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Hi,
I just noticed an issue with the latest version of FragPipe (18.0): when I launch the GUI, I see that the PTMs tab is active and I can edit fields. PTM-Shepherd is set to active. As soon as I l…
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After coming across the MCP2021 paper, I was really excited to see the implementation of an FDR-controlled MBR function for IonQuant. Figure 4 of that paper demonstrated that even with a stringent FDR…
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I am new to using Philosopher for LFQ - when using the label-free quantification function, is there a way to only quantify proteins only identified by a minimum of two unique peptides?
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Can I get sample output file(s) for a basic MSfragger search?
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Hi @anupshah14,
I have realized that if you can obtain different results (without changing any parameter obviously) just by pressing Start analysis again. These are a few screenshots just after pre…
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In this section https://github.com/wombat-p/Proline-Workflow#run-benchmarking-data-set
we give this example of nextflow execution:
```
nextflow run main.nf --raws 'RAWFOLDER/*.raw' --fasta yeast_…
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(Expert opinion required, recommendations can be implemented by developer)
When inputting parameters outside of the allowable range, the top error message is "Incorrect moving average (MA) value! P…
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I tried to Run iceR in windows with two thermo .raw. The process seems to work fine until saving quantification results after alignement scoring and filter.
Then, the programs stops with a warning.
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Greetings,
Currently, I am trying to perform non-enzyme searches using fragpipe with the default workflow (with reviewed UniProt Proteome Database) of non-specific-peptidome with the following chan…