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Description
**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.