Open Protocols

Protocol Name	Investigatory Role	Biomarkers	Data Collections
Body Fluids as a Source of Diagnostic Biomarkers	Leading	0	0
Body Fluids as a Source of Diagnostic Biomarkers: Breast	Coordinating	0	0
Collaborative study on SELDI biomarker discovery and serum protein profiling of lung cancers	Leading	0	0
Detection of Serum Markers of Breast Cancer by SELDI	Involved	0	0
EDRN Pre-Validation of Metabolic Biomarkers of Prostate Cancer: Follow up EDRN Challenge	Involved	0	0
EDRN Pre-Validation of Multiplex Biomarker in Urine	Involved	2	0
Establishment of a serum standard for use in high-throughput proteomic	Leading	0	0
HNPCC colon cancer-associated SELDI mass spectrometry protein profiles in serum	Involved	0	0
SELDI and LC-MS/MS discovery and profiling study of hepatocarcinomas	Leading	0	0
SELDI Profiling of serum and urine from patients with urologic disease in support of bladder cancer studies	Leading	0	0
Upgrading Reference Set	Involved	0	0

Closed Protocols

Protocol Name	Investigatory Role	Biomarkers	Data Collections
Body Fluids as a Source of Diagnostic Biomarkers: Prostate	Coordinating	0	0
Detecting breast cancer protein signatures in body fluid	Leading	0	0
Early Detection of Cancer by Affinity Mass Spectrometry-Set Aside funds	Leading	0	0
EDRN-WHI Pre-Clinical Colon Ca Specimens	Involved	0	1
Protein profiling for detection of high risk breast cancer	Leading	0	0
Proteomic Profiling of Serum and Other Body Fluids for the Early Detection of Colon Cancers	Leading	0	0
SELDI Phase I: Assay Validation-Prostate	Leading	1	1
SELDI Validation Study Phase II	Leading	1	1

