Probing the endogenous peptidomes of cancer for biomarkers: A new endeavor.

[1]  S. Gottesman,et al.  Regulation by proteolysis: energy-dependent proteases and their targets , 1992, Microbiological reviews.

[2]  J. Yates,et al.  Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. , 1995, Analytical chemistry.

[3]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[4]  J. Bertram The molecular biology of cancer. , 2000 .

[5]  P. Choong,et al.  The expression of the urokinase plasminogen activator system in metastatic murine osteosarcoma: an in vivo mouse model. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[6]  MS Pepper,et al.  Extracellular Proteolysis and Angiogenesis , 2001, Thrombosis and Haemostasis.

[7]  C. Southan A genomic perspective on human proteases , 2001, FEBS letters.

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

[9]  G. Berchem,et al.  Cathepsin-D affects multiple tumor progression steps in vivo: proliferation, angiogenesis and apoptosis , 2002, Oncogene.

[10]  H. Moses,et al.  Stromal fibroblasts in cancer initiation and progression , 2004, Nature.

[11]  M. Duffy The role of proteolytic enzymes in cancer invasion and metastasis , 1992, Clinical & Experimental Metastasis.

[12]  D. Hanahan,et al.  Cathepsin cysteine proteases are effectors of invasive growth and angiogenesis during multistage tumorigenesis. , 2004, Cancer cell.

[13]  E. Diamandis,et al.  The emerging roles of human tissue kallikreins in cancer , 2004, Nature Reviews Cancer.

[14]  E. Holland,et al.  Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. , 2004, Analytical chemistry.

[15]  A. Noël,et al.  Catalytically inactive human cathepsin D triggers fibroblast invasive growth , 2005, The Journal of cell biology.

[16]  J. Clements,et al.  Kallikrein 4 (hK4) and prostate-specific antigen (PSA) are associated with the loss of E-cadherin and an epithelial-mesenchymal transition (EMT)-like effect in prostate cancer cells. , 2005, Endocrine-related cancer.

[17]  Nichole L. King,et al.  The PeptideAtlas Project , 2010, Proteome Bioinformatics.

[18]  A. Olshen,et al.  Differential exoprotease activities confer tumor-specific serum peptidome patterns. , 2005, The Journal of clinical investigation.

[19]  J. Kos,et al.  Cysteine cathepsins: regulators of antitumour immune response , 2006, Expert opinion on biological therapy.

[20]  D. Saunders,et al.  Plasminogen binding and activation at the breast cancer cell surface: the integral role of urokinase activity , 2007, Breast Cancer Research.

[21]  V. Vetvicka,et al.  Role of activation peptide of procathepsin D in proliferation and invasion of lung cancer cells. , 2006, Anticancer research.

[22]  I. Brewis The human plasma proteome , 2006 .

[23]  E. Petricoin,et al.  The blood peptidome: a higher dimension of information content for cancer biomarker discovery , 2006, Nature Reviews Cancer.

[24]  M. Fälth,et al.  SwePep, a Database Designed for Endogenous Peptides and Mass Spectrometry* , 2006, Molecular & Cellular Proteomics.

[25]  E. Petricoin,et al.  Serum peptidome for cancer detection: spinning biologic trash into diagnostic gold. , 2005, The Journal of clinical investigation.

[26]  C. López-Otín,et al.  Emerging roles of proteases in tumour suppression , 2007, Nature Reviews Cancer.

[27]  P. Budde,et al.  Oncopeptidomics--a commentary on opportunities and limitations. , 2007, Cancer letters.

[28]  Timur Shtatland,et al.  PepBank - a database of peptides based on sequence text mining and public peptide data sources , 2007, BMC Bioinformatics.

[29]  J. Joyce,et al.  Cysteine Cathepsins and the Cutting Edge of Cancer Invasion , 2007, Cell cycle.

[30]  S. Baumann,et al.  Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. , 2007, Clinical chemistry.

[31]  R. Aebersold,et al.  Mass Spectrometric Detection of Tissue Proteins in Plasma*S , 2007, Molecular & Cellular Proteomics.

[32]  R. Jacob,et al.  The catalytically inactive precursor of cathepsin D induces apoptosis in human fibroblasts and HeLa cells , 2007, Journal of cellular biochemistry.

