
The San Francisco Bay Area Mass Spectrometry (BAMS)
discussion
group
Tuesday April 29, 2008
6:00 pm to 9:30 pm
Michael's Restaurant at Shoreline Park
Mountain View, CA
Dinner reservations required by
noon on Friday April 25, 2008
A technical evaluation of 2D-LC MS for clinical biomarker
discovery
Keith Wilson
Director of Computational Biology
PDL BioPharma
Redwood City, CA
Abstract
Liquid chromatograph mass spectrometry (LC-MS) proteomic analysis has
the ability to quantify and track thousands of peptides from tissues
and body fluids. We investigated the ability of LC-MS proteomics to
reproducibly detect blood-based markers in the plasma of metastatic
renal cancer patients. We used the differential quantification ability
of LC-MS to interrogate the plasma of two separate clinical site
collections of metastatic renal cancer patients and healthy individuals.
Our goal was to examine the ability of the method to reproducibly find
renal cancer specific markers. We demonstrated that there are over 100
plasma proteins enriched in renal cancer patients compared to healthy
controls and that these proteins are highly reproducibly detected in
two separate clinical collections. Regression analysis, unsupervised
hierarchical clustering and PCA detected no systematic bias in the data
related to site of sample collection and processing. Using a genetic
algorithm, support vector machine classification method we were able to
correctly classify disease samples at 88% sensitivity and 94%
specificity with an independent validation set. The disease enriched
plasma proteins included acute phase reactant proteins, multiple
proteins previously associated with renal cancer, and many others with
no previous renal cancer association. 2D-LC-MS can be a highly
reproducible biomarker discovery platform when used to assess plasma
samples.
Speaker
Background
Keith Wilson received
his Ph.D. from Oregon Health Sciences University in Biochemistry and
Molecular Biology and did his postdoctoral work at Stanford University.
He joined Eos Biotechnology in 1997 which was an early genomics company
utilizing emerging microarray technology and was involved in
technological platform design, software and algorithm development, and
applying the technology to drug discovery and clinical applications. He
has continued to be involved in applying cutting edge technology to
drug discovery and development at PDL BioPharma, including recently
proteomics, high density SNP/CNV arrays, and massively parallel
sequencing.
Dr. Wilson is Director of Computational Biology at PDL BioPharma in
Redwood City.
Meeting
details
| Date: |
Thursday |
April 29, 2008 |
| Time: |
6:00 pm |
Social hour, registration (no-host cocktails) |
|
7:00 pm |
Dinner |
|
8:00 pm |
Presentation |
Dinner:
|
featuring:
|
Salmon |
|
|
Chicken Florentine
|
|
|
Grilled Vegetable Brochette
|
| Cost: |
$30
|
BAMS members* |
|
$40
|
Non-members |
|
$60
|
BAMS membership plus dinner cost |
|
$20
|
Students only |
|
$300
|
2008 Corporate Sponsors |
|
|
Dinner reservations
required
by noon on Friday April 25, 2008
|
*Note: BAMS memberships are for the calendar
year and should
be renewed with the first event you attend in 2008. Dues ($30.00)
may be paid while registering for dinner. If you
are
unsure of your Membership status, please email
Tim Hawkins.
Maps & directions
Michael's Restaurant at Shoreline Park
2960 N.Shoreline Blvd
Mountain View, CA
Google
Map of Michael's
Restaurant Phone: 650-962-1014
If you would like to
subscribe/unsubscribe or make changes to your email address in our
distribution
list, please email
Yingying Huang.
Did you see or hear about the BAMS talk by Professor Murayama
entitled
"What is Mass?" What is it we are measuring after
all?
Check it out! Go to ctp.berkeley.edu
and click on "Popular Talks & Articles" for a QuickTime file.
As a service to our members, we post Employment
postings.
The San Francisco Bay Area Mass Spectrometry discussion group was
formed
in 1980 to provide a regular gathering for people interested in mass
spectrometry
and allied topics. BAMS currently has a membership of about 280
individual
and 20 corporate members, and meets 8-10 times per year for a midweek
dinner
and lecture. Meetings attract between 30 and 90 people, and are
held
at a restaurant or hotel in the bay area convenient for our
speaker.
We usually convene at 6:00 pm for cocktails, dinner at 7:00 pm, and
lecture
at 8:15 pm.
If you have suggestions for a meeting topic, or know of a prominent
mass spectrometrist who will be visiting the bay area, please contact
our
program
chair.
To become a member, please fill out and mail in a membership
form.
BAMS has been fortunate to have had many excellent
speakers in our history.
If you have suggestions for a meeting topic please contact our program
chair.
If you have questions or comments about BAMS, please contact one of
the BAMS officers.
Please thank our corporate sponsors who
help keep BAMS membership and dinner costs low.
Here are some internet links that may be of
interest to BAMS members.
If you have comments or suggestions for this web site, please email
me at hugh-gregg@llnl.gov
Last update: 4/21/2008