Articles

Antibody-based proteomics to identify an apoptosis signature for early recurrence of hepatocellular carcinoma

Early recurrence after surgical resection is a hallmark of poor prognosis in hepatocellular carcinoma (HCC). To determine the proteomic background of early recurrence of HCC, we focused on apoptosis-related pr...

Authors: Noriaki Morofuji, Hidenori Ojima, Nobuyoshi Hiraoka, Takuji Okusaka, Minoru Esaki, Satoshi Nara, Kazuaki Shimada, Yoshiro Kishi and Tadashi Kondo

N-glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models

Diabetic nephropathy (DN) is a late complication in both type 1 diabetes mellitus (T1DM) and T2DM. Already at an early stage of DN morphological changes occur at the cell surface and in the extracellular matri...

Authors: Leena Liljedahl, Maiken Højgaard Pedersen, Jenny Norlin, James N. McGuire and Peter James

Fibrinogen alpha C chain 5.9 kDa fragment (FIC5.9), a biomarker for various pathological conditions, is produced in post-blood collection by fibrinolysis and coagulation factors

Fibrinogen alpha C chain 5.9 kDa fragment (FIC5.9) is a new serum biomarker for chronic hepatitis that was discovered by proteomics analysis. Previous studies have shown that FIC5.9 is derived from the C-termi...

Authors: Wataru Kikuchi, Motoi Nishimura, Takahisa Kuga, Sachio Tsuchida, Tatsuya Saito, Mamoru Satoh, Kenta Noda, Yoshio Kodera, Takeshi Tomonaga and Fumio Nomura

Mass spectrometry-based approaches to targeted quantitative proteomics in cardiovascular disease

Mass spectrometry-based proteomics methodology has become an important tool in elucidating some of the underlying mechanisms involved in cardiovascular disease. The present review provides details on selected ...

Authors: Clementina Mesaros and Ian A. Blair

Plasma degradome affected by variable storage of human blood

The successful application of—omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio...

Authors: Maria Kaisar, Leon F. A. van Dullemen, Marie-Laëtitia Thézénas, M. Zeeshan Akhtar, Honglei Huang, Sandrine Rendel, Philip D. Charles, Roman Fischer, Rutger J. Ploeg and Benedikt M. Kessler

Precision medicine: from pharmacogenomics to pharmacoproteomics

Disease progression and drug response may vary significantly from patient to patient. Fortunately, the rapid development of high-throughput ‘omics’ technologies has allowed for the identification of potential ...

Authors: Allison B. Chambliss and Daniel W. Chan

Increased sialylation of site specific O-glycoforms of hemopexin in liver disease

Non-invasive monitoring of liver disease remains an important health issue. Liver secreted glycoproteins reflect pathophysiological states of the organ and represent a rational target for serologic monitoring....

Authors: Miloslav Sanda, Julius Benicky, Jing Wu, Yiwen Wang, Kepher Makambi, Jaeil Ahn, Coleman I. Smith, Peng Zhao, Lihua Zhang and Radoslav Goldman

Adapting extracellular matrix proteomics for clinical studies on cardiac remodeling post-myocardial infarction

Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of cardiac wound healing responses that involve stimulation of robust inflammation to clear necrotic myocytes and tissue debris...

Authors: Merry L. Lindsey, Michael E. Hall, Romain Harmancey and Yonggang Ma

Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations

Ebola virus like particles (EBOV VLPs, eVLPs), are produced by expressing the viral transmembrane glycoprotein (GP) and structural matrix protein VP40 in mammalian cells. When expressed, these proteins self-a...

Authors: Lisa H. Cazares, Michael D. Ward, Ernst E. Brueggemann, Tara Kenny, Paul Demond, Christopher R. Mahone, Karen A. O. Martins, Jonathan E. Nuss, Trevor Glaros and Sina Bavari

A proteomic evaluation of urinary changes associated with cardiopulmonary bypass

The urinary proteome of patients undergoing cardiopulmonary bypass (CPB) may provide important insights into systemic and renal changes associated with the procedure. Such information may ultimately provide a ...

Authors: Ravi C. Dwivedi, Mario Navarrete, Nora Choi, Victor Spicer, Claudio Rigatto, Rakesh C. Arora, Oleg Krokhin, Julie Ho and John A. Wilkins

Quantification of angiotensin II-regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring

Angiotensin-II (Ang II) mediates progression of autosomal-dominant polycystic kidney disease (ADPKD) and other chronic kidney diseases (CKD). However, markers of kidney Ang II activity are lacking. We previous...

