[Psidev-ms-dev] Essential element on mzQuantML consideration

[Mi-Youn B. <mbr...@sy...>]

Dear PSI mzQuantML discussion participants,

 

1.       Background of APML

Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008
with APML (Annotated Putative peptide Markup Language) that enables using
several different ms1 peak extraction and alignment modules. After
publication, Damon May, who is a lead developer on MSInspect from Fred
Hutchinson Cancer Research Center, initiated to use APML for broader use for
MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After
review and merging all institutions' needs for capturing MS1 dataset, we
introduced APML v2.0 schema and java written parsers
(http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch
introduced APML v2.0 to PSI in 2008.

 

2.       mzQuantML that Oliver is leading.

Recent my visit to Oliver Kohlbacher group in University of Tubingen and
meeting with Peter Horvatovich from University of Groningen in HUPO Sydney,
The mzQuantML schema and availability of its parser and validator can be an
important contribution to bioinformatician and computational biologists, who
develop or process MS1 based dataset for biological system studies.

 

3.       Essential elements in the schema

To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter's group) are
using APML v2.0, it would be nice (or rather essential) to have some of
elements that can capture essential dataset to reproduce or reprocessing
(e.g., statistical analysis on quantification etc). Thus, without further
explanation, I have absolute agreement on Dr. Kohlbacher comments on
"complexity is expected"  posted on Sep 13 to this mailing list.  The
"feature" element is an absolute "must" for MS1 based pipeline. In my
experience and perspective of continuous usage of Corra for several
biomarker discovery projects, we need the feature element for mzQuantML  and
it will help for broad future mzQuantML schema in proteomics community.

 

Thank you for reading.

 

Warm Regards,

Mi-Youn

 

Mi-Youn Brusniak, Ph.D.

Computational Biology

Seattle Proteome Center

mbr...@sy...

Tel: (206)732-1327

 

 

Mi-Youn Brusniak, Ph.D.

Computational Biology

Seattle Proteome Center

mbr...@sy...

Tel: (206)732-1327