falcon

falcon copied to clipboard

**1. Improved I/O** Write spectra to a single lance file instead of many pickle files. Fast spectrum retrieval with index. **2. Updated binning strategy** Removed assigning spectra to mass intervals,...

Janne98

MS2 spectra without a precursor charge are ignored

14

Hello, I was trying to cluster mzXML files from https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=88a7dfeeecb74131a6d6bfb7a9db0a46 in WSL:Ubuntu-22.04 but it does not seem to recognize any spectra. My parameters and output are below: ``` falcon BAX89_BA1_01_23240.mzXML...

YasinEl

NumPy 1.24.4 results in the following error: ``` 2023-07-12 15:21:00,375 WARNING [py.warnings/MainProcess] warnings._showwarnmsg : /home/wout/.conda/envs/falcon/lib/python3.11/site-packages/falcon/cluster/cluster.py:509: FutureWarning: In the future `np.object` will be defined as the corresponding NumPy scalar. neighborhoods_arr =...

bittremieux

Weird numba caching issue

2

Due to the incorrect fraction part, the resulting dim can have an error (+1/-1 difference).

tycheyoung

Make sure the correct monoisotopic precursor m/z is used. See for example [Monocle](https://github.com/gygilab/Monocle).

bittremieux

Automatically determine the precursor mass tolerance and fragment mass tolerance. Can this be done using [Param-Medic](https://github.com/dhmay/param-medic)? Porting the software to Python 3 would be necessary. Alternative, relevant code can be...

bittremieux

mzML parsing issue

1

Some mzML files are reported to have 0 MS/MS spectra. For example: [MSV000083463/Milk_final_11712.SUBJECT57.MBM.1333.mzML](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=0a4e79b555eb4987b3cd0e033f73c52d). Equivalent mzXML files do work.

bittremieux

Investigating splitting

4

Sometimes we have same precursor m/z and very similar MS/MS not ending up in the same cluster, even with high EPS values. One example here: [Falcon Clustering](https://proteomics2.ucsd.edu/ProteoSAFe/status.jsp?task=48f893dc8a4147e59798910e6c866ce2) [Networking](https://proteomics2.ucsd.edu/ProteoSAFe/result.jsp?view=network_displayer&componentindex=73&task=5fae3956b11346e4b120352b735d54b3#%7B%7D) We can...

mwang87