Legend:
required parameter
advanced parameter
+MascotAdapterAnnotates MS/MS spectra using Mascot.
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'MascotAdapter'
in
input file in mzData format.
Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is readinput file
out
output file in idXML format.
Note: In mode 'mascot_in' Mascot generic format is written.output file
mascot_infalse
if this flag is set the MascotAdapter will read in mzData and write Mascot generic formattrue,false
mascot_outfalse
if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXMLtrue,false
instrumentDefault
the instrument that was used to measure the spectra
precursor_mass_tolerance2
the precursor mass tolerance
peak_mass_tolerance1
the peak mass tolerance
taxonomyAll entries
the taxonomyAll entries,. . Archaea (Archaeobacteria),. . Eukaryota (eucaryotes),. . . . Alveolata (alveolates),. . . . . . Plasmodium falciparum (malaria parasite),. . . . . . Other Alveolata,. . . . Metazoa (Animals),. . . . . . Caenorhabditis elegans,. . . . . . Drosophila (fruit flies),. . . . . . Chordata (vertebrates and relatives),. . . . . . . . bony vertebrates,. . . . . . . . . . lobe-finned fish and tetrapod clade,. . . . . . . . . . . . Mammalia (mammals),. . . . . . . . . . . . . . Primates,. . . . . . . . . . . . . . . . Homo sapiens (human),. . . . . . . . . . . . . . . . Other primates,. . . . . . . . . . . . . . Rodentia (Rodents),. . . . . . . . . . . . . . . . Mus.,. . . . . . . . . . . . . . . . . . Mus musculus (house mouse),. . . . . . . . . . . . . . . . Rattus,. . . . . . . . . . . . . . . . Other rodentia,. . . . . . . . . . . . . . Other mammalia,. . . . . . . . . . . . Xenopus laevis (African clawed frog),. . . . . . . . . . . . Other lobe-finned fish and tetrapod clade,. . . . . . . . . . Actinopterygii (ray-finned fishes),. . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish),. . . . . . . . . . . . Danio rerio (zebra fish),. . . . . . . . . . . . Other Actinopterygii,. . . . . . . . Other Chordata,. . . . . . Other Metazoa,. . . . Dictyostelium discoideum,. . . . Fungi,. . . . . . Saccharomyces Cerevisiae (baker's yeast),. . . . . . Schizosaccharomyces pombe (fission yeast),. . . . . . Pneumocystis carinii,. . . . . . Other Fungi,. . . . Viridiplantae (Green Plants),. . . . . . Arabidopsis thaliana (thale cress),. . . . . . Oryza sativa (rice),. . . . . . Other green plants,. . . . Other Eukaryota,. . Bacteria (Eubacteria),. . . . Actinobacteria (class),. . . . . . Mycobacterium tuberculosis complex,. . . . . . Other Actinobacteria (class),. . . . Firmicutes (gram-positive bacteria),. . . . . . Bacillus subtilis,. . . . . . Mycoplasma,. . . . . . Streptococcus Pneumoniae,. . . . . . Streptomyces coelicolor,. . . . . . Other Firmicutes,. . . . Proteobacteria (purple bacteria),. . . . . . Agrobacterium tumefaciens,. . . . . . Campylobacter jejuni,. . . . . . Escherichia coli,. . . . . . Neisseria meningitidis,. . . . . . Salmonella,. . . . . . Other Proteobacteria,. . . . Other Bacteria,. . Viruses,. . . . Hepatitis C virus,. . . . Other viruses,. . Other (includes plasmids and artificial sequences),. . unclassified,. . Species information unavailable
modifications[]
the modifications i.e. Carboxymethyl (C)
variable_modifications[]
the variable modifications i.e. Carboxymethyl (C)
charges[1+, 2+, 3+]
the different charge states
dbMSDB
the database to search in
hitsAUTO
the number of hits to report
cleavageTrypsin
The enzyme descriptor to the enzyme used for digestion. (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server).Trypsin,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,CNBr+Trypsin,Formic_acid,Lys-C,Lys-C/P,PepsinA,Tryp-CNBr,TrypChymo,Trypsin/P,V8-DE,V8-E,semiTrypsin,LysC+AspN,None
missed_cleavages0
number of allowed missed cleavages0:∞
sig_threshold0.05
significance threshold
pep_homol1
peptide homology threshold
pep_ident1
peptide ident threshold
pep_rank1
peptide rank
prot_score1
protein score
pep_score1
peptide score
pep_exp_z1
peptide expected charge
show_unassigned1
show_unassigned
first_dim_rt0
additional information which is added to every peptide identification as metavalue if set > 0
boundary
MIME boundary for mascot output format
mass_typeMonoisotopic
mass typeMonoisotopic,Average
mascot_directory
the directory in which mascot is located
temp_data_directory
a directory in which some temporary files can be stored
log
Name of log file (created only when specified)
debug0
Sets the debug level
threads1
Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse
Disables progress logging to command linetrue,false
testfalse
Enables the test mode (needed for internal use only)true,false