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X!!Tandem with PTMTreeSearch


PTMTreeSearch is a program developed for identification of Post-Translational Modification in MS/MS data and it is embedded to the X!Tandem project. This server is hosted by Protein Structure and Bioinformatics Group [link]
International Centre for Genetic Engineering and Biotechnology (ICGEB) [link],
Trieste,Italy. click here for help.
Note that this server has been created for demonstration purposes and some parameters are fixed. For access to all parameters of the PTMTreeSearch, please download it from here.
  1. spectra
    common, mzXML, mzData, DTA, PKL or MGF only (Minimum number of spectra is 19.)
  2. taxon
    Select one or more.
    Eukaryotes Prokaryotes Viruses
    1. Include reversed sequences:
    2. all 15N amino acids
    		| none | mixed | only |
    with peptide log(e) < and protein log(e) <
  3.   measurement errors
    1. Fragment mass error:  
  4.   PTMTreeSearch parameters
    1. use PTMTreeSearch:
      mass lower bound: - mass upper bound:
      Two-stage search is used.
      The firs round parameters are:       PTM Bound (MB)=1,           MPE>0.99, SR=0.6, using NPM.
      The second round parameters are: PTM Bound (MB)= MPE>0.00, SR=0.3, without NPM.
      E-mail address where the link to the results will be sent: (required!)
      Note that: our privacy statement can be seen here.
  5.   residue modifications
    1. Complete modifications 1:

      specify your own
    2. Complete modifications 2:

      specify your own
    3. Potential modifications:
      specify your own
    4. Use sequence annotations yes no
  6.   refinement specification
    1. Potential modifications (unimod):
      round 1 round 2

       mods:
      motifs:
       mods: motifs:
    2. Use sequence annotations yes no
    3. Point mutations: yes no
    4. Semi-style cleavage: yes no
    5. Valid expectation: <
  7.   protein cleavage specification
    1. Cleavage site:
    2. Semi-style cleavage: yes no
  8.   spectrum conditioning
    1. Remove redundant: yes no, angle: (0-90)
    2. Spectrum synthesis: yes no
  9.   predefined methods
    1. Method: Select device & parent δm.
  10.   gpmdb
    1. Add to gpmDB: yes restricted no
    2. Archive MS/MS informationyes no
    3. Anonymous contribution: yes no

      4.   more ...