Publications

Publication Name	PubMed ID	Journal
A novel approach for clustering proteomics data using Bayesian fast Fourier transform.	15769836	Bioinformatics
A novel approach toward development of a rapid blood test for breast cancer.	14499014	Clin Breast Cancer
Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias.	17981926	Clin Chem
Application of mass spectrometry to the discovery of biomarkers for detection of prostate cancer.	16552720	J Cell Biochem
Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients.	12324514	Clin Chem
Characterization and Evidence of the miR-888 Cluster as a Novel Cancer Network in Prostate.	29330297	Mol Cancer Res
Clinical proteomics: A need to define the field and to begin to set adequate standards.	21136664	Proteomics Clin Appl
Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status.	14997503	Proteomics
Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine.	38580319
Data reduction using a discrete wavelet transform in discriminant analysis of very high dimensionality data.	12762451	Biometrics
Deconvolution filters to enhance resolution of dense time-of-flight survey spectra in the time-lag optimization range.	16636999	Rapid Commun Mass Spectrom
Defining the role of mass spectrometry in cancer diagnostics.	15466969	Cancer Epidemiol Biomarkers Prev
Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine.	11290567	Am J Pathol
Differential capture of serum proteins for expression profiling and biomarker discovery in pre- and posttreatment head and neck cancer samples.	18043497	Laryngoscope
Direct N-Glycosylation Profiling of Urine and Prostatic Fluid Glycoproteins and Extracellular Vesicles.	34646811	Front Chem
Endothelial-to-Mesenchymal Transition in Human Adipose Tissue Vasculature Alters the Particulate Secretome and Induces Endothelial Dysfunction.	31434495	Arterioscler Thromb Vasc Biol
Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques.	15550476	Clin Chem
Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility.	15613711	Clin Chem
Expression of genes and proteins specific for prostate cancer.	15535438	J Urol
Feature extraction in the analysis of proteomic mass spectra.	16502467	Proteomics
Functional clustering algorithm for high-dimensional proteomics data.	16046812	J Biomed Biotechnol
Generation of a baculovirus recombinant prostate-specific membrane antigen and its use in the development of a novel protein biochip quantitative immunoassay.	10833385	Protein Expr Purif
Identification of patients with head and neck cancer using serum protein profiles.	14732777	Arch Otolaryngol Head Neck Surg
Lectin capture strategies combined with mass spectrometry for the discovery of serum glycoprotein biomarkers.	16760258	Mol Cell Proteomics
Measurement reproducibility in the early stages of biomarker development.	15665389	Dis Markers
Mining the low molecular weight proteome of blood.	21136732	Proteomics Clin Appl
Molecular Hallmarks of Prostate-specific Membrane Antigen in Treatment-naïve Prostate Cancer.	39294048	Eur Urol
National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines for use of tumor markers in clinical practice: quality requirements.	18606634	Clin Chem
NFTest: automated testing of Nextflow pipelines.	38341660	Bioinformatics
Normal, benign, preneoplastic, and malignant prostate cells have distinct protein expression profiles resolved by surface enhanced laser desorption/ionization mass spectrometry.	12171882	Clin Cancer Res
Optimization of MALDI-TOF MS detection for enhanced sensitivity of affinity-captured proteins spanning a 100 kDa mass range.	17918874	J Proteome Res
Optimization of small extracellular vesicle isolation from expressed prostatic secretions in urine for in-depth proteomic analysis.	35119778	J Extracell Vesicles
Overexpression of alpha-defensin is associated with bladder cancer invasiveness.	16520271	Urol Oncol
Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma.	15112261	Cancer
PipeVal: light-weight extensible tool for file validation.	38341658	Bioinformatics
promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling.	36922981	Bioinform Adv
Prospective comparison of restriction spectrum imaging and non-invasive biomarkers to predict upgrading on active surveillance prostate biopsy.	36097168	Prostate Cancer Prostatic Dis
Prostate Cancer Biomarker Development: National Cancer Institute's Early Detection Research Network Prostate Cancer Collaborative Group Review.	33093161	Cancer Epidemiol Biomarkers Prev
Protein profiling in urine for the diagnosis of bladder cancer.	15277356	Clin Chem
Proteomic approaches to biomarker discovery in prostate and bladder cancers.	11721637	Proteomics
Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers.	11708463	Ann N Y Acad Sci
Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry.	34453155	Nat Rev Urol
Proteomic strategies for biomarker identification: progress and challenges.	11249741	Curr Opin Mol Ther
Proteomics in early detection of cancer.	11568117	Clin Chem
Quantitation of serum prostate-specific membrane antigen by a novel protein biochip immunoassay discriminates benign from malignant prostate disease.	11507047	Cancer Res
Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants.	34680183	Cancers (Basel)
Resampling and deconvolution of linear time-of-flight records for enhanced protein profiling.	16637003	Rapid Commun Mass Spectrom
RNA transcripts serve as a template for double-strand break repair in human cells.	40348775	Nat Commun
SELDI protein profiling of dunning R-3327 derived cell lines: identification of molecular markers of prostate cancer progression.	17705230	Prostate
SELDI-TOF MS profiling of serum for detection of the progression of chronic hepatitis C to hepatocellular carcinoma.	15726646	Hepatology
SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer.	18024530	Clin Chem
SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers.	15258337	Dis Markers
Selective capture of prostatic basal cells and secretory epithelial cells for proteomic and genomic analysis.	15283892	Urol Oncol
Serum biomarkers to differentiate benign and malignant mammographic lesions.	17481542	J Am Coll Surg
Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer.	15709174	Clin Cancer Res
Serum protein expression profiling for cancer detection: validation of a SELDI-based approach for prostate cancer.	15258333	Dis Markers
Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men.	12097261	Cancer Res
Serum protein profiles to identify head and neck cancer.	15014013	Clin Cancer Res
Serum, salivary and tissue proteomics for discovery of biomarkers for head and neck cancers.	15723595	Expert Rev Mol Diagn
Signal detection in high-resolution mass spectrometry data.	18173224	J Proteome Res
Site-Specific Intact N-Linked Glycopeptide Characterization of Prostate-Specific Membrane Antigen from Metastatic Prostate Cancer Cells.	36061737	ACS Omega
Surfaced-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer.	15383419	Ann Surg Oncol
Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype Determination.	32614141	Proteomics Clin Appl
Targeting PLOD2 suppresses invasion and metastatic potential in radiorecurrent prostate cancer.	39184453	BJC Rep
The "omics" haystack: defining sources of sample bias in expression profiling.	16120944	Clin Chem
The early detection research network surface-enhanced laser desorption and ionization prostate cancer detection study: A study in biomarker validation in genitourinary oncology.	15283893	Urol Oncol
The Germline and Somatic Origins of Prostate Cancer Heterogeneity.	39945744	Cancer Discov
The landscape of N<sup>6</sup>-methyladenosine in localized primary prostate cancer.	40128621	Nat Genet
The Proteogenomics of Prostate Cancer Radioresistance.	39166898	Cancer Res Commun

Interests

Proteomics

Study of proteins

To update protocols, publications, biomarkers, or science data, please contact the Data Management and Coordinating Center.

Site

Eastern Virginia Medical School

Degree(s)

Ph.D.

Email

semmesoj@odu.edu

Fax

757 446-5766

Person ID

1333

Note

To update contact information, please visit the Data Management and Coordinating Center .