Proteome Informatics Group > Java Proteomic Library



This application generates a decoy library from a given annotated MS library.

Please cite:
Ahrné E., Ohta Y, Nikitin F., Scherl A., Lisacek F., Müller M., An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates, Proteomics., 2011, 11 (7), pp 4085-4095


The method is based on the shuffling of each MS precursor peptide and the generation of decoy spectra obtained after the theoretical fragmentation.

Each generated spectrum fragment then follows a different fate:

  1. the mz is recalculated for any Annotated fragments
  2. the Non-Annotated (NA) fragment is kept or sampled from the overall NA distributions
The decision to sample a NA peak depends on its deviation from the overall population (of closed mz fragments sharing the same precursor charge in the precursor mz neighborhood) - The less it deviates the more probable it will be sampled.


1. parse the annotated spectra library file
   (with --etd option: precursor neighbors fragments removed)
2. make n distributions of all NA fragments by precursor charge (n charges) for future sampling 
   (example at charge +3)
   FOR each original_spectrum DO 
3.  [make decoy spectrum]
     count <- 0
3.1  shuffle precursor peptide sequence (do not shuffle N/C terminal amino-acids (peptidase footprint))
3.2  create the fragmentation spectrum from the shuffled precursor 
     /// TODO: (specific kind of fragmentation ??)
     FOR all peaks DO
       IF annotated peak THEN
         recalculate the new mzs
       ELSE IF mz closed to the baseline THEN
         pick a peak mz in the NA sample (see 2)
         keep the peak
4.   [compute spectrum match (score [0, 1[)]
     score <- original_spectrum versus decoy_spectrum (with only annotated peaks)
     IF score > dot_product_threshold (decoy ~ original) and count < 10 THEN
       count <- count + 1
       GOTO 3.1
5.     [write decoy spectrum]
       flush the most different (lowest score) decoy spectrum in output file


usage: Deliberator <mslib> [-a] [-c] [-d <arg>] [--decoy-tag]
       [--default-decoy-tag] [--default-pep-decoy-tag] [-h] [-i <arg>] [--log
       <arg>] [-o <arg>] [-p <arg>] [--pep-decoy-tag <arg>] [-q] [-r <arg>] [-s
       <arg>] [-t <arg>] [-v] [-w <arg>]
 -a,--average                         set the average mass mode for
                                      peptide mass calculation
                                      by default: MONOISOTOPIC.
 -c,--concat-libs                     concatenate libs
                                      by default: false.
 -d,--dp-threshold <arg>              define the dot-product threshold
                                      ([0-1[) for spectrum shuffling
                                      by default: 0.7.
    --decoy-tag                       set this decoy tag in 'Comments' of
                                      decoy spectra
                                      by default: No tag.
    --default-decoy-tag               set this default decoy tag in
                                      'Comments' of decoy spectra
                                      by default: 'DECOY_'.
    --default-pep-decoy-tag           set this default decoy tag in
                                      peptide 'Name' of decoy spectra
                                      by default: 'decoy_'.
 -h,--help                            print this message.
 -i,--setting-file <arg>              give a property file with all input
    --log <arg>                       define the log file.
 -o,--output <arg>                    set the output filename (.msp or
                                      .sptxt file only).
 -p,--precision <arg>                 define the number of fractional
                                      digits for output
                                      by default: 2.
    --pep-decoy-tag <arg>             set this decoy tag in peptide 'Name'
                                      of decoy spectra
                                      by default: No tag.
 -q,--quiet                           quiet mode (verbose off)
                                      by default: false.
 -r,--render-dir <arg>                render NA peak histograms
                                      (render-dir/hist) and original + decoy spectra (render-dir/scan).
                                      warning: execution time x10.
 -s,--sampling-prob <arg>             define the probability of sampling
                                      non-annotated peaks ([0-1[)
                                      by default: -1.0.
 -t,--tol <arg>                       define the tolerance for mz fragment
                                      peak comparison
                                      by default: 0.1.
 -v,--version                         print the version info.
 -w,--sampling-interval-width <arg>   define the bin width of
                                      non-annotated (NA) peaks histograms for sampling
                                      by default: 100.


The latest version is v0.19 - Download app with the default properties file.


Fixed Bug Deliberator was generating the decoy library in sptxt format only. It now produces sptxt or msp file given the file name extension.
Fixed Bug The MW is now evaluated to the "exact molar mass of the peptide ion" and not to the neutral molar mass.


Fixed Bug While shuffling peak sequence, some peak mz were becoming negative after recomputation given their fragment type. We now ignore them.


Fixed Bug MS1/MS2 dist computation sometimes crashed


Runtime behavior Change Parsed spectra (needed in MS1/MS2 distributions process) are not kept in memory anymore. They are now serialized in hadoop file reducing the memory overhead.


Decoy process progression Change The progression is now visible in a progress bar.