Degradomics in Biomarker Discovery

Aggrecanase degradation of type III collagen is associated with clinical knee pain

(2018) A.C. Bay-Jensen et al.   CLINICAL BIOCHEMISTRY

Proteolytic ectodomain shedding of membrane proteins in mammals—hardware, concepts, and recent developments

(2018) Stefan F Lichtenthaler et al.   EMBO JOURNAL

Tau Proteolysis in the Pathogenesis of Tauopathies: Neurotoxic Fragments and Novel Biomarkers

(2018) James P. Quinn et al.   JOURNAL OF ALZHEIMERS DISEASE

Comparative Degradomics of Porcine and Human Wound Exudates Unravels Biomarker Candidates for Assessment of Wound Healing Progression in Trauma Patients

(2018) Fabio Sabino et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Prognostic significance of elevated serum CD44 levels in patients with oral squamous cell carcinoma

(2018) Sharada Sawant et al.   JOURNAL OF ORAL PATHOLOGY & MEDICINE

Simple, scalable, and ultrasensitive tip-based identification of protease substrates

(2018) Gerta Shema et al.   MOLECULAR & CELLULAR PROTEOMICS

Cysteine protease cathepsins in cardiovascular disease: from basic research to clinical trials

(2018) Cong-Lin Liu et al.   Nature Reviews Cardiology

Exploring the roles of urinary HAI-1, EpCAM & EGFR in bladder cancer prognosis & risk stratification

(2018) Kym I.E. Snell et al.   Oncotarget

Proteolysis in septic shock patients: plasma peptidomic patterns are associated with mortality

(2018) J. Bauzá-Martinez et al.   BRITISH JOURNAL OF ANAESTHESIA

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

(2018) Christina Ludwig et al.   Molecular Systems Biology

Assembling the Community-Scale Discoverable Human Proteome

(2018) Mingxun Wang et al.   Cell Systems

Novel tau fragments in cerebrospinal fluid: relation to tangle pathology and cognitive decline in Alzheimer’s disease

(2018) Claudia Cicognola et al.   ACTA NEUROPATHOLOGICA

TAILS proteomics reveals dynamic changes in airway proteolysis controlling protease activity and innate immunity during COPD exacerbations

(2018) Brendan Mallia-Milanes et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

The Urokinase Plasminogen Activator System in Human Cancers: An Overview of Its Prognostic and Predictive Role

(2018) Josip Madunić   THROMBOSIS AND HAEMOSTASIS

Cell-adhesion molecules and their soluble forms: Promising predictors of “tumor progression” and relapse in leukemia

(2018) Ieda Cristina Cunha Ferreira e Fonseca et al.   TUMOR BIOLOGY

Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

(2017) Jesse G. Meyer et al.   Expert Review of Proteomics

Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis

(2017) Yijing Yu et al.   Journal of Proteomics

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

(2017) George Rosenberger et al.   NATURE BIOTECHNOLOGY

Selected reaction monitoring approach for validating peptide biomarkers

(2017) Qing Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current trends and challenges in proteomic identification of protease substrates

(2016) Matej Vizovišek et al.   BIOCHIMIE

Neuropeptide Y (NPY) in cerebrospinal fluid from patients with Huntington's Disease: increased NPY levels and differential degradation of the NPY1-30fragment

(2016) Leona Wagner et al.   JOURNAL OF NEUROCHEMISTRY

Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

(2016) Piero Giansanti et al.   Nature Protocols

Advances in targeted proteomics and applications to biomedical research

(2016) Tujin Shi et al.   PROTEOMICS

Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: Principle and applications

(2016) Adele Bourmaud et al.   PROTEOMICS

Development of a selected reaction monitoring mass spectrometry-based assay to detect asparaginyl endopeptidase activity in biological fluids

(2016) Anindita Dutta et al.   Oncotarget

TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors

(2016) Anna Prudova et al.   Cell Reports

Plasma degradome affected by variable storage of human blood

(2016) Maria Kaisar et al.   Clinical Proteomics

Legumain Protein as a Potential Predictive Biomarker for Asian Patients with Breast Carcinoma

