[Psidev-ms-dev] TraML - Multiple locations for RetentionTimeType and ConfigurationType

[Kenny H. <ken...@ug...>]

Dear community,

While working with the TraML format, I observed that there are multiple locations to place a RetentionTimeType or ConfigurationType fields.

For instance, the retention time can be described both on the PeptideType and the TransitionType. So what happens when the user specifies two different values for a single transition? And anyone help me with a use case where the TransitionType is expected to occur at a different time then the PeptideType?

Similarly, the ConfigurationTypes can be placed on the TargetType, ProductType and IntermediateProductType. When is it possible for the ProductType and the IntermediateProductType to have (e.g.) different collision energy values?

Many thanks in advance,



Kenny Helsens, PhD
 
Computational Omics and Systems Biology Group
Department of Medical Protein Research
Universiteit Gent - VIB
 
A. Baertsoenkaai 3
B9000 Gent
Belgium
 
Tel: +32-92649359
Fax: +32-92649484

Skype: kennyhelsens