main

news

software

Glossolalia

mzXML SchemaReAdWMassWolfmzStarRAMPJRAPRAMPvalidateXML mzXML ViewerInsilicosViewerreadmzXML

MS/MS Interpretation

Probability Assignment

Protein Quantification

Curation of Protein IDs

Miscellaneous

TPP

LC-MS

data repository

developers

contact

This project is hosted at


software

Glossolalia: a common language for MS data

mzXML Schema

This is the schema for mzXML (the common file format for MS data).

Stable version (2.1):
View mzXML Schema
View mzXML Schema Documentation
and even more mzXML Schema Documentation

Version 2.0 of the mzXML schema introduces the use of ontologies. Here you will find the current draft of the mzXML ontology in Excel format.

ReAdW (ThermoFinnigan Xcalibur to mzXML)

Visual C++ program to convert Xcalibur native acquisition files to mzXML. The program is based on the XRawfile dll from ThermoFinnigan. The XRawfile library can be found in the Xcalibur directory. Please see the ReAdW page on the SPC Tools wiki for more information, including download instructions.

MassWolf (Micromass MassLynx to mzXML)

Visual C++ program to convert MassLynx native acquisition files to mzXML. The program is based on the DAC library from Waters. The DAC library can be found in the MassLynx directory. Please see the massWolf page on the SPC Tools wiki for more information, including download instructions.

mzStar (SCIEX/ABI Analyst to mzXML)

Visual Basic application to convert data from a SCIEX/ABI Q-STAR instrument into mzXML format. This application is based on a VB library provided by the Analyst software, which is therefore required to be present on the same machine the converter will be used on. Please see the mzStar page on the SPC Tools wiki for more information, including download instructions.

JRAP and RAMP

This is the port of RAP to java. The jrap package is contained in the jrap.jar file. This file can just be added to your classpath to use the code in there, you can run it as an executable jar ("java -jar jrap.jar") to get guidelines on how to run the graphical spectrum viewer or you can just unpack the archive by running "jar xf jrap.jar" to take a look at the source code. There's also a readme.txt file in the root directory of the jar file. Go to download page
Read Jrap documentation online

Random Access Minimal Parser. Is a very simple C parser for mzXML files. It doesn't have the extensive controll options offered by the Xerces parser in RAP, but it is much faster. Also, it is tolerant of missing or broken indexes and will read the PSI-HUPO mzData format.
Go to the CVS repository

validateXML

Schema and sha1-sum validation of an mzXML instance document.
Go to the CVS repository

mzXML Viewer

A Java based viewer for mzXML instance documents

InsilicosViewer

A free viewer for mzXML with most of the functionalities offered by its commercial counterparts. Also, multiple runs can be loaded and visualized at the same time.
Go to the download page

readmzXML

A simple C application based on RAMP to parse mzXML files.
Please see the readmzXML page on the SPC Tools wiki for more information, including download instructions.