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Re: [Psidev-pi-dev] (no subject)
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From: Jones, A. <And...@li...> - 2008-06-02 08:29:50
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Hi Pierre-Alain,
We already have a separate mechanism for reporting mods found (1):
<Peptide identifier="3_1">
<Modification location="5">
<pf:cvParam accession="MOD:00412" name="Oxidation (M)" cvRef="PSI-MOD"/>
The discussion here is about how to record the mods searched for (2). I’ll put out a schema proposal later today but the basic idea is to encode whether a search mod is fixed/variable, with the option for adding cvParams to encode more complex rules. We also plan to encode the modification mass used by the search engine, since it might not be the exact value that is encoded in the cv.
Cheers
Andy
From: psi...@li... [mailto:psi...@li...] On Behalf Of Pierre-Alain Binz
Sent: 01 June 2008 19:57
To: Martin Eisenacher
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] (no subject)
Hi all,
I'm not sure about the goal here. Is it
1) to encode actual modifications found in the identified peptides / molecules
2) to encode the rules that the search engines are using
In the case of 1) I do not see for instance the reason for the "variable/fixed" item
In the case of 2) It looks difficult to encode all, as tools will even implement those rules in very different manner (things like maximal number of occurences per peptide, or more non-explicit searches like the error-tolerant search button in Mascot, or the default list of mods in Paragon / Modiro etc)
Maybe we should do both, but in different manners.
Please clarify here...
Pierre-Alain
Martin Eisenacher wrote:
Hi from Bochum!
Find attached a schema draft of a
<ModificationParams> element with
example.
It is for the description of
modification parameters of a search
engine.
Most characteristics of a modification
(like formula or mass shift) are part
of the PSI-MOD CV (obo cross
references).
Idea: attributes sensitivity
(fixed/variable), masstype (mono/avg)
and
origins (to specify modification sites
explicitely);
elements othersensitivity and
othermasstype for extensions or special
cases (e.g. phenyx' tolerance on
fixed/variable type).
To discuss: a special "neutral loss"
element.
Bye
Martin
________________________________
<?xml version="1.0" encoding="UTF-8"?>
<!--W3C Schema generated by XMLSpy v2007 sp1 (http://www.altova.com)-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" <http://www.w3.org/2001/XMLSchema> >
<xs:complexType name="cvParamType" abstract="false">
<xs:attribute name="cvRef" type="xs:string" use="required">
</xs:attribute>
<xs:attribute name="accession" type="xs:string" use="required">
</xs:attribute>
<xs:attribute name="value" type="xs:string">
</xs:attribute>
<xs:attribute name="name" type="xs:string" use="required">
</xs:attribute>
<xs:attribute name="unitAccession" type="xs:string">
</xs:attribute>
<xs:attribute name="unitName" type="xs:string">
</xs:attribute>
</xs:complexType>
<xs:element name="cvParam" type="cvParamType" abstract="false"/>
<xs:element name="othersensitivity">
<xs:annotation>
<xs:documentation>Specify extensions to "fixed" and "variable" or specify other sensitivities (using CV).</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="cvParam"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="othermasstype">
<xs:annotation>
<xs:documentation>Specify extensions to "monoisotopic" or "averageisotopic" or specify other mass types (using CV).</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="cvParam"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="oneModificationParam">
<xs:annotation>
<xs:documentation>Details of one modification parameter (most characteristics contained in PSI-MOD CV !).</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="cvParam"/>
<xs:element ref="othersensitivity" minOccurs="0"/>
<xs:element ref="othermasstype" minOccurs="0"/>
</xs:sequence>
<xs:attribute name="identifier" use="required">
<xs:simpleType>
<xs:restriction base="xs:string">
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="sensitivity" use="required">
<xs:annotation>
<xs:documentation>Specify whether modification occurs always ("fixed") or sometimes ("variable"). If "other", sub-element othersensitivity must be present.</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="fixed"/>
<xs:enumeration value="variable"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="masstype" use="required">
<xs:annotation>
<xs:documentation>Specify whether mass type is monoisotopic or avergaeisotopic. If "other", sub-element othermasstype must be present.</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="monoisotopic"/>
<xs:enumeration value="averageisotopic"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="origins" use="optional">
<xs:annotation>
<xs:documentation>Possible sites (amino acids).</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string"/>
</xs:simpleType>
</xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="ModificationParamsExamples">
<xs:complexType>
<xs:sequence>
<xs:element ref="ModificationParams"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="ModificationParams">
<xs:annotation>
<xs:documentation>Set of all modification parameters used for a spectrum search.</xs:documentation>
</xs:annotation>
<xs:complexType>
<xs:sequence>
<xs:element ref="oneModificationParam" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:element>
</xs:schema>
________________________________
<?xml version="1.0" encoding="UTF-8"?>
<!-- edited with XMLSpy v2007 sp1 (http://www.altova.com) by eisenach (MPC) -->
<ModificationParamsExamples xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" <http://www.w3.org/2001/XMLSchema-instance> xsi:noNamespaceSchemaLocation=".\modifications_temp.xsd">
<ModificationParams>
<oneModificationParam identifier="Oxidation_M_NL80" sensitivity="variable" masstype="monoisotopic">
<cvParam accession="MOD:00768" name="methionine oxidation with neutral loss of 80 Da" cvRef="PSI-MOD"/>
</oneModificationParam>
<oneModificationParam identifier="Oxidation_M_NL64" sensitivity="variable" masstype="monoisotopic">
<cvParam accession="MOD:00935" name="methionine oxidation with neutral loss of 64 Da" cvRef="PSI-MOD"/>
</oneModificationParam>
<oneModificationParam identifier="Carbamido" sensitivity="fixed" masstype="monoisotopic" origins="C"> <!-- MOD:00397 has possible origins H, K, C, E, D -->
<cvParam accession="MOD:00397" name="iodoacetamide derivative" cvRef="PSI-MOD"/>
</oneModificationParam>
<oneModificationParam identifier="Phospho_S" sensitivity="fixed" masstype="monoisotopic">
<cvParam accession="MOD:00046" name="O-phosphorylated L-serine" cvRef="PSI-MOD"/>
</oneModificationParam>
<oneModificationParam identifier="Phospho_T" sensitivity="fixed" masstype="monoisotopic">
<cvParam accession="MOD:00047" name="O-phosphorylated L-threonine" cvRef="PSI-MOD"/>
</oneModificationParam>
<oneModificationParam identifier="Phospho_Y" sensitivity="fixed" masstype="monoisotopic">
<cvParam accession="MOD:00048" name="O4'-phosphorylated L-tyrosine" cvRef="PSI-MOD"/>
</oneModificationParam>
<!-- example for "other" elements: phenyx -->
<oneModificationParam identifier="Fantasy" sensitivity="fixed" masstype="averageisotopic" >
<cvParam accession="" name="Fantasy" cvRef="PSI-MOD"/>
<othersensitivity>
<cvParam accession="" name="phenyx-tolerance" cvRef="PSI-MOD" value="n-1"/>
</othersensitivity>
<othermasstype>
<cvParam accession="" name="SomethingVerySpecial" cvRef="PSI-MOD" value="" unitAccession="" unitName=""/>
</othermasstype>
</oneModificationParam>
</ModificationParams>
</ModificationParamsExamples>
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