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Error importing protein prophet file

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Error importing protein prophet file g158094008  2008-01-20 18:21
Status: Closed
Assigned To: g158094008
 
With version 2.3 importing protein prophet fails with the following message:

18 一月 2008 10:28:25,577 INFO : Starting to load ProteinProphet file F:\Chi\20071204_SILAC\mascot\interact\XP0.036areainteract.prot.xml
18 一月 2008 10:28:25,624 INFO : Resolved referenced PepXML file to F:\Chi\20071204_SILAC\mascot\interact\XP0.036areainteract.pep.xml
18 一月 2008 10:28:25,624 INFO : Clearing out existing MS2 data for XP0.036areainteract.pep.xml
18 一月 2008 10:28:37,046 INFO : Finished clearing out existing MS2 data for XP0.036areainteract.pep.xml
18 一月 2008 10:28:37,124 INFO : Loading FASTA file
18 一月 2008 10:28:39,874 INFO : FASTA file "c:/Inetpub/wwwroot/ISB/data/database/SwissProt_51.6.fasta" has already been loaded
18 一月 2008 10:28:39,905 INFO : Loading MS/MS results is 0% complete
18 一月 2008 10:28:40,140 ERROR: MS2 data upload failed
org.postgresql.util.PSQLException: ERROR: value too long for type character varying(20)
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1548)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1316)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:191)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:351)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:305)
    at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:101)
    at org.labkey.api.data.ConnectionWrapper$StatementWrapper.executeUpdate(ConnectionWrapper.java:984)
    at org.labkey.ms2.PepXmlImporter.write(PepXmlImporter.java:526)
    at org.labkey.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:122)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:189)
    at org.labkey.ms2.MS2Manager.uploadRun(MS2Manager.java:413)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:404)
    at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:292)
    at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:54)
    at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:49)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
18 一月 2008 10:28:40,202 ERROR: ProteinProphet load failed
org.postgresql.util.PSQLException: ERROR: value too long for type character varying(20)
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1548)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1316)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:191)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:351)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeUpdate(AbstractJdbc2Statement.java:305)
    at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:101)
    at org.labkey.api.data.ConnectionWrapper$StatementWrapper.executeUpdate(ConnectionWrapper.java:984)
    at org.labkey.ms2.PepXmlImporter.write(PepXmlImporter.java:526)
    at org.labkey.ms2.PepXmlImporter.uploadRun(PepXmlImporter.java:122)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:189)
    at org.labkey.ms2.MS2Manager.uploadRun(MS2Manager.java:413)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:404)
    at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:292)
    at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:54)
    at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:49)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Thanks,
Amy
 
 
jeckels responded:  2008-01-21 16:48
Amy,

That error message means that there is at least one quantitation entry in your pep.xml where either the decimal_ratio or the heavy2light_ratio attributes are longer than 20 characters, most likely quite early in the file. We haven't seen any values that long before.

What parameters are you using to run XPRESS?

If you open your pep.xml file, do you see the value or values that are too long? If so, what do they look like?

Thanks,
Josh
 
donw responded:  2011-02-21 13:16
Feb 21, 2011

Hi, We are seeing this same error when trying to import pep.xml with SILAC quantitation data into cpas 10.30.

I uploaded our log file and our pep.xml

Here is the Error msg we are seeing:

21 Feb 2011 14:30:42,223 INFO : Starting to import peptide search results for fraction 1, analysis of file null
21 Feb 2011 14:30:42,223 INFO : Importing MS/MS results is 0% complete
21 Feb 2011 14:30:42,270 ERROR: Failed to insert quantitation info for scan 4855 with charge 2 from use1point0asxpresstolerance_sec20_feb21_interact_edit.pep.tgz
21 Feb 2011 14:30:42,473 ERROR: MS2 import failed
org.postgresql.util.PSQLException: ERROR: value too long for type character varying(20)


