Robert Millikin

indexed mzML is re-implemented in #1970 so this should be fixed when that gets merged

this may be because of neutral loss - I know our internal phospho definition includes neutral loss but UniProt doesn't have any neutral losses annotated for (I think) any mod....

- "Pretty" default graph styling/colors (+colorblind-friendly palette) - Multiple annotation types (ellipse, square, text, lines) for data and floating annotations - High performance with 1million+ data points (may not be...

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I think we'd treat them as any other mod, right? Being in the protein core is (to me) only relevant in a secondary+ structural sense. I guess we're assuming any...

can you give an example? I'm not sure I understand I usually just use something like myFilePath = @"C:\Users\rmillikin\myfile.txt";

strange. that path is in the mzml file itself? sounds like @dippman might be able to fix this in mzLib

maybe we can develop some kind of modification motif syntax, like @bintiibrahim did for protease cleavage specificity? So like X{P} means any amino acid except P

Thanks for the thorough investigation and the tips. We use MsConvert all the time, but lack access to WIFF files and the SCIEX converters, so these things are a bit...

I'd like to add my 2c and say that deconvolution probably shouldn't assume the monoisotopic mass is below the limit of detection if the theoretical monoisotopic intensity is above noise....