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Distributions of correct and incorrect matches
Search engines assign scores to each peptide sequence that matches the theoretical spectrum. These peptide spectrum matchings are called PSMs. All pep…
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@jadianes @jgriss @noedelta Since our last dev release, we had a lot of releases and discussions for the potential improvements. After discussing with Jose and Johannes, here are a proposed list of to…
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When generating decoy spectra the peptide sequence and modification locations are not updated. Thus the spectrum returned by com.compomics.coss.controller.decoyGeneration.GetDecoySpectrum will have t…
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This ideally would start with support for `MultiAssayExperiment` which would directly work for QFeatures
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When two candidate peptides receive the same score with respect to a single spectrum, they should receive the same rank. When top-match=1, both peptides should be reported. Tide currently reports one…
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Hi,
I found a bug.
The SetActiveRange function duplicates the peptides if the heaviest peptide (in Dalton) is smaller than the neutral mass of the heaviest spectrum (in Dalton).
Using the d…
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I have a pipeline where I search some "novel" peptides from a genomic translation, and concatenate to this DB a "normal" ENSEMBL DB to catch non-novel peptides. The strange thing is, I recently (`MSGF…
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Some pipelines need to filter PSMs taking into account the Search Engine provisioning (which search engines have identified the corresponding spectrum), we see two cased here:
- [x] Filter Peptide…
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Hello, I'm having a lot of difficulty understanding how to map pepquery output to TMT tag of GTEx so that I can correctly map peptide to sample_ID.
I know this issue was opened before, but I do not…
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Hi,
I can't figure out the mass values reported by "percolator".
The input MGF is this:
```
TITLE=RawFile: P3141_HC67_1_01_9191 Index: 29964 precursor: 2 Charge: 5
INSTRUMENT=ESI_QUAD_TOF
P…