Articles

A review of studies of the proteomes of circulating microparticles: key roles for galectin-3-binding protein-expressing microparticles in vascular diseases and systemic lupus erythematosus

Subcellular microvesicles (MVs) have attracted increasing interest during the past decades. While initially considered as inert cellular debris, several important roles for MVs in physiological homeostasis, ca...

Authors: Christoffer T. Nielsen, Ole Østergaard, Niclas S. Rasmussen, Søren Jacobsen and Niels H. H. Heegaard

Glycated lysine-141 in haptoglobin improves the diagnostic accuracy for type 2 diabetes mellitus in combination with glycated hemoglobin HbA_1c and fasting plasma glucose

Recent epidemiological studies indicate that only 30–50% of undiagnosed type 2 diabetes mellitus (T2DM) patients are identified using glycated hemoglobin (HbA_1c) and elevated fasting plasma glucose (FPG) levels. ...

Authors: Sandro Spiller, Yichao Li, Matthias Blüher, Lonnie Welch and Ralf Hoffmann

OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages

Despite recent advances in colorectal cancer (CRC) diagnosis and population screening programs, the identification of patients with preneoplastic lesions or with early CRC stages remains challenging and is imp...

Authors: Florence Quesada-Calvo, Charlotte Massot, Virginie Bertrand, Rémi Longuespée, Noëlla Blétard, Joan Somja, Gabriel Mazzucchelli, Nicolas Smargiasso, Dominique Baiwir, Marie-Claire De Pauw-Gillet, Philippe Delvenne, Michel Malaise, Carla Coimbra Marques, Marc Polus, Edwin De Pauw, Marie-Alice Meuwis…

Tubulointerstitial nephritis antigen-like 1 protein is downregulated in the placenta of pre-eclamptic women

Tubulointerstitial nephritis antigen-like 1 protein (TINAGL1), is a matricellular protein, known to play role in cell adhesion and cell receptor interaction. Research related to TINAGL1 is limited to cell cult...

Authors: Sheon Mary, Mahesh J. Kulkarni, Savita S. Mehendale, Sadhana R. Joshi and Ashok P. Giri

Cervical mucus proteome in endometriosis

Endometriosis is a chronic gynecological inflammatory disease characterized by the presence of functional endometrial glands and stroma outside of the uterine cavity. It affects 7–10% of women of reproductive ...

Authors: Giuseppe Grande, Federica Vincenzoni, Domenico Milardi, Giuseppina Pompa, Domenico Ricciardi, Erika Fruscella, Francesca Mancini, Alfredo Pontecorvi, Massimo Castagnola and Riccardo Marana

Serum proteomic-based analysis identifying autoantibodies against PRDX2 and PRDX3 as potential diagnostic biomarkers in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a major head and neck cancer with high occurrence in Southeast Asia and southern China. We aimed to identify autoantibodies that may contribute to early detection of NPC.

Authors: Lie-Hao Lin, Yi-Wei Xu, Li-Sheng Huang, Chao-Qun Hong, Tian-Tian Zhai, Lian-Di Liao, Wen-Jie Lin, Li-Yan Xu, Kai Zhang, En-Min Li and Yu-Hui Peng

Immune-enrichment of insulin in bio-fluids on gold-nanoparticle decorated target plate and in situ detection by MALDI MS

Detection of low-abundance biomarkers using mass spectrometry (MS) is often hampered by non-target molecules in biological fluids. In addition, current procedures for sample preparation increase sample consump...

Authors: Kai Liang, Hongmei Wu and Yan Li

A new enzyme-linked immunosorbent assay (ELISA) for human free and bound kallikrein 9

Kallikrein 9 (KLK9) is a member of the human kallikrein-related peptidases family, whose physiological role and implications in disease processes remain unclear. The active form of the enzyme is predicted to h...

Authors: Panagiota Filippou, Dimitrios Korbakis, Sofia Farkona, Antoninus Soosaipillai, Theano Karakosta and Eleftherios P. Diamandis

Simultaneous analyses of N-linked and O-linked glycans of ovarian cancer cells using solid-phase chemoenzymatic method

Glycans play critical roles in a number of biological activities. Two common types of glycans, N-linked and O-linked, have been extensively analyzed in the last decades. N-glycans are typically released from g...

Authors: Shuang Yang, Naseruddin Höti, Weiming Yang, Yang Liu, Lijun Chen, Shuwei Li and Hui Zhang

Redox proteomic identification of carbonylated proteins in autism plasma: insight into oxidative stress and its related biomarkers in autism

Autism is a severe childhood neurological disorder with poorly understood etiology and pathology. Currently, there is no authentic laboratory test to confirm the diagnosis of autism. Oxidative damage may play ...

