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License: MIT License
Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
License: MIT License
stuff I'd like added or changed:
Write the software version in the written files. Decide which of the output files need to have the version.
not necessarily "unique" in the sense that they match only one protein, but unique in the sense that the best scoring version of each peptide is kept and all others are dropped. This obviates grade inflation in FDR when multiple copies of the same thing are observed.
use the same output header as psms_tsv
Even with defects
Look for peptide evidence across multiple spectra files based on m/z and retention time, not requiring MS2 precursor selection. See moff algorithm
Have MS1 scan, then ms2 scans are mixed: might be cid, hcd, etc -> all from same precursor
Split into ptm, adducts, glyco, unknown, etc. This is for different kinds of runs.
Display tasks in treeview
Different ion types z,c, a, etc.
Need more complicated logic for seen peptides
Write the results summaries, decide if need to write results for each engine/task/global task. Probably all of them.
Use mzLib, and the included class generated from schema.
Dictionary<CompactPeptide, HashSet> local = compactPeptideToProteinPeptideMatching.ToDictionary(b => b.Key, b => new HashSet());
in analysis engine, method AddObservedPeptidesToDictionary
with error
An exception of type 'System.InvalidOperationException' occurred in mscorlib.dll but was not handled in user code
Additional information: Collection was modified; enumeration operation may not execute.
And if it finds too many intervals with multiple peaks, should give a meaningful error return.
Might be wise to limit the tolerance here to plus/minus 1
Put in a boolean switch in tasks
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