Hello,

I used MS-GF+ on the mzML file, using the .faa file as reference, and produce the .mzid file. All files are in the following link: https://figshare.com/s/b65fc594da19f0f9347f . The raw data was produced by Bruker Impact II (Q-TOF MS/MS), and was transformed into mzML file by ProteoWizard msconvert.

However, when I tried to use the function countIdentifications, an error popped up. I am not sure whether there was something wrong about the reducePSMs, joinSpectraData, or countIdentifications.

My codes were as below. The MS-GF+ was run in Mac terminal; other codes were in R Studio.

java -version 
java version "1.8.0_421"

java -Xmx3500M -jar MSGFPlus.jar -s "HH090441864_2024-09-09_2648.mzML" -d "protein.faa" -tda 0 -inst 2 -e 1 -maxMissedCleavages 2 -o HH090441864_2.mzid

 library(Spectra)
library(PSMatch)
sp<-Spectra("HH090441864_2024-09-09_2648.mzML")
id<-readPSMs("HH090441864_2.mzid")

id_filtered<-filterPSMs(id)
id_f_r<-reducePSMs(id_filtered)

sp_ident <- joinSpectraData(sp, id_f_r,
                      by.x = "spectrumId",
                      by.y = "spectrumID")

sp_ident_count <- countIdentifications(sp_ident)

#Error: BiocParallel errors
 # 1 remote errors, element index: 1
 # 0 unevaluated and other errors
 # first remote error:
#Error in as.vector(x, mode): coercing an AtomicList object to an atomic vector is supported only for
  #objects with top-level elements of length <= 1

Thank you in advance for any thoughts!