Alexander-Sol

Usi downloader

1

Implemented UsiLoader class that downloads spectra from various databases as JSON, then converts them into a lightweight UsiSpectrumFromJSON class. Conversion from JSON object is done using Newtonsoft, which is a...

UnimodLoader throws KeyNotFoundException

1

When MetaMorpheus calls UnimodLoader, it throws a KeyNotFoundException - "Key '2H' not found". This happens ~50 times whenever you run a test in MetaMorpheus. I would like this to not...

Implemented SpectrumTree Class

2

The spectrum tree is a basic Binary Search Tree storing mz, intensity pairs. The nodes are ordered by m.z. This data structure will allow for efficient search _and_ deletion. It...

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...

Reads output from msFragger

[WIP] Edited FlashLFQ to include option for verbose peaks

1

FlashLFQ now has the option to encode the entire isotopic envelope in the quantified peaks outputs This is done using three new columns Isotope Peak Intensity: Report the intensity of...

Issue with Write method in Readers

1

In Readers, the WriteResults methods calls CanRead to validate a file path. CanRead checks the intended output path for a given file extension from SupportedFileType. However, these types contain specific...

Peptide Level PEP-Q Value changes

1

This PR changes the way PSMs are rolled up to peptides for the purpose of PEP-Q Value calculations. When calculating PEPQ Values at the peptide level, you first have to...

[WIP] Add support for timsTOF data to MetaMorpheus

1

This PR is downstream of a related mzLib PR. It adds support for searching timsTOF data in MM. Calibration/quant is not currently supported

PR #2394 added functionality to eliminate decoy peptides that are identical to target peptides. However, this only works for single-protease searches. If there are multiple proteases, then it is possible...