Error in data.frame(retrive_ID, mod_position, one_letter, stringsAsFactors = F) : arguments imply differing number of rows: 1, 0

[MT0104]

**Dear HiTMaP Team,

Thank you so much for the excellent support and maintenance. I am running a new issue with Modifications=list(). I am trying to include oxidized peptide in the call. However, it output an error. I have also tried using the same code in the Peptide calibrant but seeing the same error. I have pasted my code below. Would you please let me know if I am calling it incorrectly? Thank you very much for your help!

My Code:**

preprocess = list(force_preprocess=TRUE, use_preprocessRDS=FALSE, smoothSignal=list(method = c("Disable", "gaussian", "sgolay", "ma")[1]), reduceBaseline=list(method = c("Disable", "locmin", "median")[1]), peakPick=list(method=c("diff", "sd", "mad", "quantile", "filter", "cwt")[3]), peakAlign=list(tolerance=5, units="ppm", level=c("local","global")[1], method=c("Enable","Disable")[1]), normalize=list(method=c("Disable","rms","tic","reference")[1], mz=NULL) )

imaging_identification( #==============Choose the imzml raw data file(s) to process make sure the fasta file in the same folder datafile=paste0(wd,datafile), threshold=0.005, ppm=5, FDR_cutoff = 0.05, #==============specify the digestion enzyme specificity Digestion_site="trypsin", #==============specify the range of missed Cleavages missedCleavages=0:1, #==============Set the target fasta file Fastadatabase="uniprotkb_human.fasta", #==============Set the possible adducts and fixed modifications adducts = c("M+H", "M+Na", "M+K"), Modifications = list( fixed = NULL, fixmod_position = NULL, variable = c("Oxidation"), # UniMod code_name (Accession 35) varmod_position = list(c("M")) # restrict to Met ), #==============The decoy mode: could be one of the "adducts", "elements" or "isotope" Decoy_mode = "isotope", use_previous_candidates=F, output_candidatelist=T, #==============The pre-processing param preprocess=preprocess, #==============Set the parameters for image segmentation spectra_segments_per_file=1, Segmentation="none", Smooth_range=1, Virtual_segmentation=FALSE, Virtual_segmentation_rankfile=NULL, #==============Set the Score method for hi-resolution isotopic pattern matching score_method="SQRTP", peptide_ID_filter=1, #==============Summarise the protein and peptide features across the project the result can be found at the summary folder Protein_feature_summary=TRUE, Peptide_feature_summary=TRUE, Region_feature_summary=TRUE, #==============The parameters for Cluster imaging. Specify the annotations of interest, the program will perform a case-insensitive search on the result file, extract the protein(s) of interest and plot them in the cluster imaging mode plot_cluster_image_grid=FALSE, ClusterID_colname="Protein", componentID_colname="Peptide", Rotate_IMG=NULL, )

I have also tried the two below:

Modifications = list( fixed = NULL, fixmod_position = NULL, variable = c(35), # UniMod record_id for Oxidation (M) varmod_position = c(2) # 2 = Anywhere )

and

Modifications = list( fixed = NULL, fixmod_position = NULL, variable = c("Oxidation"), # by code_name varmod_position = c(2) # 2 = Anywhere )

However, they give me the same output:

12 Cores detected, 4 threads will be used for computing 1 files were selected and will be used for Searching uniprotkb_human.fasta was selected as database. Candidates will be generated through Proteomics mode Found enzyme: trypsin Found rule: "" Found customized rule: "" Testing fasta sequances for degestion site: (KR)|((?<=W)K(?=P))|((?<=M)R(?=P)) Generated 205205 Proteins in total. Computing exact masses... Error in data.frame(retrive_ID, mod_position, one_letter, stringsAsFactors = F) : arguments imply differing number of rows: 1, 0

Please help me out. Thank you so much.