Going into the pep.xml file pulling out scan 1023 shows the following values for decimal_ratio and heavy2light_ratio
decimal_ratio="0.001"
heavy2light_ratio="1:19182626470973493000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000.00"


<spectrum_query spectrum="o261_08may02_18_silac_sec20.4855.4855.2" start_scan="4855" end_scan="4855" precursor_neutral_mass="763.4878" assumed_charge="2" index="8" retention_time_sec="2305.850000">
<search_result>
<search_hit hit_rank="1" peptide="AARTGLR" peptide_prev_aa="K" peptide_next_aa="I" protein="IPI:IPI00167065.3|SWISS-PROT:Q8N142-2|ENSEMBL:ENSP00000333019|REFSEQ:NP_954634" num_tot_proteins="2" num_matched_ions="5" tot_num_ions="12" calc_neutral_pep_mass="763.4567" massdiff="+0.0310" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="Tax_Id=9606 Gene_Symbol=ADSSL1 Isoform 2 of Adenylosuccinate synthetase isozyme 1">
<alternative_protein protein="IPI:IPI00170914.1|SWISS-PROT:Q8N142-1|TREMBL:B3KTV4|ENSEMBL:ENSP00000331260|REFSEQ:NP_689541|H-INV:HIT000053273|VEGA:OTTHUMP00000028412" protein_descr="Tax_Id=9606 Gene_Symbol=ADSSL1 Isoform 1 of Adenylosuccinate synthetase isozyme 1" num_tol_term="2" peptide_prev_aa="K" peptide_next_aa="I"/>
<modification_info modified_peptide="AAR[166]TGLR[166]">
<mod_aminoacid_mass position="3" mass="166.109381"/>
<mod_aminoacid_mass position="7" mass="166.109381"/>
</modification_info>
<search_score name="ionscore" value="15.82"/>
<search_score name="identityscore" value="38.06"/>
<search_score name="star" value="0"/>
<search_score name="homologyscore" value="28.49"/>
<search_score name="expect" value="8.38"/>
<analysis_result analysis="peptideprophet">
<peptideprophet_result probability="0.0106" all_ntt_prob="(0.0000,0.0030,0.0106)">
<search_score_summary>
<parameter name="fval" value="-1.1302"/>
<parameter name="ntt" value="2"/>
<parameter name="nmc" value="1"/>
<parameter name="massd" value="0.031"/>
</search_score_summary>
</peptideprophet_result>
</analysis_result>
<analysis_result analysis="xpress">
<xpressratio_result light_firstscan="4830" light_lastscan="4965" light_mass="744.448" heavy_firstscan="4830" heavy_lastscan="4965" heavy_mass="764.465" mass_tol="1.000" ratio="1:INF" heavy2light_ratio="1:19182626470973493000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000.00" light_area="0.00e+000" heavy_area="7.55e+006" decimal_ratio="0.001"/>
</analysis_result>
</search_hit>
</search_result>
</spectrum_query>

-------------------------------------------------------------------------------
So I realize now our issue is getting a 1:INF which generates the > 20 char value in heavy2light_ratio.

Do you have any XPRESS suggestions for settings or workarounds to prevent getting these 1:INF ratios or an easy way to filter your xml file so it can pass being imported.

Thanks
Don Wolfgeher (donw@uchicago.edu)
 
donw responded:  2011-02-23 13:57
Feb 23, 2011

Update:

We tested different versions of TPP builds to see if the 1:INF issue was fixed, and found out that TPP ver 4.3 and later has fixed the 1:INF issue causing this error.

If you are importing pep.xml quant interact files from TPP versions 4.2 and below you may have this error/issue.

TPP 4.3 and 4.4 import fine.

Just wanted to post this in case other users run into the same issue.
 
jeckels responded:  2011-02-24 09:51
Hi Don,

Thanks for the update. For the 11.1 release, I've added some code to handle this kind of data in pepXML files for those who are still running old releases of the TPP, or need to import existing data.

Thanks,
Josh