Dmorgen

O-Pair crashes specifically on one file

1

**Describing the issue** Getting an exception specifically on one data file. the rest are OK. the file is not corrupt and opens well in Xcalibur. **Reproducing the error** the raw...

PTM localisation?

2

Hi, I saw you've added a column for "localized score", and I'm guessing it's for PTM localization score? in our results it's not populated. is it supposed to be? or...

generating new XML libraries from search results? - feature request

2

Hi Guys, is it possible to generate new XML databases from search results? i'd be especially interested in "beefing up" the uniprot XMLs with new modification sites (especially for O-glyco)....

multiple ID files

12

Hi, I noted that you write I can use multiple Raw files, but not multiple tsv files? is there an ability to run LFQ for multiple files? if yes, does...

software threw 2 samples from quant

3

I'm running a 90 sample analysis, but the output contains only 88 columns. does the software throw outliers? D.

Baysian quantification crashed.

1

Please see attachment. Cheers, D. [ErrorReport.txt](https://github.com/smith-chem-wisc/FlashLFQ/files/4313631/ErrorReport.txt)

How to quantify cross-linked data?

2

what should be put in the base/full sequence? Thanks! D.

Hi, Where can I change the enzyme parameters in the GUI application for peptidomics data? I've tried to input in the Mokapot FASTA parameters the Enzyme as '.' (as written...

Hi, running rescore on Sage results, the program crashed trying to download something? our servers are disconnected from the web, so we can't have software connecting to the outside. ...

crash running a non-specific search.

3

I ran an analysis that includes spectra averaging, GPTMD and search. The crash occurred during the search stage, giving a "key=10" error. see the attached file. Thanks! David. [results.txt](https://github.com/user-attachments/files/16676304/results.txt)