[33]  V. Vetvicka,et al.  Ribozyme-targeting procathepsin D and its effect on invasion and growth of breast cancer cells: an implication in breast cancer therapy. , 2007, International journal of oncology.

[34]  A. Dominiczak,et al.  Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. , 2007, Journal of proteome research.

[35]  C. López-Otín,et al.  Proteases: Multifunctional Enzymes in Life and Disease* , 2008, Journal of Biological Chemistry.

[36]  F. Liu,et al.  The construction of a bioactive peptide database in Metazoa. , 2008, Journal of proteome research.

[37]  J. Tosoian,et al.  PSA and Beyond: The Past, Present, and Future of Investigative Biomarkers for Prostate Cancer , 2010, TheScientificWorldJournal.

[38]  M. Girolami,et al.  Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease* , 2010, Molecular & Cellular Proteomics.

[39]  Ronald J. Moore,et al.  Blood Peptidome-Degradome Profile of Breast Cancer , 2010, PloS one.

[40]  F. Cortés,et al.  Cellular Proteases as Cancer Biomarkers: A Review , 2010 .

[41]  N. Anderson,et al.  The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. , 2010, Clinical chemistry.

[42]  Yiping Deng,et al.  Expression of Matrix Metalloproteinase-26 promotes human glioma U251 cell invasion in vitro and in vivo. , 2009, Oncology reports.

[43]  H. Cohen,et al.  Urine peptidomics for clinical biomarker discovery. , 2010, Advances in clinical chemistry.

[44]  Jae-Wook Song,et al.  Observational Studies: Cohort and Case-Control Studies , 2010, Plastic and reconstructive surgery.

[45]  C. López-Otín,et al.  The regulatory crosstalk between kinases and proteases in cancer , 2010, Nature Reviews Cancer.

[46]  C. Overall,et al.  Matrix metalloproteinases: what do they not do? New substrates and biological roles identified by murine models and proteomics. , 2010, Biochimica et biophysica acta.

[47]  J. Joyce,et al.  Proteolytic networks in cancer. , 2011, Trends in cell biology.

[48]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[49]  Y. Abiko,et al.  MMP-10/Stromelysin-2 Promotes Invasion of Head and Neck Cancer , 2011, PloS one.

[50]  T. Song,et al.  Serum peptidome profiling in patients with gastric cancer , 2012, Clinical and Experimental Medicine.

[51]  C. Tripodo,et al.  MMP-13 stimulates osteoclast differentiation and activation in tumour breast bone metastases , 2011, Breast Cancer Research.

[52]  H. Mischak,et al.  Clinical application of urinary proteomics/peptidomics , 2011, Expert review of proteomics.

[53]  Nuno Bandeira,et al.  False discovery rates in spectral identification , 2012, BMC Bioinformatics.

[54]  M. Neumaier,et al.  Functional protease profiling for diagnosis of malignant disease , 2012, Proteomics. Clinical applications.

[55]  A. Vlahou,et al.  A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. , 2012, Journal of proteomics.

[56]  D. Turk,et al.  Protease signalling: the cutting edge , 2012, EMBO Journal.

[57]  Nai-jun Fan,et al.  Serum peptidome patterns of breast cancer based on magnetic bead separation and mass spectrometry analysis , 2012, Diagnostic Pathology.

[58]  Lingjun Li,et al.  Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery , 2012, Frontiers in Biology.

[59]  Rahul Kumar,et al.  TumorHoPe: A Database of Tumor Homing Peptides , 2012, PloS one.

[60]  M. Sarwal,et al.  Optimization for peptide sample preparation for urine peptidomics , 2014, Clinical Proteomics.

[61]  Kun He,et al.  Serum Peptidome Variations in a Healthy Population: Reference to Identify Cancer-Specific Peptides , 2013, PloS one.

[62]  C. Deng,et al.  Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis. , 2013, Chemical Society reviews.

[63]  H. Mischak,et al.  Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications , 2013, Electrophoresis.

[64]  E. Diamandis,et al.  Deciphering the peptidome of urine from ovarian cancer patients and healthy controls , 2014, Clinical Proteomics.

