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Dear PepQuery developers,
Thank you for building this valuable tool!
I am currently working with a TMT16-labeled dataset and I wanted to use PepQuery v2.0.2. to validate a list of mutated peptide …
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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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You may want to view this on GitHub since I have embedded tables and such. https://github.com/MoseleyBioinformaticsLab/MESSES/issues
I am going to start with a short description of how ISA assays w…
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In the current Tide output format, terminal PTMs cannot be distinguished from side chain PTMs. I think we should represent them using a hyphen, so a modification of XXX on the first amino acid of PEP…
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As part of our CFDE base award we planned to submit additional data to the CFDE portal using C2M2 which is currently not covered in the model. Namely protein site specific information (PTMs). This wil…
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### Description of feature
@MaLLLiYA @timosachsenberg @jpfeuffer @daichengxin :
We have been analysing some of the datasets and we found some interesting unexpected PTMs (mass shits), most of the…
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Hi,
I want to analyze LFQ-DIA global proteome and phospho-enriched proteome data separately on DIA-NN. Just want to make sure that we need two different libraries for these two different searches, r…
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added confidence measures for PTMs would be useful. For example, indicate presence of diagnostic ions or observation of expected neutral losses in PSMS.tsv.
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### Questions to answer
* What are ways we will further our product mission if we onboard PTMs?
* What are ways we'll be distracted from our product mission if we onboard PTMs?
* What kind of language…
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We should cover more PTMs in statements.py. These are easy to add and just need to be added to the modification hierarchy to be correctly handled in all contexts.