MetaMorpheus

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**What would you like to see done in MetaMorpheus?** **Please describe any alternatives you've considered** **Additional context**

trishorts

MetaDraw Fragmentation Reanalysis

2

Enables the reanalysis of a fragmentation spectrum with additional fragment ion types. The plotting methods use the MatchedIons of the psm that gets passed in to determine what to plot....

nbollis

[WIP] Kdn adding and diagnostic filtering

1

RayMSMS

Add the comment on glyco-searching and the search summary on the result file

1

1. Add lei's comment on the coding of o-pair searching. 2. Try to add the search summary information (PSMs, protein group, glycoPsms, Level1-glycoPsms) into the "AllResult.txt" file for glycoSearch (1)...

RayMSMS

Currently, the pep q-value is computed by summing the pep and dividing by row number for psms or peptides sorted in descending order by MetaMorpheus score. In this PR, pep...

trishorts

Meta Draw Quality of Life Updates

1

Added additional customization options to the meta draw spectral match plot. MetaDrawSettings is now more robust to prevent crashes due to saved parameter reading/writing. Meta Draw settings window was reorganized...

nbollis

Added new features to Top-Down PEP

1

Added the following features - Peaks in precursor envelope - Count of identifications per scan - (Still Considering) Intensity of most abundant precursor peak Removed the normalization for top down...

nbollis

YulingDai

Only quantify peptides that clear the q-value threshold

1

Previously, when we wrote the AllQuantifiedPeptides output, we filtered based off of PSM q-value. So you would have some peptides with high q-values reported in the quant results. This fixes...

Alexander-Sol

**Describing the issue** Here is an example from a classic search task. The All target XXX is what Jenkins looks for All target PSMs with q-value = 0.01: 7784 All...

nbollis