Quantitative mass spectrometry-based techniques for clinical use: Biomarker identification and quantification

[1]  Sudhir Bahadur,et al.  Discovery and Verification of Head-and-neck Cancer Biomarkers by Differential Protein Expression Analysis Using iTRAQ Labeling, Multidimensional Liquid Chromatography, and Tandem Mass Spectrometry*S , 2008, Molecular & Cellular Proteomics.

[2]  Crispin J. Miller,et al.  Eight-channel iTRAQ Enables Comparison of the Activity of Six Leukemogenic Tyrosine Kinases*S , 2008, Molecular & Cellular Proteomics.

[3]  C. Sawyers The cancer biomarker problem , 2008, Nature.

[4]  W. Hancock,et al.  A two step fractionation approach for plasma proteomics using immunodepletion of abundant proteins and multi-lectin affinity chromatography: Application to the analysis of obesity, diabetes, and hypertension diseases. , 2008, Journal of separation science.

[5]  G. Clifton,et al.  Identification of serum biomarkers in brain-injured adults: potential for predicting elevated intracranial pressure. , 2008, Journal of neurotrauma.

[6]  H. Otu,et al.  Serum Proteomics and Biomarkers in Hepatocellular Carcinoma and Chronic Liver Disease , 2008, Clinical Cancer Research.

[7]  C. Isacke,et al.  A comparative proteinomic analysis of nipple aspiration fluid from healthy women and women with breast cancer. , 2007, European journal of cancer.

[8]  A. Whetton,et al.  How will haematologists use proteomics? , 2007, Blood reviews.

[9]  R. Ahrends,et al.  A Metal-coded Affinity Tag Approach to Quantitative Proteomics* , 2007, Molecular & Cellular Proteomics.

[10]  Laura Beretta,et al.  Proteomics from the clinical perspective: many hopes and much debate , 2007, Nature Methods.

[11]  David C Muddiman,et al.  Differential protein expression in male and female human lumbar cerebrospinal fluid using iTRAQ reagents after abundant protein depletion , 2007, Proteomics.

[12]  Alexey I Nesvizhskii,et al.  Analysis and validation of proteomic data generated by tandem mass spectrometry , 2007, Nature Methods.

[13]  J. Martínková,et al.  Relative quantitation of proteins fractionated by the ProteomeLab™ PF 2D system using isobaric tags for relative and absolute quantitation (iTRAQ) , 2007, Analytical and bioanalytical chemistry.

[14]  Jens M. Rick,et al.  Quantitative mass spectrometry in proteomics: a critical review , 2007, Analytical and bioanalytical chemistry.

[15]  György Marko-Varga,et al.  Personalized medicine and proteomics: lessons from non-small cell lung cancer. , 2007, Journal of proteome research.

[16]  Jörg Grigull,et al.  Endometrial Carcinoma Biomarker Discovery and Verification Using Differentially Tagged Clinical Samples with Multidimensional Liquid Chromatography and Tandem Mass Spectrometry*S , 2007, Molecular & Cellular Proteomics.

[17]  R. Gray,et al.  Mass spectrometry to classify non-small-cell lung cancer patients for clinical outcome after treatment with epidermal growth factor receptor tyrosine kinase inhibitors: a multicohort cross-institutional study. , 2007, Journal of the National Cancer Institute.

[18]  F. Dieterle,et al.  Promises of Biomarkers in Drug Development – A Reality Check , 2007, Chemical biology & drug design.

[19]  D. Lauffenburger,et al.  Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks , 2007, Proceedings of the National Academy of Sciences.

[20]  T. Veenstra Global and targeted quantitative proteomics for biomarker discovery. , 2007, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

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

[22]  Robert E. Kearney,et al.  Quantitative Proteomics Analysis of the Secretory Pathway , 2006, Cell.

[23]  Jacob D. Jaffe,et al.  PEPPeR, a Platform for Experimental Proteomic Pattern Recognition*S , 2006, Molecular & Cellular Proteomics.

[24]  Trairak Pisitkun,et al.  Discovery of Urinary Biomarkers* , 2006, Molecular & Cellular Proteomics.

[25]  Richard D. Smith,et al.  Advances and Challenges in Liquid Chromatography-Mass Spectrometry-based Proteomics Profiling for Clinical Applications* , 2006, Molecular & Cellular Proteomics.

[26]  M. Herbster,et al.  Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum , 2006, The Lancet.

[27]  Jue-Liang Hsu,et al.  Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics , 2006, Electrophoresis.

[28]  K. Elenitoba-Johnson,et al.  Analytical characteristics of cleavable isotope-coded affinity tag-LC-tandem mass spectrometry for quantitative proteomic studies. , 2006, The Journal of molecular diagnostics : JMD.

