Presentation #1:
Profiling Multiple Myeloma: Analysis of Clinical Samples using a Proteomics Discovery Platform
Multiple Myeloma is an incurable cancer that affects plasma cells primarily in the bone marrow.  We have taken a label free proteomics approach using nano-LC/MS and a LTQ Orbitrap to obtain protein profiles from isolated plasma cells. Plasma (myeloma) cells are purified from bone marrow aspirates of patients suffering from various stages of Multiple Myeloma; these plasma cells are then digested and analyzed by nanoscale LC/MS/MS. The peptide/protein profiles across hundreds of patients are compared and correlated to gene expression profile data and clinical outcome.

Ricky D. Edmondson, PhD
Director, The Nancy and Stephen Grand Laboratory for Myeloma Proteomics
Associate Professor of Medicine
Myeloma Institute for Research and Therapy
University of Arkansas for Medical Sciences

Presentation #2:
Investigation of Tissue Interstitial Fluid from Kidney Cancer using High Resolution Differential Mass Spectrometry and SRM-Based Protein Confirmation
Renal cell carcinoma (RCC) is the predominant form of kidney cancer, responsible for over twelve thousand deaths in the US in 2007. Prognosis depends on stage at diagnosis and due to a dearth of symptoms, most patients are diagnosed at advanced stages of the disease. The usual course of treatment begins with total removal of the kidney, or radical nephrectomy. We have designed label-free proteomics experiments using high resolution mass spectrometry to analyze the changes in peptide and protein profiles in tissue interstitial fluid (TIF) from RCC and adjacent normal kidney (ANK) tissues. Tumor and ANK tissues were diced and incubated in PBS to collect secreted and shed proteins followed by trypsin digestion and nanoflow reversed-phase liquid chromatography (nRPLC) coupled to an LTQ-Orbitrap mass spectrometer. Data analysis using SIEVE provided statistical significance of the changes in peptides observed between the RCC and ANK samples, resulting in several protein candidates to target by selected reaction monitoring (SRM) using a triple quadrupole mass spectrometer.

Susan E. Abbatiello, Ph.D.
Postdoctoral Associate
Department of Pharmacology
University of Pittsburgh Cancer Institute Clinical Proteomics Facility Magee Women's Research Institute

Enhancing Linear Ion Trap Mass Spectrometry ETD Performance Using Supplemental Activation - Zhiqi Hao, High Performance MS Technologies oral presentation session, Monday, 3–3:15 pm

Building an SRM-based Targeted MS quantitation assay for the anti-aging hormone Klotho - Amol Prakash, Poster No. 26

Characterization of stress hormone-mediated drug resistance in breast cancer cells using SILAC combined with high resolution mass spectrometry - Jennifer Sutton, Poster No. 86

Simplifying the Hunt for Optimal SRM Transitions:  Utilizing Discovery Data to Expedite Targeted Peptide Quantitation Methods - Scott Peterman, Poster No. 100

Early markers of kidney transplant rejection: Quantitative proteomic workflows for discovery and the development of non-invasive, targeted assays - David Sarracino, Poster No. 125

In-Depth Analysis of the Arabidopsis thaliana Proteome using Electron Transfer Dissociation - Kai Scheffler, Poster No. 133

Quantitative Profiling of DNA Damage Response Proteins Using iTRAQ Labeling and LTQ Orbitrap XL - Rosa Viner, Poster No. 166

Building Improved Coverage and PTM Characterization of Complex Samples Through the Use of Complementary Proteases and Fragmentation Methods – Michael Rosenblatt, Poster No. 226

The following proteomics products are being featured at HUPO:

• Electron Transfer Dissociation (ETD): new technology enables ECD-like fragmentation using an ion trap
• LTQ Orbitrap: superior accurate mass alternative to time-of-flight mass spectrometry
• LTQ XL: next-generation LTQ with three dissociation techniques (ETD-enabled, CID and PQD standard)
• LTQ FT Ultra: hybrid FTICR with new ICR cell design for higher resolution and mass accuracy
• TSQ Quantum Ultra for absolute quantitation of proteins and peptides
• SIEVE: for label-free, semi-quantitative differential expression analysis
• Custom HeavyPeptide kits: for relative or absolute protein quantification