Authors: Ana Konvalinka, Ihor Batruch, Tomas Tokar, Apostolos Dimitromanolakis, Shelby Reid, Xuewen Song, York Pei, Andrei P. Drabovich, Eleftherios P. Diamandis, Igor Jurisica and James W. Scholey

Identification of potential protein biomarkers for early detection of pregnancy in cow urine using 2D DIGE and label free quantitation

An early, reliable and noninvasive method of early pregnancy diagnosis is prerequisite for efficient reproductive management in dairy industry. The early detection of pregnancy also help in to reduce the calvi...

Authors: Preeti Rawat, Shveta Bathla, Rubina Baithalu, Munna Lal Yadav, Sudarshan Kumar, Syed Azamal Ali, Anurag Tiwari, Masoud Lotfan, Jasmine Naru, Manoj Jena, Pradip Behere, Ashok K. Balhara, Rajesh Vashisth, Inderjeet Singh, Ajay Dang, Jai K. Kaushik…

Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines

The refractory nature of many cancers remains the main health challenge over the past century. The epigenetic drug, decitabine (DAC), represents one of the most promising therapeutic agents in cancers particul...

Authors: Chunchao Zhang, Jinfeng Suo, Hiroyuki Katayama, Yue Wei, Guillermo Garcia-Manero and Samir Hanash

Phosphotyrosine profiling of curcumin-induced signaling

Curcumin, derived from the rhizome Curcuma longa, is a natural anti-cancer agent and has been shown to inhibit proliferation and survival of tumor cells. Although the anti-cancer effects of curcumin are well esta...

Authors: Gajanan Sathe, Sneha M. Pinto, Nazia Syed, Vishalakshi Nanjappa, Hitendra S. Solanki, Santosh Renuse, Sandip Chavan, Aafaque Ahmad Khan, Arun H. Patil, Raja Sekhar Nirujogi, Bipin Nair, Premendu Prakash Mathur, T. S. Keshava Prasad, Harsha Gowda and Aditi Chatterjee

Synovial fluid proteome in rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic autoinflammatory disorder that affects small joints. Despite intense efforts, there are currently no definitive markers for early diagnosis of RA and for monitoring the p...

Authors: Mitali Bhattacharjee, Lavanya Balakrishnan, Santosh Renuse, Jayshree Advani, Renu Goel, Gajanan Sathe, T. S. Keshava Prasad, Bipin Nair, Ramesh Jois, Subramanian Shankar and Akhilesh Pandey

Identification of brain-enriched proteins in the cerebrospinal fluid proteome by LC-MS/MS profiling and mining of the Human Protein Atlas

Cerebrospinal fluid (CSF) is a proximal fluid which communicates closely with brain tissue, contains numerous brain-derived proteins and thus represents a promising fluid for discovery of biomarkers of central...

Authors: Ilijana Begcevic, Davor Brinc, Andrei P. Drabovich, Ihor Batruch and Eleftherios P. Diamandis

Clinical proteomics of enervated neurons

The dynamic field of neurosciences entails ever increasing search for molecular mechanisms of disease states, especially in the domain of neurodegenerative disorders. The previous century heralded the techniqu...

Authors: Mohor Biplab Sengupta, Arunabha Chakrabarti, Suparna Saha and Debashis Mukhopadhyay

Challenges and opportunities of bovine milk analysis by mass spectrometry

Bovine milk and its products (e.g. cheese, yoghurt) are an important part of human diet with beneficial effects for all ages. Although analyses of different milk components (e.g. proteins, lipids) pose huge ch...

Authors: Aparna Verma and Kiran Ambatipudi

Clinical utility of serum biomarkers in Duchenne muscular dystrophy

Assessments of disease progression and response to therapies in Duchenne muscular dystrophy (DMD) patients remain challenging. Current DMD patient assessments include complex physical tests and invasive proce...

Authors: Yetrib Hathout, Haeri Seol, Meng Hsuan J. Han, Aiping Zhang, Kristy J. Brown and Eric P. Hoffman

Targeted quantification of N-1-(carboxymethyl) valine and N-1-(carboxyethyl) valine peptides of β-hemoglobin for better diagnostics in diabetes

N-1-(Deoxyfructosyl) valine (DFV) β-hemoglobin (β-Hb), commonly referred as HbA1c, is widely used diagnostic marker in diabetes, believed to provide glycemic status of preceding 90–120...

Authors: Mashanipalya G. Jagadeeshaprasad, Kedar B. Batkulwar, Nishita N. Meshram, Shalbha Tiwari, Arvind M. Korwar, Ambika G. Unnikrishnan and Mahesh J. Kulkarni

Extracellular vesicle proteomes reflect developmental phases of Bacillus subtilis

Extracellular vesicles (EV) are spherical membrane-bound vesicles with nano-scale diameters, which are shed to the extracellular region by most eukaryotic and prokaryotic cells. Bacterial EV are proposed to co...

