Modifications.xml - Revision history

Mtrevisan at 10:16, 26 May 2017

2017-05-26T10:16:28Z

Mtrevisan at 10:05, 26 May 2017

2017-05-26T10:05:07Z

Mtrevisan at 09:56, 26 May 2017

2017-05-26T09:56:58Z

Mtrevisan at 09:54, 26 May 2017

2017-05-26T09:54:50Z

Mtrevisan: Created page with "'''modifications.xml''' is a configuration file used by QuiXoT and pRatio. It includes information about the modifications considered in the experiment. QuiXoT tags se..."

2017-05-26T09:52:47Z

Created page with "'''modifications.xml''' is a configuration file used by QuiXoT and pRatio. It includes information about the modifications considered in the experiment. QuiXoT tags se..."

New page

'''modifications.xml''' is a configuration file used by [[QuiXoT]] and [[pRatio]]. It includes information about the modifications considered in the experiment. QuiXoT tags sequence post-translational modifications using the former SEQUEST notation, with a non-alphanumerical ASCII character (such as @#*^) following the single-character code of the modified amino acid; for example, IM@ADDYGWDVTDAR is the peptide IMADDYGWDVTDAR with a modification in methionine (which could be, for example, a methionine oxidation).

When pRatio finds a modification while generating the QuiXML file, it will first look into the modifications.xml file to check if it has been already assigned a character there. If no character is found for the corresponding modification, pRatio will assign a new character by order of appearance, including it in this file. To avoid confusion, it is convenient to use always the same modifications.xml file with the common modifications along a project.

Currently, up to 30 modifications are usable; each of them is used by pRatio in the following default order:

*#@^-${_!=|(){}][:;+0123456789

← Older revision		Revision as of 10:05, 26 May 2017
Line 7:		Line 7:

	*#@^-${_!=\|(){}][:;+0123456789		*#@^-${_!=\|(){}][:;+0123456789
		+
		+	You can find here a sample file: [[File:Modifications.zip]].

	[[Category:Configuration files]]		[[Category:Configuration files]]

← Older revision		Revision as of 09:56, 26 May 2017
Line 1:		Line 1:
		+	{{lowercase}}
	'''modifications.xml''' is a configuration file used by [[QuiXoT]] and [[pRatio]]. It includes information about the modifications considered in the experiment. QuiXoT tags sequence post-translational modifications using the former SEQUEST notation, with a non-alphanumerical ASCII character (such as @#*^) following the single-character code of the modified amino acid; for example, IM@ADDYGWDVTDAR is the peptide IMADDYGWDVTDAR with a modification in methionine (which could be, for example, a methionine oxidation).		'''modifications.xml''' is a configuration file used by [[QuiXoT]] and [[pRatio]]. It includes information about the modifications considered in the experiment. QuiXoT tags sequence post-translational modifications using the former SEQUEST notation, with a non-alphanumerical ASCII character (such as @#*^) following the single-character code of the modified amino acid; for example, IM@ADDYGWDVTDAR is the peptide IMADDYGWDVTDAR with a modification in methionine (which could be, for example, a methionine oxidation).

← Older revision		Revision as of 09:54, 26 May 2017
Line 6:		Line 6:

	*#@^-${_!=\|(){}][:;+0123456789		*#@^-${_!=\|(){}][:;+0123456789
		+
		+	[[Category:Configuration files]]

@@ Line 2: / Line 2: @@
 '''modifications.xml''' is a configuration file used by [[QuiXoT]] and [[pRatio]]. It includes information about the modifications considered in the experiment. QuiXoT tags sequence post-translational modifications using the former SEQUEST notation, with a non-alphanumerical ASCII character (such as @#*^) following the single-character code of the modified amino acid; for example, IM@ADDYGWDVTDAR is the peptide IMADDYGWDVTDAR with a modification in methionine (which could be, for example, a methionine oxidation).
-When pRatio finds a modification while generating the QuiXML file, it will first look into the modifications.xml file to check if it has been already assigned a character there. If no character is found for the corresponding modification, pRatio will assign a new character by order of appearance, including it in this file. To avoid confusion, it is convenient to use always the same modifications.xml file with the common modifications along a project.
+When pRatio finds a modification while generating the QuiXML file, it will first look into the modifications.xml file to check if it has been already assigned a character there. If no character is found for the corresponding modification, pRatio will assign a new character by order of appearance, including it in this file. To avoid confusion, '''it is convenient to use always the same modifications.xml file with the common modifications along a project'''.
 Currently, up to 30 modifications are usable; each of them is used by pRatio in the following default order: