Recent advances in clinical proteomics using mass spectrometry.

The ultimate objective of clinical proteomics is the successful discovery, validation and translation of biomarkers, together with new therapeutic targets into medical practices. New highly developed technologies in proteomics and their use in understanding tumor biology have significant clinical potential in the diagnosis, prognosis and treatment of disease. Areas such as MS, new labeling technologies and advancements in bioinformatics systems are now used to successfully detect disease-associated biomarkers together with therapeutic targets in complex biological specimens, including biofluids, cell lysates and tissue biopsies. Recent improvements in sample preparation (specifically focused on fractionation and enrichment) are enabling the analysis of low-abundance proteins together with many types of post-translational modifications. Targeted proteomic diagnostics will play a significant role in the development of personalized molecular medicine, a process that will be vital in modernizing healthcare structures.

[1]  Jeroen Krijgsveld,et al.  Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics , 2003, Nature Biotechnology.

[2]  Rong Zeng,et al.  Effect of peptide-to-TiO2 beads ratio on phosphopeptide enrichment selectivity. , 2009, Journal of proteome research.

[3]  Amanda G. Paulovich,et al.  An Automated and Multiplexed Method for High Throughput Peptide Immunoaffinity Enrichment and Multiple Reaction Monitoring Mass Spectrometry-based Quantification of Protein Biomarkers* , 2009, Molecular & Cellular Proteomics.

[4]  M. Kubbutat,et al.  Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. , 2010, Journal of proteome research.

[5]  Christoph H Borchers,et al.  Accurate quantitation of standard peptides used for quantitative proteomics , 2009, Proteomics.

[6]  Lennart Martens,et al.  Peptide and protein quantification: A map of the minefield , 2010, Proteomics.

[7]  John R Yates,et al.  Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)* , 2006, Molecular & Cellular Proteomics.

[8]  A. Sickmann,et al.  Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications , 2008, Proteomics.

[9]  P. Tempst,et al.  A Sequence-specific Exopeptidase Activity Test (SSEAT) for “Functional” Biomarker Discovery*S , 2008, Molecular & Cellular Proteomics.

[10]  M. Neumaier,et al.  Spiking of serum specimens with exogenous reporter peptides for mass spectrometry based protease profiling as diagnostic tool. , 2008, Rapid communications in mass spectrometry : RCM.

[11]  Xiangmin Zhang,et al.  On‐plate‐selective enrichment of glycopeptides using boronic acid‐modified gold nanoparticles for direct MALDI‐QIT‐TOF MS analysis , 2009, Proteomics.

[12]  Christoph H Borchers,et al.  Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma* , 2009, Molecular & Cellular Proteomics.

[13]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[14]  G. Giaccone,et al.  Prediction of outcome of non-small cell lung cancer patients treated with chemotherapy and bortezomib by time-course MALDI-TOF-MS serum peptide profiling , 2009, Proteome Science.

[15]  J. Tommassen,et al.  Candidate verification of iron-regulated Neisseria meningitidis proteins using isotopic versions of tandem mass tags (TMT) and single reaction monitoring. , 2009, Journal of proteomics.

[16]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[17]  Y. Shiloh,et al.  Citrate boosts the performance of phosphopeptide analysis by UPLC-ESI-MS/MS. , 2009, Journal of proteome research.

[18]  P. Aukrust,et al.  Folic Acid Treatment Reduces Chemokine Release From Peripheral Blood Mononuclear Cells in Hyperhomocysteinemic Subjects , 2002, Arteriosclerosis, thrombosis, and vascular biology.

[19]  Soyoung Ryu,et al.  Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method , 2008, Cancer informatics.

[20]  Je-Hyun Baek,et al.  Multiple products monitoring as a robust approach for peptide quantification. , 2009, Journal of proteome research.

[21]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[22]  Marcus Schmidt,et al.  Surface-enhanced Laser Desorption/Ionisation Time-of-flight Mass Spectrometry to Detect Breast Cancer Markers in Tears and Serum. , 2009, Cancer genomics & proteomics.

[23]  D. Chan,et al.  Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias. , 2008, Clinical chemistry.

[24]  J. Kellermann ICPL--isotope-coded protein label. , 2008, Methods in molecular biology.

[25]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian Cancer , 2002 .

[26]  M. Neumaier,et al.  Mass spectrometry-based clinical proteomics profiling: current status and future directions , 2009, Expert review of proteomics.

[27]  Terence C W Poon,et al.  Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices , 2007, Expert review of proteomics.

[28]  Nasreen S Jessani,et al.  A streamlined platform for high-content functional proteomics of primary human specimens , 2005, Nature Methods.

[29]  M. Clench,et al.  MALDI-ion mobility separation-mass spectrometry imaging of glucose-regulated protein 78 kDa (Grp78) in human formalin-fixed, paraffin-embedded pancreatic adenocarcinoma tissue sections. , 2009, Journal of proteome research.