[65]  D. Quail,et al.  Microenvironmental regulation of tumor progression and metastasis , 2014 .

[66]  E. Diamandis,et al.  Deciphering the ovarian cancer ascites fluid peptidome , 2014, Clinical Proteomics.

[67]  K. Gevaert,et al.  Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation. , 2013, Journal of proteome research.

[68]  Lei Wu,et al.  Serum peptidome patterns of hepatocellular carcinoma based on magnetic bead separation and mass spectrometry analysis , 2013, Diagnostic Pathology.

[69]  S. V. Heesch,et al.  University of Groningen Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis , 2018 .

[70]  A. Facchiano,et al.  Rapid peptidomic profiling of peritoneal fluid by MALDI-TOF mass spectrometry for the identification of biomarkers of endometriosis , 2014, Gynecological Endocrinology.

[71]  M. Ferrari,et al.  Circulating proteolytic products of carboxypeptidase N for early detection of breast cancer. , 2014, Clinical chemistry.

[72]  A. Sood,et al.  Kallikrein family proteases KLK6 and KLK7 are potential early detection and diagnostic biomarkers for serous and papillary serous ovarian cancer subtypes , 2014, Journal of Ovarian Research.

[73]  H. Zou,et al.  Analysis of the human urine endogenous peptides by nanoparticle extraction and mass spectrometry identification. , 2014, Analytica chimica acta.

[74]  Xiaomei Yan,et al.  Liquid chromatography-mass spectrometry based serum peptidomic approach for renal clear cell carcinoma diagnosis. , 2014, Journal of pharmaceutical and biomedical analysis.

[75]  L. Fricker,et al.  Intracellular peptides: From discovery to function , 2014 .

[76]  E. Diamandis,et al.  Peptidomics of urine and other biofluids for cancer diagnostics. , 2014, Clinical chemistry.

[77]  H. Mischak,et al.  Comparison of CE‐MS/MS and LC‐MS/MS sequencing demonstrates significant complementarity in natural peptide identification in human urine , 2014, Electrophoresis.

[78]  J. Joyce,et al.  Pericellular proteolysis in cancer , 2014, Genes & development.

[79]  C. Lebrilla,et al.  Current peptidomics: Applications, purification, identification, quantification, and functional analysis , 2015, Proteomics.

[80]  Gordon W. Slysz,et al.  Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes , 2014, Journal of proteome research.

[81]  F. Magni,et al.  Intraluminal proteome and peptidome of human urinary extracellular vesicles , 2015, Proteomics. Clinical applications.

[82]  Gajendra P. S. Raghava,et al.  CancerPPD: a database of anticancer peptides and proteins , 2014, Nucleic Acids Res..

[83]  Richard D Smith,et al.  An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics , 2015, Journal of The American Society for Mass Spectrometry.

[84]  Feng Wang,et al.  Serum peptidome profiling analysis for the identification of potential biomarkers in cervical intraepithelial neoplasia patients. , 2015, Biochemical and biophysical research communications.

[85]  R. Sallam Proteomics in Cancer Biomarkers Discovery: Challenges and Applications , 2015, Disease markers.

[86]  M. Ferrari,et al.  Circulating Peptidome to Indicate the Tumor-resident Proteolysis , 2015, Scientific Reports.

[87]  J. Polańska,et al.  Identification of serum proteome signatures of locally advanced and metastatic gastric cancer: a pilot study , 2015, Journal of Translational Medicine.

[88]  O. Schilling,et al.  The emerging role of the peptidome in biomarker discovery and degradome profiling , 2015, Biological chemistry.

[89]  G. Mauri,et al.  Tumor size, stage and grade alterations of urinary peptidome in RCC , 2015, Journal of Translational Medicine.

[90]  M. Peake,et al.  Stage at diagnosis and early mortality from cancer in England , 2015, British Journal of Cancer.

[91]  J. Parsons,et al.  4-Kallikrein Test and Kallikrein Markers in Prostate Cancer Screening. , 2016, The Urologic clinics of North America.

[92]  Emile G Magny,et al.  New Peptides Under the s(ORF)ace of the Genome. , 2016, Trends in biochemical sciences.

