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Biomarker Profiling, Discovery and Identification
The goal of our past and ongoing research is to understand,
explore, and evaluate the existence of previously unknown
biomarker information within the lower molecular weight range
of the circulating proteome (e.g. serum, plasma, nipple fluid).
None of this work should be construed or represented as a
clinical test, or the evaluation of a commercial clinical
test.
We are currently focused on sequencing and identifying
the low molecular weight biomarkers that underlie the mass
spectral signatures. For this goal we are taking advantage
of our recent finding that indicates that the vast majority
of the low molecular weight biomarker proteins are amplified
by binding to circulating carrier proteins such as albumin.
We plan to post lists of differentially expressed peptide
sequences for a variety of diseases. Currently we are in
the process of antibody based validation for many low abundance
novel markers.
Proteomic Fingerprinting
The following study sets were independently obtained using
different experimental conditions, mass spectrometry platforms,
different sampling handling conditions, and employ different
clinical study sets. These samples come from both human and
animal sources and are provided anonymized. It is widely
known that MALDI-TOF spectra are highly dependant on the
specific conditions used to generate the signal. Moreover,
each of these study sets are different in one or more important
parameters (e.g. type of chip surface, type of mass spectrometer,
sample handling, source and type of body fluid) . In fact,
most of our studies were generated with the expressed intent
to study and evaluate the effect of the changing experimental
conditions on the characteristics of the spectra. Thus, while
we offer these study sets to the scientific community in
an unrestricted manner, we caution against any direct comparative
analysis within or between sets. Certainly, we highly recommend
that you contact us before making such comparisons, and that
you employ appropriate normalization, baseline correction,
and alignment prior to any such analysis.
High Resolution SELDI-TOF Study Sets
- Ovarian cancer case vs. high-risk control: This study was published
in The Endocrine Related Cancer Journal in June 2004. We have attached as well
an example report on the quality control/quality assurance for this set. Please
click on "Ovarian cancer QA/QC report" for a Word download.
GOALS OF STUDY: We generated this data, using a
non-randomized study set of ovarian cancers and control specimens
on an ABI Qstar fitted with a SELDI-TOF
source to begin to collect data relative to critical unanswered
questions in the field of proteomic profiling as follows:
A. Does the use of high-resolution time-of-flight
(TOF) mass spectrometry (MS) for gathering proteomic fingerprints
from surface-enhanced laser/desorption
ionization (SELDI) ProteinChip arrays yield better analytical and clinical
sensitivity and specificity compared to low-resolution instrumentation, at
least for the set of serum samples analyzed within this study? According
to NCCLS experimental design criteria, a single variable was isolated
(i.e., the
type of mass spectrometer) to answer this question. Since we were able to
analyze the exact same SELDI ProteinChip spot with two different
mass spectrometers,
a direct comparison could be attempted.
B. Which contributes the greatest source of variability: the heterogeneity
within and between clinical serum sets (i.e., normal study set vs. cancer study
set) or the sample application/MS process itself? To address this question,
reference standards were used and the variable to be tested was fixed and isolated.
Thus, we could not randomize and co-mingle the cancers and controls at the
same time since we wanted to determine the variability within the mass spectrometer/sample
application within a given run cycle and test that variable on a common set
of samples - we chose not to co-vary two independent variables at one (run
date and phenotype). This experimental design allowed us to answer the important
question and show that for this study set, the variability within the process
itself was greater than the variability within the samples sets.
C. Does the development of spectral QA/QC procedures positively
impact the modeling performance? In other words, does elimination
of “bad looking
spectra” contribute to better performing models?
Acquire High Resolution Ovarian Data (Zip Format, 275 MB)
- Premalignant Pancreatic Cancer Detection: Published Cancer Cell, December 2003
GOALS OF THIS STUDY:
The goals of this study, using a randomly commingled study set of murine
sera, were to explore the ability of the low molecular weight information
archive to classify and discriminate premalignant pancreatic cancer compared
to control animals.
