Alexander-Sol

Added isotopic envelope information to PSMs for use in PEP calculations

1

Appveyor wasn't building, hoping re-opening the PR will help

Adding a new option in the search task window to adjust the required isotope threshold in FlashLFQ. MzLib still needs to be updated to accommodate this parameter.

Implementing spectral library search for mbr results

Spectral decon

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This is the minimal viable implementation of a new deconvolution method, spectral deconvolution. Spectral Deconvolution works by generating theoretical isotopic distributions for each peptide/proteoform in a given library, generating isotopic...

We like to enable re-analysis of an MBR Chromatographic peak once it is created & passed to MetaMorpheus. We add retention time hypothesis and retention time std dev, which can...

This refactor was necessary to enable further changes to the deconvolution algorithm. The folder path to proteases.tsv was changed as a result of this refactor, so ProteaseDictionary.ProteaseDictionary() was changed to...

[WIP] Multiplex reporting

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Small refactor to multiplex ion quantification to increase speed and code quality. Introduced MultiplexMod class to handle all multiplex operations.

Added option to quantify ambiguous peptides

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This PR includes all the commits from nbollis's 539 update PR.

Spectral recovery update

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Previously, spectral recovery was dependent on deconvolution. The updated version uses isolation windows, not deconvoluted precursors, to locate Ms2 spectra associated with MBR-transferred identifications. This change results in increased performance,...