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### PXD001819 Analysis
Currently, we have a workflow that can perform peptide identification using: `-> ms2rescore -> SNR + spectrum properties -> percolator`
Here the results can be found (http…
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Greetings,
I am a new user to nf-core and currently trying to establish nf-core proteomicslfq pipeline on my personal local PC. Unfortunately, I am facing error with search engine comet. I have att…
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Thank you for developing such a promising software for the scientific community.
I tried running Alphalink2 with several datasets, including the rpoa-rpoc dataset used in the bioRxiv manuscript but …
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Hi all,
I made a pull request with three exemplary annotations for MSI data to start a discussion: https://github.com/bigbio/proteomics-metadata-standard/pull/450
Here are some thoughts about t…
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@jpfeuffer sometimes the pipeline fails in the id part because of the peak-peaking step by the ThermoRawFileParser. Would be great to "restart" the pipeline, same parameters but with the openms peak p…
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This morning I am feeling very inspired by some work that @anastasiyaprymolenna , @sierra-moxon and others were doing last night. I'm talking about reviewing a [PR I made for simplifying ChemicalConve…
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# DeepScore: Community curated scoring, supercharged with AI
![EJ2PqRjXsAIQrb6](https://user-images.githubusercontent.com/16521288/195572456-62ab95bf-d0bc-4f70-b5e4-272cb509eff4.jpeg)
(Image taken f…
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Workflow
The search engine definitely plays the most important role in the peptide identification process. As illustrated below, what the search engine itself does is bascically first in silico diges…
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```
Eric posted this to the PSI-PI list, so copied here for tracking:
By way of background, we at ISB have been testing to the ProteoWizard idconvert
tool to convert our TPP output (pepXML & protXML…
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```
Eric posted this to the PSI-PI list, so copied here for tracking:
By way of background, we at ISB have been testing to the ProteoWizard idconvert
tool to convert our TPP output (pepXML & protXML…