[29]  Steven A Carr,et al.  Protein biomarker discovery and validation: the long and uncertain path to clinical utility , 2006, Nature Biotechnology.

[30]  A. Whetton,et al.  Relative quantification in proteomics: new approaches for biochemistry. , 2006, Trends in biochemical sciences.

[31]  Leigh Anderson,et al.  Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins* , 2006, Molecular & Cellular Proteomics.

[32]  P. Righetti,et al.  Decoding 2D-PAGE complex maps: relevance to proteomics. , 2006, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[33]  Jos H Beijnen,et al.  Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface-enhanced laser desorption ionisation-time of flight mass spectrometry. , 2006, World journal of gastroenterology.

[34]  A. Denizli,et al.  Efficient removal of albumin from human serum by monosize dye-affinity beads. , 2006, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[35]  J. Sung,et al.  Serum Proteomic Fingerprints of Adult Patients with Severe Acute Respiratory Syndrome , 2006, Clinical chemistry.

[36]  S. Hanash,et al.  Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study , 2006, Nature Biotechnology.

[37]  E. Sheta,et al.  2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases , 2006, Expert review of proteomics.

[38]  Chun-Ta Liao,et al.  Oral cancer plasma tumor marker identified with bead-based affinity-fractionated proteomic technology. , 2005, Clinical chemistry.

[39]  D. Chan,et al.  Identification of Biomarkers for Breast Cancer in Nipple Aspiration and Ductal Lavage Fluid , 2005, Clinical Cancer Research.

[40]  Liang Li,et al.  Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis. , 2005, Journal of proteome research.

[41]  K. Resing,et al.  Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics*S , 2005, Molecular & Cellular Proteomics.

[42]  Henrik Zetterberg,et al.  Proteomic analysis using protein chips to detect biomarkers in cervical and amniotic fluid in women with intra-amniotic inflammation. , 2005, Journal of proteome research.

[43]  Ruedi Aebersold,et al.  A Software Suite for the Generation and Comparison of Peptide Arrays from Sets of Data Collected by Liquid Chromatography-Mass Spectrometry*S , 2005, Molecular & Cellular Proteomics.

[44]  D. Driesch,et al.  ProteinChip technology reveals distinctive protein expression profiles in the urine of bladder cancer patients. , 2005, European urology.

[45]  P. Speckman,et al.  Proteomic analysis of nipple aspirate fluid using SELDI‐TOF‐MS , 2005, International journal of cancer.

[46]  J. Listgarten,et al.  Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry , 2005, Molecular & Cellular Proteomics.

[47]  T. Colgan,et al.  Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. , 2005, Journal of proteome research.

[48]  R. T. Carruth,et al.  Proteolytic 18O labeling by peptidyl-Lys metalloendopeptidase for comparative proteomics. , 2005, Journal of proteome research.

[49]  O John Semmes,et al.  SELDI‐TOF MS profiling of serum for detection of the progression of chronic hepatitis C to hepatocellular carcinoma , 2005, Hepatology.

[50]  Steven P Gygi,et al.  The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. , 2005, Methods.

[51]  D. Driesch,et al.  Proteome Analysis of Maternal Serum Samples for Trisomy 21 Pregnancies Using ProteinChip Arrays and Bioinformatics , 2005, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[52]  Jeffrey S. Morris,et al.  Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. , 2005, Journal of the National Cancer Institute.

[53]  Jing Zhang,et al.  Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid , 2005, Neurobiology of Aging.

[54]  Ruedi Aebersold,et al.  High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry *S , 2005, Molecular & Cellular Proteomics.

[55]  Pierre Bedossa,et al.  Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases , 2005, Hepatology.

[56]  G. Omenn,et al.  HUPO 3rd Annual World Congress on Proteomics , 2005 .

[57]  Sang-Won Lee,et al.  Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability. , 2004, Rapid communications in mass spectrometry : RCM.

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

[59]  Yongyi Mao,et al.  Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry*S , 2004, Molecular & Cellular Proteomics.

[60]  R. Bast,et al.  Three Biomarkers Identified from Serum Proteomic Analysis for the Detection of Early Stage Ovarian Cancer , 2004, Cancer Research.

[61]  T. Poon,et al.  Serial Analysis of Plasma Proteomic Signatures in Pediatric Patients with Severe Acute Respiratory Syndrome and Correlation with Viral Load , 2004, Clinical chemistry.

[62]  J. Lapidus,et al.  Diagnosis of intra-amniotic infection by proteomic profiling and identification of novel biomarkers. , 2004, JAMA.

[63]  J. Yates,et al.  A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.

[64]  George G Klee,et al.  Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. , 2004, Journal of proteome research.

[65]  Werner Zolg,et al.  Quantification of C‐reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C‐labeled peptide standards , 2004, Proteomics.

