Convert speclib to tsv format

[Niveda-S]

Hi,

I am interested in doing a comparison between two pre-existing libraries. Is there a way to convert library in the speclib format to a readable format such as tsv?

[vdemichev]

Yes, just specify an output library in the GUI

[Niveda-S]

Okay thanks! Is there a way to directly read the speclib format also (with the help of some sort of a database)?

[vdemichev]

No, the only way is to convert with DIA-NN

[wolski]

Dear @vdemichev

Although I specify the "\report-lib.tsv" in the GUI, and the options seem to be passed to the diann.exe

diann.exe --lib "" --threads 16 --verbose 1 --out "D:\WEW_o29132_\BENCHMARKING\report.tsv" --qvalue 0.01 --matrices  --out-lib "D:\WEW_o29132_\BENCHMARKING\report-lib.tsv" --gen-spec-lib --predictor --prosit --fasta "D:\WEW_o29132_\BENCHMARKING\UP000000625_83333.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 --use-quant --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal 

neither the report.tsv file nor the report-lib.tsv is being written by DIA-NN (see log below).

0 files will be processed
[0:00] Loading FASTA D:\WEW_o29132_\BENCHMARKING\UP000000625_83333.fasta
[0:00] Processing FASTA
[0:02] Assembling elution groups
[0:03] 498603 precursors generated
[0:04] Prosit input saved to D:\WEW_o29132_\BENCHMARKING\report-lib.prosit.csv
[0:04] Gene names missing for some isoforms
[0:04] Library contains 4392 proteins, and 4392 genes
[0:04] Encoding peptides for spectra and RTs prediction
[0:05] Predicting spectra and IMs
[5:27] Predicting RTs
[5:56] Decoding predicted spectra and IMs
[5:58] Decoding RTs
[5:58] Saving the library to D:\WEW_o29132_\BENCHMARKING\report-lib.predicted.speclib
[6:00] Initialising library

[6:00] Log saved to D:\WEW_o29132_\BENCHMARKING\report-lib.log.txt
Finished

[Arthfael]

Same problem here, the report-lib.tsv is not being written: diann.exe --lib "MYPATHWITHOUTSPACES\report-lib.predicted.speclib" --threads 28 --verbose 1 --out "MYPATHWITHOUTSPACES\report.tsv" --qvalue 0.01 --matrices --out-lib "MYPATHWITHOUTSPACES\report-lib.tsv" --gen-spec-lib --predictor --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal I have tried 1.8.1 and 1.8.2 (beta) but got the same result.

[wolski]

@Arthfael

Running the command

diann.exe --lib "D:\WEW_o29132_\BENCHMARKING\report-lib.predicted.speclib" --threads 16 --verbose 1 --out "D:\WEW_o29132_\BENCHMARKING\report.tsv" --qvalue 0.01 --matrices  --out-lib "D:\WEW_o29132_\BENCHMARKING\report-lib.tsv" --gen-spec-lib --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal

On the generated speclib file generates then the report-lib.tsv file. (Some of the options I guess are not needed).

[Arthfael]

It worked, thanks for your swift reply! So the "--predictor" flag was the issue.

On Wed, Sep 20, 2023 at 9:22 AM Witold Wolski @.***> wrote:

@Arthfael https://github.com/Arthfael

Running the command

diann.exe --lib "D:\WEW_o29132_\BENCHMARKING\report-lib.predicted.speclib" --threads 16 --verbose 1 --out "D:\WEW_o29132_\BENCHMARKING\report.tsv" --qvalue 0.01 --matrices --out-lib "D:\WEW_o29132_\BENCHMARKING\report-lib.tsv" --gen-spec-lib --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal

On the generated speclib file generates then the report-lib.tsv file. (Some of the options I guess are not needed).

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