- Toxicoproteomic analysis of anthracycline-induced cardiotoxicity: Published Toxicological Pathology, March 2004
GOALS OF THIS STUDY:
The goals of this study, using a randomly commingled study set of murine
sera, were to explore the ability of the low molecular weight information
archive to classify and discriminate animals exposed to cardiotoxic compounds
vs vehicle alone. This study employed a randomized and double blinded design
with a blinded validation set.
Wegeners Disease Study. This study is in press at Arthritis
and Rheumatism. For collaborative contacts and study details
please email Dr. John Stone, the Director of the The Johns
Hopkins Vasculitis Center at : jstone@jhmi.edu.
Acquire High Resolution
Wegeners Data (467 MB Zip File)
GOALS OF THIS STUDY:
The goals of this
study were to explore the ability of the low molecular
weight information archive to discriminate
patients with active Wegeners granulomatosis from those
in remisssion using a randomly commingled study set of
serum from patients. Wegeners granulomatosis, is a vasculitic
inflammatory
condition.
Low Resolution SELDI-TOF Datasets
- Ovarian Cancer Studies
- Data from publications: Download .pdf of Lancet
paper, published February 2002
GOALS OF THIS STUDY:
This data was collected using the H4 protein chip and a Ciphergen
PBS1 SELDI-TOF mass spectrometer. The chip was prepared
by hand using the recommended protocol. The spectra were
exported with the baseline subtracted. The goal of this
feasibility study was to explore the existence of low molecular
weight information that could serve as a diagnostic classifier,
using a defined study set as a test ground.
- Data from unpublished experimental
studies
- 4/3/02 Ovarian Study set
GOALS OF THIS STUDY:
Due to the discontinuation of the H4
chip, the WCX2 chip was chosen as
a replacement. The Lancet study was
repeated
using the WCX2 chip. These samples were processed by
hand and the baseline was subtracted
creating the negative intensities seen
for some values.
Ovarian
Dataset 4-3-02.zip (31 MB)
- Ovarian Dataset 8-7-02: x
GOALS OF THIS STUDY: This
dataset while produced using the
WCX2 protein chip, differed
greatly
from the 4/3/02
study set. The goal of this study was to explore the impact
of robotic sample handling (washing, incubation, etc.)
on the spectral quality. We employed an upgraded
PBSII SELDI-TOF mass spectrometer to generate the spectra.
Different sets of ovarian serum samples were used compared
to previous studies. The sample set
included 91 controls and
162 ovarian cancers, which were not randomized so that
we could evaluate the effect of robotic automation on the
spectral variance within each phenotypic group.
Ovarian Dataset 8-7-02.zip (31 MB)
- Prostate Cancer Studies
Download .pdf of JNCI paper, published October 2002 GOALS OF THIS STUDY:
This data was collected using the H4 protein chip and a Ciphergen
PBS1 SELDI-TOF mass spectrometer. The chip was prepared
by hand using the recommended protocol. The spectra were
exported with the baseline subtracted. The goal of this
feasibility study was to explore the existence of low molecular
weight information that could serve as a diagnostic classifier,
using a defined study set as a test ground.
JNCI Dataset 7-3-02.zip
(46 MB)
Other Recent Publications from our Laboratory
- BMC
Bioinformatics Rebuttal
- OvaCheck Question and Answer
- Carrier Protein Binding and Biomarker
Amplification
- Written in Blood- Nature Concepts
- Current Opinion in Biotechnology
- Cancer Diagnosis Using Proteomic Pattern
- Proteomic Applications for the Early
Detection of Cancer
- Mass Spectrometry-based Diagnostics:
The Upcoming Revolution in Disease Detection
- SELDI-TOF Fingerprinting
and Pattern Profiling of Human Cancer Tissue
We welcome any comments or suggestions about how we can improve the website.
We are attempting to provide a useful and current database that will allow
investigators to perform their own analysis. Please send your comments to Dr. Gordon Whiteley.
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