(2015) Mei Wu et al.   Asian Pacific Journal of Cancer Prevention

US Food and Drug Administration Perspectives on Clinical Mass Spectrometry

(2015) J. T. Lathrop et al.   CLINICAL CHEMISTRY

High expression of the cysteine proteinase legumain in colorectal cancer – Implications for therapeutic targeting

(2015) Mads H. Haugen et al.   EUROPEAN JOURNAL OF CANCER

Advances in high-resolution quantitative proteomics: implications for clinical applications

(2015) Sebastien Gallien et al.   Expert Review of Proteomics

Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry

(2015) Navin Rauniyar   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

(2015) Florian Meier et al.   JOURNAL OF PROTEOME RESEARCH

Proteomic Identification of Cysteine Cathepsin Substrates Shed from the Surface of Cancer Cells

(2015) Barbara Sobotič et al.   MOLECULAR & CELLULAR PROTEOMICS

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma

(2015) Susan E. Abbatiello et al.   MOLECULAR & CELLULAR PROTEOMICS

Secretome Analysis Identifies Novel Signal Peptide Peptidase-Like 3 (SPPL3) Substrates and Reveals a Role of SPPL3 in Multiple Golgi Glycosylation Pathways

(2015) Peer-Hendrik Kuhn et al.   MOLECULAR & CELLULAR PROTEOMICS

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events inArabidopsis thaliana

(2015) A. Saskia Venne et al.   PROTEOMICS

Advances in high-resolution accurate mass spectrometry application to targeted proteomics

(2015) Antoine Lesur et al.   PROTEOMICS

Toward the definition of a peptidome signature and protease profile in chronic periodontitis

(2015) Fábio Trindade et al.   Proteomics Clinical Applications

Recent advances in targeted proteomics for clinical applications

(2015) Bruno Domon et al.   Proteomics Clinical Applications

Using data-independent, high-resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications

(2015) Tatjana Sajic et al.   Proteomics Clinical Applications

Urinary TIMP-1 and MMP-2 levels detect the presence of pancreatic malignancies

(2014) R Roy et al.   BRITISH JOURNAL OF CANCER

Proteomic cancer biomarkers from discovery to approval: it’s worth the effort

(2014) Danni Li et al.   Expert Review of Proteomics

Prostate cancer: measuring PSA

(2014) C. Pezaro et al.   INTERNAL MEDICINE JOURNAL

Global PROTOMAP Profiling to Search for Biomarkers of Early-Recurrent Hepatocellular Carcinoma

(2014) Masato Taoka et al.   JOURNAL OF PROTEOME RESEARCH

In VivoAssessment of Protease Dynamics in Cutaneous Wound Healing by Degradomics Analysis of Porcine Wound Exudates

(2014) Fabio Sabino et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometry based biomarker discovery, verification, and validation - Quality assurance and control of protein biomarker assays

(2014) Carol E. Parker et al.   Molecular Oncology

LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification

(2014) Pitter F Huesgen et al.   NATURE METHODS

Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events

(2014) Nikolaus Fortelny et al.   NUCLEIC ACIDS RESEARCH

A Soluble Form of the Giant Cadherin Fat1 Is Released from Pancreatic Cancer Cells by ADAM10 Mediated Ectodomain Shedding

(2014) Nathalie Wojtalewicz et al.   PLoS One

Identification of Urinary Peptide Biomarkers Associated with Rheumatoid Arthritis

(2014) Angelique Stalmach et al.   PLoS One

Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling

(2014) A. P. Wiita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

C-terminomics: Targeted analysis of natural and posttranslationally modified protein and peptide C-termini

(2014) Sebastian Tanco et al.   PROTEOMICS

Ensembles of protein termini and specific proteolytic signatures as candidate biomarkers of disease

(2014) Pitter F. Huesgen et al.   Proteomics Clinical Applications

Cysteine cathepsins and their potential in clinical therapy and biomarker discovery

(2014) Marko Fonović et al.   Proteomics Clinical Applications

Urinary peptidomics identifies potential biomarkers for major depressive disorder

(2014) Ying Wang et al.   PSYCHIATRY RESEARCH

Urinary EpCAM in urothelial bladder cancer patients: characterisation and evaluation of biomarker potential

