needles in the migraine haystack, cerebrospinal fluid biomarkers

Needles in the migraine haystack, cerebrospinal fluid biomarkers

Company: Huntington Medical Research InstitutesMentors:

Alfred Fonteh Ph.D., Mike Harrington M.B. Ch.B., F.R.C.P.

Intern: Samuel WeinEarlham College, IN. USA

Uncovering the protein changes brought about by migraine

Goal: To process MS/MS data to graph the levels of proteins from cerebrospinal fluid (CSF) during migraine and then combine these graphs with protein protein interaction data to create a map

of expressions.

Why do we care?

Chronic Migraine is a debilitating disorder affecting as many as 10% of people

Migraine has a direct medical cost of over $1 billion dollars

By understanding how the brain changes during migraine we come closer to finding better treatments

CSF is a likely pool for biomarkers as it is within the blood brain barrier

What is migraine?

A neurological disorder which manifests in severe headaches, photophobia, phonophobia, and nausea

Caused by over-excitation of various nerves

What is CSF?

Produced in the brain Pushed down spinal

column where it is absorbed

Physically protects the brain

Acts as a conduit for signals

What I am doing

Taking protein sequence data from CSF samples taken over a four day period

Using existing databases to find how the proteins interact

Mapping expression levels of each protein every day onto their interactions

Grouping proteins by expression profile over time

Grouping proteins by presence in specific pathways

Protein sequence data

Data was collected from a stent inserted

into the spinal column

CSF was harvested every four hours

Protein sequence was obtained using

liquid chromatography and mass spectrometry

Input:

MS/MS data

Proteins were digested with trypsin MS/MS data was interpreted using BioWorks

SEQUEST algorithm was used to determine protein composition as well as frequency of protein appearance

Protein abundance was measured by height of peaks

Raw Ms/MsData Parser

Return SeparatedList of Protein names

CSV file withProtein name

number of expressions

PICR List ofsynonyms

APID2Net& Cytoscape

Interactionsbetweenproteins

VANTED

Final Graph

Protein similarities

Python & Shell Scripts• Used to

convert between different formats

• Populate VANTED templates

• Creates a list of proteins

Raw Ms/MsData Parser

Return SeparatedList of Protein names

CSV file withProtein name

number of expressions

PICR List ofsynonyms

APID2Net& Cytoscape

Interactionsbetweenproteins

VANTED

Final Graph

Protein similarities

Cytoscape

Raw Ms/MsData Parser

Return SeparatedList of Protein names

CSV file withProtein name

number of expressions

PICR List ofsynonyms

APID2Net& Cytoscape

Interactionsbetweenproteins

VANTED

Final Graph

Protein similarities

Apid2NET

Proteins are tagged based upon what known pathways they participate in

Can also be tagged by structural homology

Apid2NET

Raw Ms/MsData Parser

Return SeparatedList of Protein names

CSV file withProtein name

number of expressions

PICR List ofsynonyms

APID2Net& Cytoscape

Interactionsbetweenproteins

VANTED

Final Graph

Protein similarities

PICR

Protein identifier cross-reference service Finds synonyms of protein names and uniprot

numbers

Raw Ms/MsData Parser

Return SeparatedList of Protein names

CSV file withProtein name

number of expressions

PICR List ofsynonyms

APID2Net& Cytoscape

Interactionsbetweenproteins

VANTED

Final Graph

Protein similarities

VANTED

Links represent known protein interactions

Colors represent similar expression profiles

Line graphs show the expression levels

VANTED

Raw Ms/MsData Parser

Return SeparatedList of Protein names

CSV file withProtein name

number of expressions

PICR List ofsynonyms

APID2Net& Cytoscape

Interactionsbetweenproteins

VANTED

Final Graph

A schematic procedure

Protein similarities

Conclusion

Automated generation of protein expression graphs

Automated ability to search protein functions

These tools will be invaluable in searching the migraine haystack

Thanks and acknowledgements

• Drs Fonteh and Harrington

• HMRI

• All of the SocalBSI staff

• All of my fellow students

• NSF and NIH