document how to pull dat out of mascot

[alexmasselot]

how to get MGF and mzId
And, how to get the fasta too (is there a web service?)

[rmylonas]

For the MGF and mzd, we can call a "service" (perl-cgi script) which gives a result file. An example:

http://mascot.vital-it.ch/mascot/cgi/export_dat_2.pl?file=..%2Fdata%2F20141212%2FF002111.dat;_ignoreionsscorebelow=14;_minpeplen=5;_noerrortolerant=0;_onlyerrortolerant=0;_prefertaxonomy=0;_requireboldred=0;_server_mudpit_switch=0.000000001;_show_decoy_report=0;_showallfromerrortolerant=0;_showsubsets=1;_sigthreshold=0.05;_target_fdr=;do_export=1;export_format=mzIdentML;group_family=1;pep_exp_mz=1;pep_isbold=1;pep_isunique=1;pep_query=1;pep_rank=1;peptide_master=1;prot_acc=1;prot_desc=1;prot_hit_num=1;report=0;sessionID=all_secdisabledsession;show_pep_dupes=1;use_homology=1;generate_file=1

[alexmasselot]

This link returns only the mzId, or is the mgf hidden somewhere?

[rmylonas]

The following link should work to download an mgf:

http://mascot.vital-it.ch/mascot/cgi/export_dat_2.pl?group_family=1&_showsubsets=1&file=..%2Fdata%2F20141218%2FF002148.dat&use_homology=1&_server_mudpit_switch=0.000000001&export_format=MGF&generate_file=1