stefanks

Yeah. The inputs would be identified peptide/proteoform spectrum matches, that come from any source. Could come from a MetaMorpheus search, or use a search result from the northwestern software. I...

It's python...

Regarding the first two, I believe the deconvolution output returns enough to extract this information. Intensity ratio setting is a hard limit on how different relative intensities are allowed to...

Ah, you're right, the peak objects are hidden in private fields. I will make those public to expose all the information. Yes, it is deconvoluting across the entire RT range....

All issues fixed here: https://github.com/smith-chem-wisc/mzLib/commit/91b805c762f3dbffa356b6f07bbf086260fbf482

Sorry, I don't understand

The way I understand this: We would like to explore whether sometimes imputed peaks are above the expected noise level, thus should have been present in the spectrum in the...

Another thought: the "intensity ratio" parameter, that decides how stringent we are with the requirement that intensities match averagine, should be computed automatically/dynamically based on things like TIC/mass/ratio of isotope...

Maybe instead of writing index it is easier to write an unindexed mzml file

Rough structure of a method for writing indexed mzmls: 1. Write non-indexed mzML to memory 2. Calculated indices of scans by reading the stream as a binary stream 3. Discard...