Introduction:
Prostate cancer is the second leading cause of cancer deaths among
males in the United States. The identification and validation of novel
protein biomarkers will play an important role in treating
life-threatening forms of this disease in men. However, obtaining
sufficient amounts of diseased specimens to interrogate the robustness
of protein biomarkers poses a serious limitation in protein biomarker
development in prostate cancer. In this study, we have extracted
proteins from formalin-fixed paraffin embedded prostate tissues and
identified a complement of proteins through tandem mass spectrometry
(MS/MS) in a process called the Direct Tissue Proteomics (DTP) method.
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Methods:
We have employed a multi-step approach to identify potential protein
biomarkers in formalin-fixed human prostate tissues using the DTP
method. First, proteins were extracted from commercially available
prostate cancer tissue microarrays. A total of 38 prostate cancer and 8
normal tissue samples were analyzed by tandem MS/MS. RAW MS files were
converted to mzXML format and searched using the SEQUEST, and
subsequently processed through the transproteomic pipeline (TPP)
(PeptideProphet, ProteinProphet). Results were uploaded into the
Computational Portal and Analysis System (CPAS) database and
subsequently interrogated to look for individual proteins or protein
signatures that were unique to cancerous and normal prostate tissue
samples.
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Preliminary Results:
This proof-of-principle analysis utilizes our workflow to elucidate
potential protein biomarkers in prostate cancer, and greater than 2,000
unique proteins were robustly detected (ProteinProphet ≥0.95). We have
corroborated previously published data and have identified candidate
proteins and/or protein signatures/networks as candidate biomarkers in
prostate cancer. Lastly, these studies identified a subset of proteins
that were capable of segregating prostate cancers of different Gleason
grades.
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