Authors: Chengyun Feng, Youjiao Chen, Jintao Pan, Aochu Yang, Li Niu, Jie Min, Xianling Meng, Liping Liao, Kaoyuan Zhang and Liming Shen

Development of a microarray-based method for allergen-specific IgE and IgG4 detection

sIgE and sIgG4 detection is necessary for more accurate and effective type I hypersensitivity diagnostics and the estimation of disease development. Typically, the analyses of these antibodies are performed se...

Authors: Guzel Feyzkhanova, Sergei Voloshin, Olga Smoldovskaya, Alla Arefieva, Marina Filippova, Viktor Barsky, Ludmila Pavlushkina, Veronika Butvilovskaya, Alexei Tikhonov, Yuri Reznikov and Alla Rubina

Cardiovascular proteomics in the era of big data: experimental and computational advances

Proteomics plays an increasingly important role in our quest to understand cardiovascular biology. Fueled by analytical and computational advances in the past decade, proteomics applications can now go beyond ...

Authors: Maggie P. Y. Lam, Edward Lau, Dominic C. M. Ng, Ding Wang and Peipei Ping

Mesoporous silica chip: enabled peptide profiling as an effective platform for controlling bio-sample quality and optimizing handling procedure

High quality clinical samples are critical for meaningful interpretation of data obtained in both basic and translational medicine. More specifically, optimized pre-analysis handling to bio-sample is crucial ...

Authors: Kai Liang, Hongmei Wu, Tony Y. Hu and Yan Li

Proteome analysis of excretory-secretory proteins of Entamoeba histolytica HM1:IMSS via LC–ESI–MS/MS and LC–MALDI–TOF/TOF

Excretory-secretory (ES) proteins of E. histolytica are thought to play important roles in the host invasion, metabolism, and defence. Elucidation of the types and functions of E. histolytica ES proteins can furt...

Authors: Jorim Anak Ujang, Soon Hong Kwan, Mohd Nazri Ismail, Boon Huat Lim, Rahmah Noordin and Nurulhasanah Othman

Integrated glycomic analysis of ovarian cancer side population cells

Ovarian cancer is the most lethal gynecological malignancy due to its frequent recurrence and drug resistance even after successful initial treatment. Accumulating scientific evidence indicates that subpopulat...

Authors: Ran Zhao, Xiaoxia Liu, Yisheng Wang, Xiaoxiang Jie, Ruihuan Qin, Wenjun Qin, Mengyu Zhang, Haiyan Tai, Caiting Yang, Lili Li, Peike Peng, Miaomiao Shao, Xingwang Zhang, Hao Wu, Yuanyuan Ruan, Congjian Xu…

Proteomics in India: the clinical aspect

Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is ...

Authors: Somaditya Mukherjee and Arun Bandyopadhyay

Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival

Lung cancer is the leading cause of cancer mortality in the United States. Non-small cell lung cancer accounts for 85% of all lung cancers for which adenocarcinoma is the most common histological type. Managem...

Authors: Johannes F. Fahrmann, Dmitry Grapov, Brett S. Phinney, Carol Stroble, Brian C. DeFelice, William Rom, David R. Gandara, Yanhong Zhang, Oliver Fiehn, Harvey Pass and Suzanne Miyamoto

Implementation and evaluation of amyloidosis subtyping by laser-capture microdissection and tandem mass spectrometry

Correct identification of the amyloidosis-causing protein is crucial for clinical management. Recently the Mayo Clinic reported laser-capture microdissection (LCM) with liquid chromatography-coupled tandem mas...

Authors: Peter Mollee, Samuel Boros, Dorothy Loo, Jayde E. Ruelcke, Vanessa A. Lakis, Kim-Anh Lê Cao, Patricia Renaut and Michelle M. Hill

Proteomic profiling of retinoblastoma by high resolution mass spectrometry

Retinoblastoma is an ocular neoplastic cancer caused primarily due to the mutation/deletion of RB1 gene. Due to the rarity of the disease very limited information is available on molecular changes in primary r...

Authors: Ravikanth Danda, Kalaivani Ganapathy, Gajanan Sathe, Anil K. Madugundu, Sharavan Ramachandran, Uma Maheswari Krishnan, Vikas Khetan, Pukhraj Rishi, T. S. Keshava Prasad, Akhilesh Pandey, Subramanian Krishnakumar, Harsha Gowda and Sailaja V. Elchuri

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