FP 22.0, plexDIA & MSBooster

[kabalak]

log_2024-06-19_10-51-42.zip

Hi,

I am using FragPipe 22.0 on a triplex plexDIA (L=+28, M=+32, H=+36 Da, semi-specific Nt. search strategy with ArgC) HUNTER sample, measured on an Exploris480 with FAIMS and split into the single CVs. The MSFragger search works fine, but subsequently MSBooster does not work and crashes with the error:

[0:00] Loading spectral library F:\Fatih\240618_M1\spectraRT.tsv
[0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete)
[0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 95179 precursors in 93786 elution groups.
[0:00] Encoding peptides for spectra and RTs prediction
[0:00] Predicting spectra and IMs
[0:17] Predicting RTs
[0:24] Decoding predicted spectra and IMs
[0:27] Decoding RTs
[0:27] Saving the list of predictions to F:\Fatih\240618_M1\spectraRT.predicted.bin
Finished
java.lang.NullPointerException
	at Features.MassCalculator.calcMass(MassCalculator.java:165)
	at Features.MassCalculator.<init>(MassCalculator.java:118)
	at Features.DiannSpeclibReader.<init>(DiannSpeclibReader.java:81)
	at Features.SpectralPredictionMapper.createSpectralPredictionMapper(SpectralPredictionMapper.java:47)
	at Features.PercolatorFormatter.editPin(PercolatorFormatter.java:90)
	at Features.MainClass.main(MainClass.java:647)
Done generating DIA-NN predictions
Model running took 28417 milliseconds
Generating edited pin with following features: [brayCurtis, pearsonCorr, dotProduct, unweightedSpectralEntropy, deltaRTLOESS, deltaRTLOESSnormalized, RTprobabilityUnifPrior]
Loading predicted spectra
Process 'MSBooster' finished, exit code: 1
Process returned non-zero exit code, stopping

If I switch off MSBooster in the Validation tab, all the other steps in the workflow work nicely (is MSBooster working nicely on semi-specific peptides at all?) and the search finishes. Also interesting is the PDV viewer component does not define the N-terminal modifications in the output list, it only features [29]... peptides, but none starting with the heavier dimethyl labels on the N-terminus - is this a bug?