Error when filling in missing precursor info: ufunc 'isnan' not supported for the input types

[singjc]

Hi,

I'm re-analyzing the immunopeptidomics data from the Thunder DDA-PASEF paper with Sage, and performing rescoring with MS2Rescore / TIMS2Rescore (v3.1.4), but I get the following error below.

I'm not entirely sure what the issue is, but seems to be an error when checking for retention and ion mobility? I have looked at the rt and ion_mobility columns in the input file (results.sage.tsv), but they don't contain any NaNs.

Best,

Justin

TIMS²Rescore (v3.1.4)
MS²Rescore tuned for timsTOF DDA-PASEF data.
Developed at CompOmics, VIB / Ghent University, Belgium.
Please cite: Declercq & Devreese et al. bioRxiv (2024)

2024-12-10 15:56:01 INFO     ms2rescore.parse_psms // Reading PSMs from PSM file
                             (1/1): 'results.sage.tsv'...                       
2024-12-10 15:57:26 INFO     ms2rescore.parse_psms // Removed 0 PSMs with rank  
                             >= 10.                                             
2024-12-10 15:57:29 WARNING  ms2rescore.parse_psms // Removed 2 PSMs with       
                             invalid amino acids.                               
2024-12-10 15:57:42 INFO     ms2rescore.parse_psms // Found 1152514 PSMs, of    
                             which 29.02% are decoys.                           
2024-12-10 15:57:49 WARNING  ms2rescore.parse_psms // Non-mapped modifications  
                             found: {'-18.010565', '+42.010567', '+119.0041',   
                             '-17.026548'}                                      
                             This can be ignored if they are Unimod modification
                             labels.                                            
2024-12-10 15:57:54 INFO     ms2rescore.core // Found 335390 identified PSMs    
                             with rank <= 1 at 0.01 FDR before rescoring.       
2024-12-10 15:57:57 INFO     ms2rescore.core // Parsing missing retention time  
                             and/or ion mobility values from spectra...         
2024-12-10 16:02:40 ERROR    ms2rescore.__main__ // ufunc 'isnan' not supported 
                             for the input types, and the inputs could not be   
                             safely coerced to any supported types according to 
                             the casting rule ''safe''
                             ╭─────── Traceback (most recent call last) ───────╮
                             │ /home/singjust/.local/lib/python3.11/site-packa │
                             │ ges/ms2rescore/__main__.py:237 in main          │
                             │                                                 │
                             │   234 │   │   │   profiled_rescore = profile(re │
                             │   235 │   │   │   profiled_rescore(configuratio │
                             │   236 │   │   else:                             │
                             │ ❱ 237 │   │   │   rescore(configuration=config) │
                             │   238 │   except Exception as e:                │
                             │   239 │   │   LOGGER.exception(e)               │
                             │   240 │   │   sys.exit(1)                       │
                             │                                                 │
                             │ /home/singjust/.local/lib/python3.11/site-packa │
                             │ ges/ms2rescore/core.py:65 in rescore            │
                             │                                                 │
                             │    62 │   )                                     │
                             │    63 │                                         │
                             │    64 │   # Add missing precursor info from spe │
                             │ ❱  65 │   psm_list = _fill_missing_precursor_in │
                             │    66 │                                         │
                             │    67 │   # Add rescoring features              │
                             │    68 │   for fgen_name, fgen_config in config[ │
                             │                                                 │
                             │ /home/singjust/.local/lib/python3.11/site-packa │
                             │ ges/ms2rescore/core.py:198 in                   │
                             │ _fill_missing_precursor_info                    │
                             │                                                 │
                             │   195 │   │   if required and (                 │
                             │   196 │   │   │   0.0 in psm_list[value_name]   │
                             │   197 │   │   │   or None in psm_list[value_nam │
                             │ ❱ 198 │   │   │   or np.isnan(psm_list[value_na │
                             │   199 │   │   ):                                │
                             │   200 │   │   │   if all(v is None or v == 0.0  │
                             │   201 │   │   │   │   raise exceptions.MissingV │
                             ╰─────────────────────────────────────────────────╯
                             TypeError: ufunc 'isnan' not supported for the     
                             input types, and the inputs could not be safely    
                             coerced to any supported types according to the    
                             casting rule ''safe''