I got two outputs named phospho with 90 and 99. Are the numbers localization probability?

Thanks Maithy

[vdemichev]

Yes, exactly!

[Maithy15]

That was super fast! Just for me to understand, do you recommend to be this stringent? is it possible to set a different value like 0.75 for the output?