Authors: Yeji Kim, Nathan Edwards and Catherine Fenselau

The proteomics of lung injury in childhood: challenges and opportunities

Proteomics, the large-scale study of the structure and function of proteins of a cell or organism, is a rapidly developing area of biomedical research which is perfectly suited to the study of pediatric lung i...

Authors: Prue M. Pereira-Fantini and David G. Tingay

Targeting LAMP2 in human cerebrospinal fluid with a combination of immunopurification and high resolution parallel reaction monitoring mass spectrometry

Alzheimer’s disease is the most common form of dementia. An increasing body of evidence suggests that endo-lysosomal dysfunction is a pathogenic mechanism of Alzheimer’s disease. Thus there is a potential for...

Authors: Simon Sjödin, Annika Öhrfelt, Gunnar Brinkmalm, Henrik Zetterberg, Kaj Blennow and Ann Brinkmalm

Erratum to: ENOX2-based early detection (ONCOblot) of asbestos-induced malignant mesothelioma 4–10 years in advance of clinical symptoms

Authors: D. James Morré, Brandon Hostetler, David J. Taggart, Dorothy M. Morré, A. W. Musk, Bruce W. S. Robinson and Jenette Creaney

ENOX2-based early detection (ONCOblot) of asbestos-induced malignant mesothelioma 4–10 years in advance of clinical symptoms

Malignant mesothelioma is an aggressive, almost uniformly fatal tumor, caused primarily by exposure to asbestos. In this study, serum presence of mesothelioma-specific protein transcript variants of ecto-nicot...

Authors: D. James Morré, Brandon Hostetler, David J. Taggart, Dorothy M. Morré, A. W. Musk, Bruce W. S. Robinson and Jenette Creaney

Advances in mass spectrometry-based clinical biomarker discovery

The greatest unmet needs in biomarker discovery are those discoveries that lead to the development of clinical diagnostic tests. These clinical diagnostic tests can provide early intervention when a patient wo...

Authors: Christopher A. Crutchfield, Stefani N. Thomas, Lori J. Sokoll and Daniel W. Chan

Mass spectrometry-based analyses showing the effects of secretor and blood group status on salivary N-glycosylation

The carbohydrate portions of salivary glycoproteins play important roles, including mediating bacterial and leukocyte adhesion. Salivary glycosylation is complex. Many of its glycoproteins present ABO and Lewi...

Authors: Matthew E. Albertolle, Maria E. Hassis, Connie Jen Ng, Severino Cuison, Katherine Williams, Akraporn Prakobphol, Andrew B. Dykstra, Steven C. Hall, Richard K. Niles, H. Ewa Witkowska and Susan J. Fisher

A microfluidic multiplex proteomic immunoassay device for translational research

Microfluidic technology has the potential to miniaturize and automate complex laboratory procedures. The objective of this study was to assess a microfluidic immunoassay device, Simple Plex, which simultaneous...

Authors: Jing Cao, Jesse Seegmiller, Naomi Q. Hanson, Christopher Zaun and Danni Li

Label-free mass spectrometric analysis reveals complex changes in the brain proteome from the mdx-4cv mouse model of Duchenne muscular dystrophy

X-linked muscular dystrophy is a primary disease of the neuromuscular system. Primary abnormalities in the Dmd gene result in the absence of the full-length isoform of the membrane cytoskeletal protein dystrophin...

Authors: Sandra Murphy, Margit Zweyer, Michael Henry, Paula Meleady, Rustam R. Mundegar, Dieter Swandulla and Kay Ohlendieck

Histone post-translational modifications in frontal cortex from human donors with Alzheimer’s disease

Alzheimer’s disease (AD) is the sixth leading cause of death and the most costly disease in the US. Despite the enormous impact of AD, there are no treatments that delay onset or stop disease progression curre...

Authors: Kyle W. Anderson and Illarion V. Turko

New biomarkers for primary mitral regurgitation

Mitral regurgitation is a frequent valvular heart disease affecting around 2.5 % of the population with prevalence directly related to aging. Degeneration of mitral valve is broadly considered as a passive ong...

