enzyme Trypsin, no P rule

[jflucier]

Hi,

how can I specify the enzyme "Trypsin, no P rule". Since it has a comma in the name this generates the following error when I call eu.isas.searchgui.cmd.IdentificationParametersCLI:

` export ENZYME_LIST="Trypsin, no P rule" export __FIXED_MODS="Carbamidomethylation of C" export VARIABLE_MODS="Deamidation of N, Deamidation of Q, Oxidation of M, Pyrolidone from Q, Pyrolidone from E, Acetylation of protein N-term"

.....

|15:02:52|jflucier@ip32-centos7:[20180929_QEHFX3_ML_DH_EXP133_highPHrp_FRAC9]> java -cp $SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI \

-ms_low_mem_mode $MS_LOW_MEM_MODE \ -max_charge $MAX_CHARGE \ -xtandem_min_frag_mz $XTANDEM_MIN_FRAG_MZ \ -msgf_num_ptms $MSGF_NUM_PTMS \ -myrimatch_num_ptms $MYRIMATCH_NUM_PTMS \ -ms_amanda_instrument "'$MS_AMANDA_INSTRUMENT'" \ -comet_num_ptms $COMET_NUM_PTMS \ -comet_remove_meth $COMET_REMOVE_METH \ -tide_num_ptms $TIDE_NUM_PTMS \ -tide_use_neutral_losses $TIDE_USE_NEUTRAL_LOSSES \ -db $TEMPDIR/db/searchgui_db_concatenated_target_decoy.fasta \ -out $TEMPDIR/searchgui.parameters \ -enzyme "$ENZYME_LIST" \ -fixed_mods '"'"$FIXED_MODS"'"' \ -variable_mods '"'"$VARIABLE_MODS"'"' \ -frag_tol $FRAG_TOL \ -frag_ppm $FRAG_PPM \ -prec_tol $PREC_TOL \ -prec_ppm $__PREC_PPM \ -protein_fdr 0.001 \ -msgf_instrument $__MSGF_INSTRUMENT

Enzyme Trypsin, no P rule not recognized. Please add enzyme using the EnzymeCLI command.

Run -usage to see the list of supported options and their input.

`

thanks for your help.

JF

[hbarsnes]

Hi JF,

Some of the enzymes were renamed a long time ago to avoid this particular issue. Try replacing "Trypsin, no P rule" with "Trypsin (no P rule)" and it should work.

Where did you find the enzyme name "Trypsin, no P rule" btw? Did we forget to update the documentation somewhere?

Best regards, Harald

[jflucier]

Hi Harald,

this information was taken from :

[https://github.com/compomics/searchgui/blob/master/resources/Andromeda/windows/conf/enzymes.xml]

Can you point me to a github file where all enzymes are defined?

I guess for these enzyme, the same naming rules apply:

• Thermolysin (no P rule)

• Lys-C (no P rule)

For this one, what is the valid name: Chymotrypsin, no P rule (FYWL) --> Chymotrypsin (no P rule (FYWL))??

thanks again for your help, JF

[hbarsnes]

Hi JF,

this information was taken from : [https://github.com/compomics/searchgui/blob/master/resources/Andromeda/windows/conf/enzymes.xml]

Those are the Andromeda enzyme names, not the SearchGUI ones. :)

Can you point me to a github file where all enzymes are defined?

You can find all of the names at the end of this file: https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/biology/EnzymeFactory.java.

Or by running java -cp SearchGUI-3.3.17.jar com.compomics.cli.enzymes.EnzymesCLI -l

Best regards, Harald

[jflucier]

thanks alot for your help Harald.