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• Harald Marx

[Harald Marx]

Questions and Answers

Q: How to start MScDB?

A: Open a console, navigate to the directory containing MScDB.v1.00.jar, type

java -jar MScDB.v1.00.jar

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Q: Starting errors?

A: Maybe a version issue (< 1.6), check the java version in console, type

java -version

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Q: How to create the settings.xml?

A: Open a text editor, copy the default settings, save the file as settings.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
<properties>
<comment/>
<entry key="PROTEASE">(?!RP)(?!KP)[K,R]</entry>
<entry key="IN_DIR_OR_FILE">ABSOLUTE PATH TO FILE OR DIRECTORY</entry>
<entry key="META_FILE"></entry>
<entry key="IN_FILE_FORMAT">1</entry>
<entry key="LENGTH_MIN">8</entry>
<entry key="LENGTH_MAX">26</entry>
<entry key="PROTEIN_CLUSTERING">true</entry>
<entry key="OUT_FILE_FORMAT">1</entry>
<entry key="MASS_MIN">883.4605</entry>
<entry key="MASS_MAX">2825.4963</entry>
<entry key="THRESHOLD_MISMATCH">2</entry>
<entry key="THRESHOLD_DETECTABILITY">0.8</entry>
<entry key="LENGTH">false</entry>
<entry key="MISS_CLEAVAGES">1</entry>
<entry key="VERSION">1.00</entry>
<entry key="META_FILE_FORMAT">2</entry>
<entry key="META">false</entry>
<entry key="MASS">true</entry>
<entry key="THRESHOLD">true</entry>
<entry key="OUT_DIR">ABSOLUTE PATH DIRECTORY</entry>
</properties>

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Q: Important parameters?

IN_DIR_OR_FILE, META_FILE, OUT_DIR

have to be absolute paths (with trailing slash), e.g. /home/user/IN_DIR/ or C:\home\user\OUT_DIR\ . To omit meta information, use an empty entry (see above).

PROTEIN_CLUSTERING
has to be true, otherwise MScDB generates only the in-silico digest.

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Q: How to start MScDB with settings?

A: Open a console, navigate to the directory containing MScDB.v1.00.jar, type

java -jar MScDB.v1.00.jar settings.xml