compomics/reporter

Protein quantification based on reporter ions

Reporter

This project aims to provide a user friendly environment to perform protein quantification based on reporter ions (iTRAQ, TMT).

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	v0.12.6 (beta) - All platforms	ReleaseNotes

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Beta Testing

Please note that Reporter is still in a beta testing mode. If you come across any issues please set up an issue using the issue tracker.

For general questions or comments please use the Reporter Google Group.

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reporter's Issues

SQL error message when saving psdb

When saving a Reporter psdb, the following error message in the log is obtained:

Windows GUI:

org.sqlite.SQLiteException: [SQLITE_CONSTRAINT_PRIMARYKEY]  A PRIMARY KEY constraint failed (UNIQUE constraint failed: data.id)
	at org.sqlite.core.DB.newSQLException(DB.java:909)
	at org.sqlite.core.DB.newSQLException(DB.java:921)
	at org.sqlite.core.DB.throwex(DB.java:886)
	at org.sqlite.core.DB.executeBatch(DB.java:774)
	at org.sqlite.core.CorePreparedStatement.executeBatch(CorePreparedStatement.java:79)
	at com.compomics.util.db.object.ObjectsCache.saveObjects(ObjectsCache.java:350)
	at com.compomics.util.db.object.ObjectsCache.saveCache(ObjectsCache.java:411)
	at com.compomics.util.db.object.ObjectsDB.lock(ObjectsDB.java:784)
	at eu.isas.peptideshaker.export.PsdbExporter.saveAs(PsdbExporter.java:130)
	at eu.isas.peptideshaker.utils.PsdbParent.saveProject(PsdbParent.java:371)
	at eu.isas.reporter.io.ProjectSaver.saveProject(ProjectSaver.java:76)
	at eu.isas.reporter.gui.ReporterGUI$19.run(ReporterGUI.java:1106)

linux command-line (different psdb file than above):

org.sqlite.SQLiteException: [SQLITE_CONSTRAINT_PRIMARYKEY]  A PRIMARY KEY constraint failed (UNIQUE constraint failed: data.id)
        at org.sqlite.core.DB.newSQLException(DB.java:909)
        at org.sqlite.core.DB.newSQLException(DB.java:921)
        at org.sqlite.core.DB.throwex(DB.java:886)
        at org.sqlite.core.DB.executeBatch(DB.java:774)
        at org.sqlite.core.CorePreparedStatement.executeBatch(CorePreparedStatement.java:79)
        at com.compomics.util.db.object.ObjectsCache.saveObjects(ObjectsCache.java:350)
        at com.compomics.util.db.object.ObjectsCache.saveCache(ObjectsCache.java:411)
        at com.compomics.util.db.object.ObjectsDB.lock(ObjectsDB.java:784)
        at eu.isas.peptideshaker.export.PsdbExporter.saveAs(PsdbExporter.java:130)
        at eu.isas.peptideshaker.utils.PsdbParent.saveProject(PsdbParent.java:371)
        at eu.isas.reporter.io.ProjectSaver.saveProject(ProjectSaver.java:76)
        at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:557)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)

I don't know what this affects exactly as the output file is generated but I wanted to mention it.

Pom problems of PeptideShaker

Hi,

I tried to compile PeptideShaker by myself in recent days, but from last week it had some problems to compile. The problem is that I cannot download some repositories online. Such as http://genesis.UGent.be/maven2/batik/batik-all/1.6/batik-all-1.6.pom and many ones on 'http://www.ebi.ac.uk/'. But it could work friendly one week ago. Do you have any idea to help me?
I will appreciate it if you have any advice.

Ken

raw/corrected TMT intensities with reporter

Hi, is it possible to export raw/corrected TMT intensities with reporter? I haven't seen an option for this. It would be nice for further processing with e.g. limma.

CLI options display

reporter/src/main/java/eu/isas/reporter/cli/ReporterCLIParameters.java

Line 132 in a7e09fc

output += "\nFor report export options:\nReplace eu.isas.reporter.cli.ReporterCLI with eu.isas.reporter.cli.ReporterCLI\n";

I think this line is supposed to say "replace eu.isas.reporter.cli.ReporterCLI with eu.isas.reporter.cli.ReportCLI"

display issue with Peptide Ratio Normalization

This is a duplicate of the same issue with Peptideshaker (that was fixed).

When doing Peptide Ratio Normalization, you'll see the following (some of it is truncated because it went off the screen to the side):

Peptide Ratio Normalization. Please Wait...
110% 120% 130% 140% 150% 160% 170% 180% 190% 200% 210% 220% 230% 240% 250% 260% 270% 280% 290% 300% 310% 320% 330% 340% 350% 360% 370% 380% 390% 400% 410% 420% 430% 440% 450% 460% 470% 480% 490%>
1010%
1020%
1030%
1040%
1050%
1060%
1070%
1080%
1090%
1100%
1110%
1120%

(it continues on for quite a while).

