|Title||»||Fix MaxQuant library builder to extract original spectra from source data files|
It has been pointed out many times over many years now that the MaxQuant Andromeda output BiblioSpec uses for spectra in its spectral libraries (found in the msms.txt file) are actually isotope deconvoluted spectra and not the original raw spectra. This is not a huge problem for doubly charged precursors where doubly charged fragments are infrequent, but with triply charged and higher it becomes a bigger problem.
For a number of years, we have hoped the MaxQuant team would offer us a solution that would provide the raw spectra in the msms.txt file, but this has not happened, and both MaxQuant and Skyline have become more popular, along with DIA methods that rely heavily on library spectra.
So, we need to fix the MaxQuant parser in BiblioSpec to get its spectra from the source data files and error if they cannot be found, as we do for other results parsers, such as pepXML and mzIdentML. We should leave the code in place to get spectra from msms.txt for when/if we get a better solution from MaxQuant. Though, even then, we will want to keep code for returning to source files in order to handle MaxQuant results that are either older or just don't contain raw spectra for some reason.