(2013) R T Bryan et al.   BRITISH JOURNAL OF CANCER

Peptidomics of Urine and Other Biofluids for Cancer Diagnostics

(2013) J. M. Bauca et al.   CLINICAL CHEMISTRY

Peptidomics methods for the identification of peptidase–substrate interactions

(2013) Anna Mari Lone et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Novel Highly Sensitive, Specific, and Straightforward Strategy for Comprehensive N-Terminal Proteomics Reveals Unknown Substrates of the Mitochondrial Peptidase Icp55

(2013) A. Saskia Venne et al.   JOURNAL OF PROTEOME RESEARCH

Sources of Technical Variability in Quantitative LC–MS Proteomics: Human Brain Tissue Sample Analysis

(2013) Paul D. Piehowski et al.   JOURNAL OF PROTEOME RESEARCH

Mapping Proteolytic Processing in the Secretome of Gastric Cancer-Associated Myofibroblasts Reveals Activation of MMP-1, MMP-2, and MMP-3

(2013) Christopher Holmberg et al.   JOURNAL OF PROTEOME RESEARCH

Absolute proteomic quantification of the activity state of proteases and proteolytic cleavages using proteolytic signature peptides and isobaric tags

(2013) Richard P. Fahlman et al.   Journal of Proteomics

Functional Interplay between Caspase Cleavage and Phosphorylation Sculpts the Apoptotic Proteome

(2012) Melissa M. Dix et al.   CELL

The Riddle of Protein Diagnostics: Future Bleak or Bright?

(2012) N. L. Anderson et al.   CLINICAL CHEMISTRY

Secretome protein enrichment identifies physiological BACE1 protease substrates in neurons

(2012) Peer-Hendrik Kuhn et al.   EMBO JOURNAL

Protease signalling: the cutting edge

(2012) Boris Turk et al.   EMBO JOURNAL

Unbiased plasma proteomics for novel diagnostic biomarkers in cardiovascular disease: identification of quiescin Q6 as a candidate biomarker of acutely decompensated heart failure

(2012) Alexandre Mebazaa et al.   EUROPEAN HEART JOURNAL

High-Throughput SISCAPA Quantitation of Peptides from Human Plasma Digests by Ultrafast, Liquid Chromatography-Free Mass Spectrometry

(2012) Morteza Razavi et al.   JOURNAL OF PROTEOME RESEARCH

Unbiased Selective Isolation of Protein N-terminal Peptides from Complex Proteome Samples Using Phospho Tagging (PTAG) and TiO2-based Depletion

(2012) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

The DegraBase: A Database of Proteolysis in Healthy and Apoptotic Human Cells

(2012) Emily D. Crawford et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

ALCAM (CD166) Expression and Serum Levels in Pancreatic Cancer

(2012) Michael Tachezy et al.   PLoS One

Mass spectrometry-based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins

(2012) Emily S. Boja et al.   PROTEOMICS

Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network

(2012) Chengpin Shen et al.   PROTEOMICS

Applying selected reaction monitoring to targeted proteomics

(2011) Enrique Calvo et al.   Expert Review of Proteomics

A Quantitative Proteomics Design for Systematic Identification of Protease Cleavage Events

(2010) Francis Impens et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Profiling of Proteolysis during Rupture ofPlasmodium falciparumfrom the Host Erythrocyte

(2010) Paul W. Bowyer et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics

(2010) Anna Prudova et al.   MOLECULAR & CELLULAR PROTEOMICS

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Complementary positional proteomics for screening substrates of endo- and exoproteases

(2010) Petra Van Damme et al.   NATURE METHODS

Proteome-wide analysis of protein carboxy termini: C terminomics

(2010) Oliver Schilling et al.   NATURE METHODS

Matrix Metalloproteinases As Novel Biomarker s and Potential Therapeutic Targets in Human Cancer

(2009) Roopali Roy et al.   JOURNAL OF CLINICAL ONCOLOGY

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini

(2008) Sami Mahrus et al.   CELL

Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis

(2008) Melissa M. Dix et al.   CELL

Analysis of Protein Processing by N-terminal Proteomics Reveals Novel Species-specific Substrate Determinants of Granzyme B Orthologs

(2008) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

Mechanistic insight into taxol-induced cell death

(2008) F Impens et al.   ONCOGENE