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Proteomics:
- [x] Send demonstration for SPPCA @austinTalbot7241993
- [ ] (stretch) Follow Eric Dammer's pipeline @akotlar
- [ ] (stretch) Replace Eric Dammer's network analysis with SPPCA and compa…
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Hi,
How is the Q.Value in the report.tsv calculated?
I noticed across multiple experiments that the Q.Values have a strange distribution. For instance, I searched the "RD139_Narrow_UPS1_25fmol_inj…
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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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Hi,
Thank you for the great tool!
When running the same analysis one two different computers the number of identified proteins changed a lot. This trend was observed repeatedly, one computer al…
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To connect the PASS1B-06 DEA results data to the phenotypic data, we need to map each unique `feature_id` (present in the DEA results) to a list of associated `vial_label` (present in the phenotypic d…
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Hi Phil,
I am starting to use PAW pipeline in my TMT studies. The transparency of the workflow and the flexibility is awesome! Although I am not acquainted with Python scripts, I think it is possible…
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Hi,
I am executing the portal_client tool (with my iHMP username and password) to download the files using a manifest file as follows:
portal_client -m hmp_cart_e0473170e2.tsv --endpoint-priority FA…
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# Abstract
Methods to represent multiple spectra
Spectral library searching offers a sensitive yet fast method to match spectra from mass spectrometry-based proteomics experiments. The techn…
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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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There are substantial differences between SynergyFinderPlus ([www.synergyfinder.org](http://www.synergyfinder.org/)) and SynergyFinder2 (https://synergyfinder.fimm.fi/). For assessing the degree of sy…