Difficulty loading a new ref-annotion for proteomics

[rlr...@umich.edu]

All-

I have tried loading some proteomic data into an instance of TranSMART, but it appears that I do not have the correct annotation loaded in order to map the readings to proteins.  I can see that I am able to search for the proteins that I know were measured in my dataset, but when I look for the information in the annotation tables for proteomics annotations, I cannot find these proteins.  

In order to understand whether I was loading the dataset correctly, I have loaded the SanofiV14Proteomics sample dataset and the ref_annotation that goes with that dataset (the msproteomics annotation), but this annotation does not contain the proteins that are measured in the dataset I am trying to load.

I have searched to understand how to create my own ref-annotation, but when I try to load one that I have created, I don't see the ref-annotation in the database in the same place as I saw the msproteomics one.  I was hoping someone out there could help me understand what the annotation definition file should look like, and how to load it.  The one piece of information that I am missing, and am unable to get is the peptide sequence that is associated with the given protein measured.  I am unsure if this is the reason I am unable to load this annotation correctly, or if there is something else happening.

Any help would be greatly appreciated!  

Thanks!

Becky Reamy