Authors: Céline Deroyer, Julien Magne, Marie Moonen, Caroline Le Goff, Laura Dupont, Alexia Hulin, Marc Radermecker, Alain Colige, Etienne Cavalier, Philippe Kolh, Luc Pierard, Patrizio Lancellotti, Marie-Paule Merville and Marianne Fillet

Proteins from formalin-fixed paraffin-embedded prostate cancer sections that predict the risk of metastatic disease

Prostate cancer is the most frequently diagnosed cancer in men and the third leading cause of cancer related deaths among men living in developed countries. Biomarkers that predict disease outcome at the time ...

Authors: Jonathan C. Dunne, David S. Lamb, Brett Delahunt, Judith Murray, Peter Bethwaite, Peter Ferguson, John N. Nacey, Sven Sondhauss and T. William Jordan

Comparative proteomic network signatures in seminal plasma of infertile men as a function of reactive oxygen species

Reactive oxygen species (ROS) plays a major role in the pathology of male infertility. It is an independent biomarker of sperm function. Seminal plasma is a natural reservoir of antioxidants responsible for th...

Authors: Ashok Agarwal, Ahmet Ayaz, Luna Samanta, Rakesh Sharma, Mourad Assidi, Adel M. Abuzenadah and Edmund Sabanegh

Proteomic profiling identifies specific histone species associated with leukemic and cancer cells

Chromatin is an extraordinarily complex structure. Much of this complexity results from the presence of numerous histone post-translational modifications and histone variants. Alterations in the patterns of hi...

Authors: Rajbir Singh, Sean W. Harshman, Amy S. Ruppert, Amir Mortazavi, David M. Lucas, Jennifer M. Thomas-Ahner, Steven K. Clinton, John C. Byrd, Michael A. Freitas and Mark R. Parthun

Urinary proteomics in chronic kidney disease: diagnosis and risk of progression beyond albuminuria

The contrast between a high prevalence of chronic kidney disease (CKD) and the low incidence of end-stage renal disease highlights the need for new biomarkers of progression beyond albuminuria testing. Urinary...

Authors: Marius A Øvrehus, Petra Zürbig, Bjørn E Vikse and Stein I Hallan

A proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritis

Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial joints. Early intervention followed by early diagnosis can result in disease remission; however,...

Authors: Junji Hayashi, Makoto Kihara, Harubumi Kato and Toshihide Nishimura

Blood-sampling collection prior to surgery may have a significant influence upon biomarker concentrations measured

Biomarkers can be subtle tools to aid the diagnosis, prognosis and monitoring of therapy and disease progression. The validation of biomarkers is a cumbersome process involving many steps. Serum samples from l...

Authors: Nicolas Kahn, Julia Riedlinger, Markus Roeßler, Christina Rabe, Michael Lindner, Ina Koch, Sabine Schott-Hildebrand, Felix J Herth, Marc A Schneider, Michael Meister and Thomas R Muley

Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium

Support for early detection of lung cancer has emerged from the National Lung Screening Trial (NLST), in which low-dose computed tomography (LDCT) screening reduced lung cancer mortality by 20 % relative to ch...

Authors: Charles E. Birse, Robert J. Lagier, William FitzHugh, Harvey I. Pass, William N. Rom, Eric S. Edell, Aaron O. Bungum, Fabien Maldonado, James R. Jett, Mehdi Mesri, Erin Sult, Elizabeth Joseloff, Aiqun Li, Jenny Heidbrink, Gulshan Dhariwal, Chad Danis…

Glycomic profiling of carcinoembryonic antigen isolated from human tumor tissue

Carcinoembryonic antigen (CEA) is a protein commonly found in human serum, with elevated CEA levels being linked to the progression of a wide range of tumors. It is currently used as a biomarker for malign tum...

Authors: Chuncui Huang, Tiancheng Zhan, Yaming Liu, Qianqian Li, Hongmei Wu, Dengbo Ji and Yan Li

Acute-phase ITIH4 levels distinguish multi-system from single-system Langerhans cell histiocytosis via plasma peptidomics

Langerhans cell histiocytosis (LCH) is a proliferative disorder in which abnormal Langerhans cell (LC)-like cells (LCH cells) intermingle with inflammatory cells. Whether LCH is reactive or neoplastic remains ...

Authors: Ichiro Murakami, Yukiko Oh, Akira Morimoto, Hitoshi Sano, Susumu Kanzaki, Michiko Matsushita, Takeshi Iwasaki, Satoshi Kuwamoto, Masako Kato, Keiko Nagata, Kazuhiko Hayashi, Shinsaku Imashuku, Jean Gogusev, Francis Jaubert, Takashi Oka and Tadashi Yoshino

Syringe-push membrane absorption as a simple rapid method of urine preparation for clinical proteomics

The analysis of urinary proteome might reveal biomarkers of clinical value. However, current methods of urine preparation for down-stream proteomic analysis are complicated, time-consuming, and/or expensive. T...