Thanks for fixing all the issues with reporter. I appreciate it!

problems exporting PSM reports

Hello,

I can successfully export Peptide/Protein reports (both in windows and linux), but cannot export any form of a PSM report regardless of the psdb used.

Here's a sample error log from trying in Windows GUI:

java.lang.NullPointerException: Cannot read the array length because "keys" is null
	at eu.isas.reporter.export.report.sections.ReporterPsmSection.writeSection(ReporterPsmSection.java:188)
	at eu.isas.reporter.export.report.ReporterExportFactory.writeExport(ReporterExportFactory.java:482)
	at eu.isas.reporter.gui.export.ReportDialog$11.run(ReportDialog.java:447)

Here's a sample error log from trying in linux command-line with a different psdb:

java.lang.NullPointerException
        at eu.isas.reporter.export.report.sections.ReporterPsmSection.writeSection(ReporterPsmSection.java:188)
        at eu.isas.reporter.export.report.ReporterExportFactory.writeExport(ReporterExportFactory.java:482)
        at eu.isas.reporter.cli.CLIExportMethods.exportReport(CLIExportMethods.java:91)
        at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:581)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)

Thanks!

Label that should be zero shows ratios up to 50%?

We have a test plate that was done with 10 of the 11plex TMT labels. So, the intensities of the 11th label should be almost zero, plus the leakage from the 10th label due to 13C content. Although we observe a substantial drop in the intensities, we see ratios up to 50 percent compared to the highest reference intensity, which is the maximum of the intensities of the other labels. Is that something you would expect? Is this due to the normalization?

I was using Reporter 0.7.17 from command line without specifying a reference sample. Pretty much default configuration, created the default protein report.

How to export TMT11plex quantification?

I wonder whether it is possible to export the quantification results from shaker. I saw the reports that can be exported, but they seem to be identical to the once that PeptideShaker creates? Ideally, I am looking for a way to do export the quantification data from the commandline in linux.

An error occurred while generating the output

Hello,

For several samples Reporter gives me this error message (in the title of this issue) for no obvious reason. They were created on a Galaxy instance wiht SearchGUI 3.2.13.4 and PeptideShaker 1.16.17.

Here is a sample I gave as an input file to Reporter: https://drive.google.com/file/d/19XjNknhqBE1qhEhWPTQZF5C7IpqM6Xtw

Is it because Reporter can't read output of old SearchGUI and PeptideShaker versions ?

Best regards,
David S.

linux command-line requires data folder

Hello,

When importing a psdb in linux (command line), it's required that the data folder inside searchgui_out.zip is present.

For example, if the psdb file is at /data/test, there needs to be a folder /data/test/data containing the files from the data folder inside searchgui_out.zip

There also doesn't seem to be an option to do -identification_files to select the searchgui_out.zip as with peptideshaker.

Thanks!

problem using custom exports

I have not been able to use custom exports when using Reporter from (linux) command line.

It works successfully in Windows GUI (creating exportFactory.json and exporting the report) and then I will use the same exportFactory.json from the command line.

paths.txt contains the proper directory:

reporter_exports=/home/jamie/jcms_projects/jc/pnnl/scripts/reporter

Within this directory is exportFactory.json generated as mentioned above.

Running reporter then generates the log entry showing the custom report isn't recognized:

java.lang.IllegalArgumentException: Unrecognized report type: 13. Available reports are: 0: Certificate of Analysis, 1: Default Hierarchical Report, 2: Default PSM Phosphorylation Report, 3: Default PSM Report, 4: Default PSM Report with non-validated matches, 5: Default Peptide Phosphorylation Report, 6: Default Peptide Report, 7: Default Peptide Report with non-validated matches, 8: Default Protein Phosphorylation Report, 9: Default Protein Report, 10: Default Protein Report with non-validated matches, 11: Extended PSM Report, 12: Fractions Report.
        at eu.isas.peptideshaker.export.PSExportFactory.getExportTypeFromCommandLineOption(PSExportFactory.java:749)
        at eu.isas.reporter.cli.ReportCLIInputBean.<init>(ReportCLIInputBean.java:68)
        at eu.isas.reporter.cli.ReporterCLIInputBean.<init>(ReporterCLIInputBean.java:335)
        at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:352)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)

I noticed paths.txt also has a peptideshaker_exports entry so I manually updated it to be the directory above.

