Timo Sachsenberg

using msconvert with "combine IM scans" but without scan summing I get: ``` ``` seems to be a scan property not a precursor property

sage mzML vs. d: mzML 980s [2024-04-02T19:19:23Z INFO sage] discovered 209898 target peptide-spectrum matches at 1% FDR [2024-04-02T19:19:23Z INFO sage] discovered 45417 target peptides at 1% FDR [2024-04-02T19:19:23Z INFO sage]...

@jcharkow @cbielow maybe sage merges by precursor I did not enable MS2 scan summing. Maybe this is needed?  and if this can be used. What are reasonable settings for...

output by sage in results.sage.tsv | psm_id | peptide | proteins | num_proteins | filename | scannr | rank | label | expmass | calcmass | charge | peptide_len |...

Here with summing (msconvert defaults if PASEF is selected 0.05MZ, 5s RT, 0.1 IM tolerance) [2024-04-03T14:18:58Z INFO sage] discovered 83451 target peptide-spectrum matches at 1% FDR [2024-04-03T14:18:58Z INFO sage] discovered...

Here with summing (msconvert defaults. all dimensions, but very tight tolerances (0.01 in RT,MZ,IM)) [2024-04-03T15:00:17Z INFO sage] discovered 222551 target peptide-spectrum matches at 1% FDR [2024-04-03T15:00:17Z INFO sage] discovered 47290...

k seems the "collapse" option without summing is most suitable @cbielow do you know why I get this error for MS2 if I want to display the IM frame? 

@cbielow what are these 3 scans? 

@jcharkow I think basic support for writing ion mobility out is there. If you have capacities, it would be great if you could look into how IM can be added...

ah ok, from the tests I see that we need to add the ion mobility to the ExtractionCoordinates ``` ChromatogramExtractorAlgorithm::ExtractionCoordinates coord; coord.mz = 618.31; coord.rt_start = 0; coord.rt_end = -1;...