[93]  Gajendra P. S. Raghava,et al.  SATPdb: a database of structurally annotated therapeutic peptides , 2015, Nucleic Acids Res..

[94]  Gajendra P. S. Raghava,et al.  PEPlife: A Repository of the Half-life of Peptides , 2016, Scientific Reports.

[95]  R. Dziadziuszko,et al.  Serum mass profile signature as a biomarker of early lung cancer. , 2016, Lung cancer.

[96]  W. Dyszkiewicz,et al.  Identification of Serum Peptidome Signatures of Non-Small Cell Lung Cancer , 2016, International journal of molecular sciences.

[97]  A. Goy,et al.  The serine protease prostasin (PRSS8) is a potential biomarker for early detection of ovarian cancer , 2016, Journal of Ovarian Research.

[98]  W. Grizzle,et al.  Surveying the serologic proteome in a tissue‐specific kras(G12D) knockin mouse model of pancreatic cancer , 2016, Proteomics.

[99]  A. Pauli,et al.  Decoding sORF translation – from small proteins to gene regulation , 2016, RNA biology.

[100]  T. Song,et al.  Identification of novel serum peptides biomarkers for female breast cancer patients in Western China , 2016, Proteomics.

[101]  M. Ferrari,et al.  Alterations of the Plasma Peptidome Profiling in Colorectal Cancer Progression , 2016, Journal of cellular physiology.

[102]  A. Heck,et al.  Six alternative proteases for mass spectrometry–based proteomics beyond trypsin , 2016, Nature Protocols.

[103]  M. Ferrari,et al.  Profiling of Cross-Functional Peptidases Regulated Circulating Peptides in BRCA1 Mutant Breast Cancer. , 2016, Journal of proteome research.

[104]  Chuanhao Tang,et al.  Mass spectrometry-based serum peptidome profiling accurately and reliably predicts outcomes of pemetrexed plus platinum chemotherapy in patients with advanced lung adenocarcinoma , 2017, PloS one.

[105]  R. Kumar,et al.  CancerPDF: A repository of cancer-associated peptidome found in human biofluids , 2017, Scientific Reports.

[106]  A. Walch,et al.  Tissue kallikrein-related peptidase 4 (KLK4), a novel biomarker in triple-negative breast cancer , 2017, Biological chemistry.

[107]  Youxin Wang,et al.  Serum peptidome profiling for the diagnosis of colorectal cancer: discovery and validation in two independent cohorts , 2017, Oncotarget.

[108]  R. Simpson,et al.  Characterization of the Low-Molecular-Weight Human Plasma Peptidome. , 2017, Methods in molecular biology.

[109]  B. Garcia,et al.  Monitoring proteolytic processing events by quantitative mass spectrometry , 2017, Expert review of proteomics.

[110]  G. Yousef,et al.  An integrated proteomic and peptidomic assessment of the normal human urinome , 2017, Clinical chemistry and laboratory medicine.

[111]  Christopher J. Lyon,et al.  Circulating Peptidome and Tumor-Resident Proteolysis. , 2017, The Enzymes.

[112]  Xue Zhou,et al.  Potential Significance of Peptidome in Human Ovarian Cancer for Patients With Ascites , 2017, International Journal of Gynecologic Cancer.

[113]  H. Motaln,et al.  Proteases and cytokines as mediators of interactions between cancer and stromal cells in tumours , 2017, Biological chemistry.

[114]  Eugene A. Kapp,et al.  The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome. , 2017, The Enzymes.

[115]  S. Anant,et al.  Stromal contributions to the carcinogenic process , 2017, Molecular carcinogenesis.

[116]  K. Blennow,et al.  Expanding the cerebrospinal fluid endopeptidome , 2017, Proteomics.

[117]  Neil D. Rawlings,et al.  The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database , 2017, Nucleic Acids Res..

[118]  A. Jemal,et al.  Cancer statistics, 2018 , 2018, CA: a cancer journal for clinicians.

[119]  S. Bhatia,et al.  Harnessing Protease Activity to Improve Cancer Care , 2018 .

[120]  R. Jamal,et al.  Probing the colorectal cancer proteome for biomarkers: Current status and perspectives. , 2018, Journal of proteomics.