trishorts

is there any way to share your data with me? i'd like to try and search them to reproduce your error.

1. yes you can modify your installation so that it doesn't pause to ask about the thermo license. You need to find the folder where MetaMorpheus is installed. That directory...

in windows, the "MaxThreadsToUsePerFile" parameter in the toml file adds more cores. This is line 50 in the latest version. Here, I show 7, which is all my laptop will...

Running MM in HPC may not accomodate the use of threads in the same way as for windows. I have almost no experience w/ HPC. Some collaborators worked to adapt...

Quantification with FlashLFQ occurs by setting the "DoQuantification" setting in the toml to true (Line 18 in the latest release) 

However, this doesnt do the bayesian thing. You can add a ExperimentalDesign file to the same directory as your raw files and MM will use that in the quant. It...

Here is an example ExperimentalDesign.tsv file: [ExperimentalDesign.zip](https://github.com/smith-chem-wisc/MetaMorpheus/files/10758814/ExperimentalDesign.zip)

MM will do FlashLFQ and provide quantitative protein values. But it will NOT do the bayesian thing. For that, you have to run FlashLFQ separately. I made an issue to...

Sorry for the slow response. You can perform qunatitative analysis of the output with our companion software FlashLFQ. You only need the metamorpheus glyco search results and the raw files...

pretty cool. i only ever see yAmmoniaLoss. maybe we need unit tests for each of the ion types? sounds like lots of work...... I wonder if we paste a couple...