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Peptides FDRs do not correspond to protein FDRs.
Currently, large-scale studies often have dozens or hundreds of LC-MS runs that are being accumulated. Repeated measurements lead to an accumulation o…
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Hello!
Thanks for developing this tool. It is nice to see this rescoring approach finally packaged in an easily distributed and reproducible manner.
I have a question regarding the fragment ion …
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A few of the PRs I still have open and am working on have all ran into this issue, and I need some input from you guys to resolve it.
In tests/validators/test_validate_test_data.py there are tests…
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We recently are trying to reproduce the results of a published study with TMT-10. We used MSFraggerAdapter, followed by Percolator to calculate PEP, and ProteinProphet to do protein grouping. If we ta…
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Blender relies on PSMs shared between multiple search engines to construct and apply its FDR scoring model, and it currently uses Comet, XTandem with k-scoring, and MS-GF+.
For best performance, th…
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Hi, Thank the developer for providing so a fantastic tool for DIA data analysis.
Is there a way to match th…
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Hello there.
We'd like to use the xQuest importer for our searches. However, we are using a light-heavy workflow for our samples.
Unfortunately the importer only supports light-light searches at t…
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ping @chambm
Still having problems with MPA. Input is a 600MB fasta file and 441MB mgf. Might be a memory problem, but -Xmx 70GB is already quite a lot (actual available memory was 3 * 37GB).
…
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We have a routine to do charge deconvolution on our spectra such that all the fragments are set to be +1 ms2 fragmention ions only (ie no +2 or +3 ms2 fragments etc.). However, we couldn't determine i…
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Hi, we have a few term requests that are not exactly protein modifications, but we use them in our data in a similar way that we use PSI-MOD terms, so we are hoping that you can help us with them. If …