Abacus error

[Jimmy]

So I got roped into running Abacus for a former colleague of mine.  I took a stab at entering all required values in the GUI but there's a good chance I did something wrong given I'm not sure what I need to be entering.  Anyways, it seems to run for awhile, parsing pep.xml files.  Then it kicks out with this message left on the console:

---------------------------------------------

prompt> java -jar abacus.jar interact-COMBINED.prot.xml

ERROR: mod_aminoacid_mass line pepXML::record_AA_mod()

basename.18165.18165.3

---------------------------------------------

Any idea what this error message is implying?  Possible I entered the "Req. AA Mod." list wrong?  That entry in the pep.xml file looks fine.

Here's what I entered for "Req. AA Mod."

+M[147];+K[142];+R[170];+K[156];+R[184];+K[170];+R[198];+K[242];+S[166];+T[181];+Y[243]

Here's the crazy list of mods from the head of a pep.xml file:

<aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0354" variable="Y" symbol="*"/>

<aminoacid_modification aminoacid="K" massdiff="14.0156" mass="142.1106" variable="Y" symbol="#"/>

<aminoacid_modification aminoacid="R" massdiff="14.0156" mass="170.1167" variable="Y" symbol="#"/>

<aminoacid_modification aminoacid="K" massdiff="28.0313" mass="156.1263" variable="Y" symbol="@"/>

<aminoacid_modification aminoacid="R" massdiff="28.0313" mass="184.1324" variable="Y" symbol="@"/>

<aminoacid_modification aminoacid="K" massdiff="42.0470" mass="170.1419" variable="Y" symbol="^"/>

<aminoacid_modification aminoacid="R" massdiff="42.0470" mass="198.1481" variable="Y" symbol="^"/>

<aminoacid_modification aminoacid="K" massdiff="114.0429" mass="242.1379" variable="Y" symbol="~"/>

<aminoacid_modification aminoacid="S" massdiff="79.9663" mass="166.9984" variable="Y" symbol="$"/>

<aminoacid_modification aminoacid="T" massdiff="79.9663" mass="181.0140" variable="Y" symbol="$"/>

<aminoacid_modification aminoacid="Y" massdiff="79.9663" mass="243.0297" variable="Y" symbol="$"/>

<aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" variable="N"/>

<aminoacid_modification aminoacid="X" massdiff="9000.0000" mass="9000.0000" variable="N"/>

Any insight is appreciated.

[Damian]

Hi.
Sorry to here you are having a problem with Abacus.

First off, the command line just has to be: java -jar abacus.jar

After that the GUI should start up.

Now onto your error:
The message is indicating which spectrum 'basename.18165.18165.3' has a formatting problem in it's AA modification line in the prot.xml file.

My guess is that something is weird about that modification tag in the XML file.
If you can send me the pep.xml file you are having issues with I can figure out what's causing the problem.

Alternatively email me just that spectrum's entire record. The data between <spectrum_query> </spectrum_query> tags.

Damian

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