Software:ProbID
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| + | ==Overview== | ||
| + | ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence database. It computes z scores for the identifications and output the results in pepXML format, which subsequently can be analyzed by the [[Software:TPP|TPP]] (Trans-Proteomic Pipeline). ProbID is written in Java. | ||
| + | |||
| ==Getting the software== | ==Getting the software== | ||
| - | You can also download from the [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=156703 Sashimi File Release page on SourceForge] and access source code at [http://sashimi.cvs.sourceforge.net/sashimi/ProbID/ SourceForge cvs]. | + | ===Downloading the package=== |
| + | You can download from the [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=156703 Sashimi File Release page on SourceForge]. The package includes | ||
| + | *ProbIDALL.jar This is the main package of software to identify peptides from MS/MS spectra using protein sequence database (FASTA format). This jar file includes both the source code and binary class files. | ||
| + | * probid.param This is the parameter file for doing peptide searches. | ||
| + | * example.dta This is the file format of MS/MS spectra that ProbID takes. | ||
| + | * runprobid.pl This is the script that takes a your_file.mzXML and returns a your_file.xml which can be analyzed by TPP (Trans-Proteomic Pipeline). | ||
| + | * runprobiddta.pl This is a script that batch processes all your .dta files in a directory. | ||
| + | * README basic information. | ||
| + | |||
| + | ===Source Code=== | ||
| + | Source is accessible from Sashimi SVN ('''add svn link'''). | ||
| + | |||
| + | ==Installation== | ||
| + | Assuming you've downloaded the package, first unzip ProbID.tgz: | ||
| + | tar -xzf ProbID.tgz | ||
| + | * set up "CLASSPATH" environment variable for ProbIDALL.jar | ||
| + | * you need either jre1.4 (or above) or j2sdk1.4 (or above) installed on your machine. | ||
| + | * ProbID was written in java and can be run on almost any OS. | ||
| + | |||
| + | ==Running ProbID== | ||
| + | ProbID may be run in single-spectrum or batch processing modes. ''Both options require you to have probid.param in the same directory where your data is located.'' | ||
| + | |||
| + | ===single MS/MS spectrum processing=== | ||
| + | java org.systemsbiology.dbsearch.ProbID your_file.dta | ||
| + | OR if you didn't set up the "CLASSPATH" variable | ||
| + | Java -cp where_ProbIDALL.jar_is org.systemsbiology.dbsearch.ProbID your_file.dta | ||
| + | |||
| + | ===batch processing of many .dta files on one computer=== | ||
| + | perl runprobid.pl your_file.mzXML. | ||
| + | You do need "mzxml2other" installed on your machine to start from your_file.mzXML. If you already have all .dta files in current directory, use runprobiddta.pl. | ||
| + | perl runprobiddta.pl | ||
| - | ==In a nutshell== | + | '''Note: should we recommend MzXML2Search instead of mzxml2other?''' |
| - | ProbID is an open-source search engine | + | |
| - | ==More info== | + | ===ProbID and the TPP=== |
| - | Coming soon... | + | Please see the [[TPP:ProbID and the TPP|ProbID and the TPP]] page. |
| ==Reference== | ==Reference== | ||
| Coming soon... | Coming soon... | ||
Current revision
Contents |
[edit]
Overview
ProbID is a software tool designed to identify peptides from tandem mass spectra using a protein sequence database. It computes z scores for the identifications and output the results in pepXML format, which subsequently can be analyzed by the TPP (Trans-Proteomic Pipeline). ProbID is written in Java.
[edit]
Getting the software
[edit]
Downloading the package
You can download from the Sashimi File Release page on SourceForge. The package includes
- ProbIDALL.jar This is the main package of software to identify peptides from MS/MS spectra using protein sequence database (FASTA format). This jar file includes both the source code and binary class files.
- probid.param This is the parameter file for doing peptide searches.
- example.dta This is the file format of MS/MS spectra that ProbID takes.
- runprobid.pl This is the script that takes a your_file.mzXML and returns a your_file.xml which can be analyzed by TPP (Trans-Proteomic Pipeline).
- runprobiddta.pl This is a script that batch processes all your .dta files in a directory.
- README basic information.
[edit]
Source Code
Source is accessible from Sashimi SVN (add svn link).
[edit]
Installation
Assuming you've downloaded the package, first unzip ProbID.tgz:
tar -xzf ProbID.tgz
- set up "CLASSPATH" environment variable for ProbIDALL.jar
- you need either jre1.4 (or above) or j2sdk1.4 (or above) installed on your machine.
- ProbID was written in java and can be run on almost any OS.
[edit]
Running ProbID
ProbID may be run in single-spectrum or batch processing modes. Both options require you to have probid.param in the same directory where your data is located.
[edit]
single MS/MS spectrum processing
java org.systemsbiology.dbsearch.ProbID your_file.dta
OR if you didn't set up the "CLASSPATH" variable
Java -cp where_ProbIDALL.jar_is org.systemsbiology.dbsearch.ProbID your_file.dta
[edit]
batch processing of many .dta files on one computer
perl runprobid.pl your_file.mzXML.
You do need "mzxml2other" installed on your machine to start from your_file.mzXML. If you already have all .dta files in current directory, use runprobiddta.pl.
perl runprobiddta.pl
Note: should we recommend MzXML2Search instead of mzxml2other?
[edit]
ProbID and the TPP
Please see the ProbID and the TPP page.
[edit]
Reference
Coming soon...