[66]  Jeffrey S. Morris,et al.  Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments , 2004, Bioinform..

[67]  David C Muddiman,et al.  Evaluation of a cleavable stable isotope labeled synthetic peptide for absolute protein quantification using LC-MS/MS. , 2004, Journal of proteome research.

[68]  Darryl B. Hardie,et al.  Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). , 2004, Journal of proteome research.

[69]  Shu-Hui Chen,et al.  Stable-isotope dimethyl labeling for quantitative proteomics. , 2003, Analytical chemistry.

[70]  D. Hochstrasser,et al.  A panel of cerebrospinal fluid potential biomarkers for the diagnosis of Alzheimer's disease , 2003, Proteomics.

[71]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[72]  B. Subramanian,et al.  A comparison of drug-treated and untreated HCT-116 human colon adenocarcinoma cells using a 2-D liquid separation mapping method based upon chromatofocusing PI fractionation. , 2003, Analytical chemistry.

[73]  T. Yip,et al.  Comprehensive proteomic profiling identifies serum proteomic signatures for detection of hepatocellular carcinoma and its subtypes. , 2003, Clinical chemistry.

[74]  Robert J Chalkley,et al.  Mass Spectrometric Analysis of Protein Mixtures at Low Levels Using Cleavable 13C-Isotope-coded Affinity Tag and Multidimensional Chromatography* , 2003, Molecular & Cellular Proteomics.

[75]  Ruth Etzioni,et al.  Early detection: The case for early detection , 2003, Nature Reviews Cancer.

[76]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[77]  Andrew H. Thompson,et al.  Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. , 2003, Analytical chemistry.

[78]  Daniel C Liebler,et al.  Quantitative analysis of modified proteins by LC-MS/MS of peptides labeled with phenyl isocyanate. , 2003, Journal of proteome research.

[79]  S. Carr,et al.  N-Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry. , 2002, Rapid communications in mass spectrometry : RCM.

[80]  Kan Zhu,et al.  Two-dimensional liquid separations-mass mapping of proteins from human cancer cell lysates. , 2002, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[81]  N. Anderson,et al.  The Human Plasma Proteome , 2002, Molecular & Cellular Proteomics.

[82]  P. Schellhammer,et al.  Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. , 2002, Cancer research.

[83]  Lloyd D. Fricker,et al.  Quantitation of Neuropeptides in Cpefat/Cpefat Mice Using Differential Isotopic Tags and Mass Spectrometry , 2002 .

[84]  S. Kingsmore,et al.  Multiplexed protein profiling on microarrays by rolling-circle amplification , 2002, Nature Biotechnology.

[85]  X. Yao,et al.  Proteolytic 18O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent. , 2002, Journal of proteome research.

[86]  X. Yao,et al.  Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. , 2001, Analytical chemistry.

[87]  G. Wright,et al.  Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. , 2001, The American journal of pathology.

[88]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[89]  F. Regnier,et al.  Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. , 2000, Journal of chromatography. B, Biomedical sciences and applications.

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

[91]  L L Needham,et al.  Isotope dilution--mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. , 1996, Clinical chemistry.

[92]  D. Suckau,et al.  Molecular characterization of surface topology in protein tertiary structures by amino-acylation and mass spectrometric peptide mapping. , 1994, Bioconjugate chemistry.

[93]  Shu Zheng,et al.  Detection and significance of serum protein markers of small‐cell lung cancer , 2008, Journal of clinical laboratory analysis.

[94]  Ruedi Aebersold,et al.  Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. , 2007, Methods in molecular biology.

[95]  F. Bertucci,et al.  Postoperative serum proteomic profiles may predict metastatic relapse in high-risk primary breast cancer patients receiving adjuvant chemotherapy , 2006, Oncogene.

[96]  D. Chan,et al.  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. , 2005, Clinical chemistry.

[97]  T. Colgan,et al.  Proteomic analysis of the proliferative and secretory phases of the human endometrium: Protein identification and differential protein expression , 2005, Proteomics.

[98]  Joachim Klose,et al.  Application of proteomics and protein analysis for biomarker and target finding for immunotherapy. , 2005, Methods in molecular medicine.

[99]  A. Schmidt,et al.  A novel strategy for quantitative proteomics using isotope‐coded protein labels , 2005, Proteomics.

[100]  R. Aebersold,et al.  Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. , 2005, Journal of Alzheimer's disease : JAD.

[101]  Kelly K. Hunt,et al.  Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry , 2004, Breast Cancer Research and Treatment.

[102]  J. Lill,et al.  Proteomic tools for quantitation by mass spectrometry. , 2003, Mass spectrometry reviews.

[103]  E. Petricoin,et al.  Use of proteomic patterns in serum to identify ovarian cancer , 2002, The Lancet.