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I have enriched acetylated peptides using PTMScan acetyl antibody beads and analyzed the peptides using ddaPASEF and diaPASEF.
diaPASEF data was analyzed using DIA-NN in library-free mode but found…
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Dear Vadim, many thanks for DiaNN which has really opened a new chapter for DIA processing.
I would like to ask you some guidance on how to calculate protein level FDR using DiaNN PSM scores from…
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Vadim,
Thanks for keeping improving the performance of DIA-NN. We are using spectral libraries generated from Spectronaut. And DIA-NN older version (1.7.10 or 1.7.12) has no problem in recognizing a…
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Hi Alex,
I am using the newest version of Spectronaut to process phospho enriched DIA data. Unfortunately, I am getting the new error; please see the image. Do you have any thoughts? Appreciate your…
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Hi Alex,
Thanks again for developing this very useful tool.
I am analyzing the PhosphoDIA data with Spectronaut/Perseus using the plugin to collapse the peptides (using the linear model). Everythi…
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Hi Vadim,
Generated spectral library using Fragpipe (easyPQP). However, I can't process DIA runs using this library. Please see the log. Any suggestions or help is greatly appreciated. Had a luck i…
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Hi ,
Thank you for your good job!
I have read the article”Generating high quality libraries for DIA MS with empirically corrected peptide predictions ”.And I’m very interested to this project.And I …
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1) I generated a user defined modification file modification_ck.txt where I defined the N-terminal acetylation as follows:
cat modification_ck.txt
modified-AA TPP-nomenclature Unimod-Acc…
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Dear Peptideshaker team,
I have been trying to import SearchGui output (analysis of 6 MS raw files) files to peptide shaker, however I have been experiencing a memory issue at the step of: "Validatin…
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What happened: I uploaded a CSV file generated using EncyclopeDIA to create a predicted library. I got the error shown in the image below.
What should have happened: I expected a predicted library…