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Hello everyone,
I am using DIA-NN to analyze ultralow sample data acquired with diaPASEF and VistaScan modes from timsTOF Ultra 2.
Multiple peptides of interest fall outside of the fragmentation win…
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Hi Johan,
I'm working with peptide samples metabolically labelled with heavy hydrogen. Dinosaur is doing a good job of detecting peptide features in these samples but is commonly dropping the first i…
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Hi,
I am using DIAmeter for peptide identification from my data, in the original paper (https://academic.oup.com/bioinformatics/article/37/Supplement_1/i434/6319661) I found the mention of pepXML …
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For a user provided spectral library, how does DIA-NN select fragment ions in the library for peptide detection?
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#### Current behavior:
Hi all,
The reactions in the subsystem `Peptide metabolism` are all **reversible**, meaning that peptides can be formed from individual amino acids without an ATP cost. Also…
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I would like to download my file "all ambiguous peptides" from SQLshare but the download directly from the site didn't seem to be progressing. I tried fetchdata in the sql python tools, but it timed …
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Peptide bond is way larger than normal (1.88 A) between A:78 and A:79 in 1byi. This in turn messes up the topology detection, either using residue/atom names or guessing, because the corresponding is …
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This issue is about mass spectrometry data (MS), we have not made a decision about whether to include the data or not. We want our affinity predictor to have no bias towards peptides that are processe…
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Catherine Kaczorowski is going to be uploading mass spec proteomics:
Level 0 ... Raw data
Level 1 ... Skyline documents
Level 2 ... CSV of raw peptide intensities from Skyline
Le…
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There is the Condition
`any(k != border for k in pep_lens[border:]) `
in the predict function of lstm_utils.py and ae_utils.py.
What is the purpose of this condition?