Authors: Somchai Chutipongtanate, Channarong Changtong, Churat Weeraphan, Suradej Hongeng, Chantragan Srisomsap and Jisnuson Svasti

Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues

Post-translational modification by ubiquitin is a fundamental regulatory mechanism that is implicated in many cellular processes including the cell cycle, apoptosis, cell adhesion, angiogenesis, and tumor grow...

Authors: Stefani N Thomas, Hui Zhang and Robert J Cotter

Changes in glycoprotein expression between primary breast tumour and synchronous lymph node metastases or asynchronous distant metastases

Breast cancer is a very heterogeneous disease and some patients are cured by the surgical removal of the primary tumour whilst other patients suffer from metastasis and spreading of the disease, despite adjuva...

Authors: Emila Kurbasic, Martin Sjöström, Morten Krogh, Elin Folkesson, Dorthe Grabau, Karin Hansson, Lisa Rydén, Sofia Waldemarson, Peter James and Emma Niméus

Comparative proteomic analysis of hypertrophic chondrocytes in osteoarthritis

Osteoarthritis (OA) is a multi-factorial disease leading progressively to loss of articular cartilage and subsequently to loss of joint function. While hypertrophy of chondrocytes is a physiological process im...

Authors: Konstantinos C Tsolis, Ekaterini S Bei, Ioanna Papathanasiou, Fotini Kostopoulou, Vassiliki Gkretsi, Kalliopi Kalantzaki, Konstantinos Malizos, Michalis Zervakis, Aspasia Tsezou and Anastassios Economou

Identification of sialylated glycoproteins from metabolically oligosaccharide engineered pancreatic cells

In this study, we investigated the use of metabolic oligosaccharide engineering and bio-orthogonal ligation reactions combined with lectin microarray and mass spectrometry to analyze sialoglycoproteins in the ...

Authors: Yuan Tian, Ruben T Almaraz, Caitlin H Choi, Qing Kay Li, Christopher Saeui, Danni Li, Punit Shah, Rahul Bhattacharya, Kevin J Yarema and Hui Zhang

A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes’ stages A-D colorectal cancers

Current methods widely deployed for colorectal cancers (CRC) screening lack the necessary sensitivity and specificity required for population-based early disease detection. Cancer-specific protein biomarkers a...

Authors: Sadia Mahboob, Seong Beom Ahn, Harish R Cheruku, David Cantor, Emma Rennel, Simon Fredriksson, Gabriella Edfeldt, Edmond J Breen, Alamgir Khan, Abidali Mohamedali, Md Golam Muktadir, Shoba Ranganathan, Sock-Hwee Tan, Edouard Nice and Mark S Baker

Direct and rapid mass spectral fingerprinting of maternal urine for the detection of Down syndrome pregnancy

The established methods of antenatal screening for Down syndrome are based on immunoassay for a panel of maternal serum biomarkers together with ultrasound measures. Recently, genetic analysis of maternal plas...

Authors: Ray K Iles, Maryam E Shahpari, Howard Cuckle and Stephen A Butler

Proteomics profiling identify CAPS as a potential predictive marker of tamoxifen resistance in estrogen receptor positive breast cancer

Despite the success of tamoxifen since its introduction, about one-third of patients with estrogen (ER) and/or progesterone receptor (PgR) - positive breast cancer (BC) do not benefit from therapy. Here, we ai...

Authors: Henrik J Johansson, Betzabe C Sanchez, Jenny Forshed, Olle Stål, Helena Fohlin, Rolf Lewensohn, Per Hall, Jonas Bergh, Janne Lehtiö and Barbro K Linderholm

Serum biomarkers of Burkholderia mallei infection elucidated by proteomic imaging of skin and lung abscesses

The bacterium Burkholderia mallei is the etiological agent of glanders, a highly contagious, often fatal zoonotic infectious disease that is also a biodefense concern. Clinical laboratory assays that analyze bloo...

Authors: Trevor G Glaros, Candace D Blancett, Todd M Bell, Mohan Natesan and Robert G Ulrich

Identification of Nocardia species using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry

The MALDI (matrix-assisted laser desorption/ionization) Biotyper system for bacterial identification has already been utilized in clinical microbiology laboratories as a successful clinical application of prot...

Authors: Shunsuke Segawa, Motoi Nishimura, Kazuyuki Sogawa, Sachio Tsuchida, Shota Murata, Masaharu Watanabe, Kazuyuki Matsushita, Katsuhiko Kamei and Fumio Nomura