peptideshaker_exports=/home/jamie/jcms_projects/jc/pnnl/scripts/reporter

Now if I run reporter, I get the following log entry:

java.io.FileNotFoundException: File resources not found.
        at eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.loadPathParametersFromLine(PeptideShakerPathParameters.java:214)
        at eu.isas.reporter.preferences.ReporterPathPreferences.loadPathParametersFromLine(ReporterPathPreferences.java:153)
        at eu.isas.reporter.preferences.ReporterPathPreferences.loadPathParametersFromFile(ReporterPathPreferences.java:126)
        at eu.isas.reporter.cli.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:132)
        at eu.isas.reporter.cli.PathSettingsCLI.extractAndUpdatePathOptions(PathSettingsCLI.java:275)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:822)

Furthermore, now within the exports directory listed above is the file: reporter_exportFactory.cus containing:

{
  "userSchemes": {}
}

The next thing I tried is renaming exportFactory.json that I generated to both reporter_exportFactory.json and reporter_exportFactory.cus but neither helped (same log entries mentioned above).

Anyway, I haven't been able to find any sort of workaround to get this issue resolved to be able to suggest how it can be fixed.

I'll also note that I have no problems using exportFactory.json (generated in Windows PeptideShaker) in the command-line version of PeptideShaker.

Thanks!

Support for MS3-based quantification

Hi reporter-team,

I'm encountering an error when processing PeptideShaker results. I've attached the bug report, I'd gladly share the PeptideShaker reults, but they are too big (even when compressed) to attach them here. I can send them via e.g. wetransfer.
Reporter 0.9.7 log.txt
Your help would be much appreciated!!

Best regards,
David

Unrecognized option: -id, -isotopes, -methods_file

Good day,

I am running Reporter-0.7.15 on a server and I have installed it on each computer node, so all should be running fine. According the the info page in cmd line for Reporter the input options "-id" is mandatory, and either "-isotopes" OR "-methods_file" should identify the .xml file with isotope specifications ( I have tried both, with reference to #6 recommendations). Except that the following errors are still occurring. What could the reason for this be? Are there any alternate options?

Fri May 03 10:36:31 SAST 2019: Reporter version 0.7.15.
Memory given to the Java virtual machine: 28631367680 b.
Total amount of memory in the Java virtual machine: 2022178816 b.
Free memory: 1958823720 b.
Java version: 1.8.0_181.
org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -id
at org.apache.commons.cli.Parser.processOption(Parser.java:363)
at org.apache.commons.cli.Parser.parse(Parser.java:199)
at org.apache.commons.cli.Parser.parse(Parser.java:85)
at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Fri May 03 10:38:12 SAST 2019: Reporter version 0.7.15.
Memory given to the Java virtual machine: 28631367680 b.
Total amount of memory in the Java virtual machine: 2022178816 b.
Free memory: 1958823720 b.
Java version: 1.8.0_181.
org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -isotopes
at org.apache.commons.cli.Parser.processOption(Parser.java:363)
at org.apache.commons.cli.Parser.parse(Parser.java:199)
at org.apache.commons.cli.Parser.parse(Parser.java:85)
at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Fri May 03 10:41:11 SAST 2019: Reporter version 0.7.15.
Memory given to the Java virtual machine: 28631367680 b.
Total amount of memory in the Java virtual machine: 2022178816 b.
Free memory: 1958823720 b.
Java version: 1.8.0_181.
org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -methods_file
at org.apache.commons.cli.Parser.processOption(Parser.java:363)
at org.apache.commons.cli.Parser.parse(Parser.java:199)
at org.apache.commons.cli.Parser.parse(Parser.java:85)
at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Here is my bash command(s):
java -cp $REPORTER eu.isas.reporter.cli.ReporterCLI -in "/nlustre/users/dwilson/peptideshaker_output/MGF_100/FU_100/CDK/HDB/Rep1/ps_output_CDK100HDB_SM_FT_1_1.cpsx" -methods_file "/nlustre/users/dwilson/ZippedData/defaultMethods.xml" -out "/nlustre/users/dwilson/Reporter_Output/MGF_100/FU_100/CDK/HDB/FT/Rep1/Quant_output_CDK100HDB_SM_FT_1_1.cpsx" -zip "/nlustre/users/dwilson/Reporter_Output/MGF_100/FU_100/CDK/HDB/FT/Rep1/Quant_output_CDK100HDB_SM_FT_1_1.zip" -threads 8 -temp_folder "/nlustre/users/dwilson/Reporter_Output/TEMPSTORE/HDB/FU_100/FT/Rep1" -log "/nlustre/users/dwilson/Reporter_Output/logs/HDB/FU_100/FT/Rep1"

There is only 1 method listed in the methods file.
Thanks!
Denise

Reporter error

Hi,

I tried to use reporter for my iTRAQ8 experiment. I tried to open the Peptideshaker results with reporter. But reporter is constantly giving this error message. The number of clusters cannot be bigger than the number of samples: #clusters:18, #samples:14. It also says please contact the developers if this persists.

