MetaMorpheus

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PEP in calibration, glyco [GUI: separation type missing in some tasks]

1

Separation type isn't populated for calibration, isn't present at all for GPTMD or Glyco

zrolfs

Normalizing protein intensities

1

[iBAQ protein quantification](https://www.nature.com/articles/nature10098) excludes missed cleavages and normalizes intensities by the number of theoretical peptides, which correlates with length. It looks like proteins with many quantified missed cleavages peptides and...

acesnik

This is the clearest explanation of a newer version of xcorr that has been implemented in a few different search algorithms including crux-tide. it is described in this paper: https://www.ncbi.nlm.nih.gov/pubmed/24895379...

trishorts

If a peptide corresponds to the same range of multiple protein entries, the range of start-to-end only includes the unique ranges. I think having the start to end for each...

acesnik

Calibration fails for phospho-enriched TMT run

15

I'm trying to run calibration on a published phospho-enriched TMT dataset, and all but two of the files fail to calibrate. Has anyone else tried to run calibration on such...

acesnik

Add command to download the latest version of MetaMorpheus to the command-line version. This will let us test the autoupdate function via appveyor and other automatic scripting/tests

rmillikin

trishorts

Write file-specific mass tolerances to prose output and change "Gptmd" to G-PTM-D

1

Search tolerances used in the .toml should be written to the results file description of the output. Also change Gptmd to G-PTM-D

trishorts

Set global default to output excel compatible

13

All files - psms, protein groups, peptides.

leahvschaffer

It'd be nice to add information on the estimated time remaining for completing the search in the Tasks section. The estimate could be based on 1) files already completed, 2)...

acesnik