I appreciate your help

Thanks

Nijat

How to set the labelling method (TMT10/11, iTRAQ, ...) on command line

Hi,

Can the labelling method be set when running Reporter command line? If so, how is this done? I can't find that info when using either PathSettingsCLI or ReporterCLI

Kind regards,
Steve

Reporter report not containing per-sample ratios following demultiplexing

Hi,

We're running the following Reporter commands to obtain a report containing the individual sample ratios using a TMT 11-plex pool

java -cp Reporter-0.12.0/Reporter-0.12.0.jar eu.isas.reporter.cli.ReporterCLI -method 'TMT 11-plex' -id sample.psdb -out sample_reporter.psdb -temp_folder /var/tmp

java -cp Reporter-0.12.0/Reporter-0.12.0.jar eu.isas.reporter.cli.ReportCLI -in sample_reporter.psdb -out ./ -report_prefix Reporter_ -reports 6,12 -temp_folder /var/tmp

However, this results in the default peptide report not containing any per-sample ratios. It only has the following columns, of which the 'Raw Ratios' and 'Normalized Ratios' columns are empty

Protein(s)
Unique Protein Group
Protein Group(s)
#Validated Protein Group(s)
Position
AAs Before
Sequence
AAs After
Modified Sequence
Fixed Modifications
Variable Modifications
Localization Confidence
#Validated PSMs
#PSMs
Confidence [%]
Validation
Raw Ratios
Normalized Ratios

What command do we need to run to obtain a report containing values for each individual label?

Thanks in advance,
Steve

ReporterCLI parameters call error

Not sure if you are interested in hearing about errors in the CLI version of Reporter, but I have been playing around with the CLI version a bit on a linux cluster.

But just in case, just when trying to look up some more detailed input parameters:

java -cp /projects/ptx_analysis/chughes/software/reporter_apr2018/Reporter-0.7.9/Reporter-0.7.9.jar eu.isas.reporter.cli.ReporterCLIParameters
Error: Main method not found in class eu.isas.reporter.cli.ReporterCLIParameters, please define the main method as:
public static void main(String[] args)

Error when exporting paths.txt

Hello,

If I try to use eu.isas.peptideshaker.cmd.PathSettingsCLI to export paths.txt, I get the following error:

An error occurred when saving the path preference to /dir/Reporter-0.9.1/lib/resources/conf/paths.txt.

Here is the relevant log info:

java.lang.RuntimeException: java.io.FileNotFoundException: /dir/Reporter-0.9.1/lib/resources/conf/paths.txt (No such file or directory)
        at com.compomics.util.io.flat.SimpleFileWriter.<init>(SimpleFileWriter.java:59)
        at eu.isas.peptideshaker.preferences.PeptideShakerPathParameters.writeConfigurationToFile(PeptideShakerPathParameters.java:391)
        at eu.isas.peptideshaker.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:114)
        at eu.isas.peptideshaker.cmd.PathSettingsCLI.call(PathSettingsCLI.java:47)
        at eu.isas.peptideshaker.cmd.PathSettingsCLI.main(PathSettingsCLI.java:200)
Caused by: java.io.FileNotFoundException: /dir/Reporter-0.9.1/lib/resources/conf/paths.txt (No such file or directory)
        at java.base/java.io.FileOutputStream.open0(Native Method)
        at java.base/java.io.FileOutputStream.open(FileOutputStream.java:291)
        at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:234)
        at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:184)
        at java.base/java.io.FileWriter.<init>(FileWriter.java:96)
        at com.compomics.util.io.flat.SimpleFileWriter.<init>(SimpleFileWriter.java:53)
        ... 4 more

I notice that Peptideshaker saves to resources/conf/paths.txt whereas Reporter is trying to save to lib/resources/conf/paths.txt so perhaps that is part of the issue (no conf dir in lib/resources?). The Reporter log is also going into lib/resources/ rather than just resources.

Thanks!

Manual available?

We are trying to find a manual, documentation for Reporter. Is it able to do TMT11plex MS3 quantification?
kind regards

Isotopes XML file

Greetings

I'm trying to perform quantification with ReporterCLI, and would like to know if there is an example available of an isotope correction factors xml file to give as input. Are these files usually supplied by the laboratories performing the mass spectrometry? Also, what separates the "isotopes" file from the "methods_file"?

Thank you for your attention