Articles

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

Proteomic analysis of human follicular fluid from fertile women

Follicular fluid is a unique biological fluid in which the critical events of oocyte and follicular maturation and somatic cell-germ cell communication occur. Because of the intimate proximity of follicular fl...

Authors: Alberuni M Zamah, Maria E Hassis, Matthew E Albertolle and Katherine E Williams

Impact of precise modulation of reactive oxygen species levels on spermatozoa proteins in infertile men

Elevated levels of reactive oxygen species (ROS) are detected in 25% to 80% of infertile men. They are involved in the pathology of male infertility. Understanding the effect of increasing levels of ROS on the...

Authors: Ahmet Ayaz, Ashok Agarwal, Rakesh Sharma, Mohamed Arafa, Haitham Elbardisi and Zhihong Cui

An integrated quantification method to increase the precision, robustness, and resolution of protein measurement in human plasma samples

Current quantification methods for mass spectrometry (MS)-based proteomics either do not provide sufficient control of variability or are difficult to implement for routine clinical testing.

Authors: Xiao-jun Li, Lik Wee Lee, Clive Hayward, Mi-Youn Brusniak, Pui-Yee Fong, Matthew McLean, JoAnne Mulligan, Douglas Spicer, Kenneth C Fang, Stephen W Hunsucker and Paul Kearney

Proteomic signatures of serum albumin-bound proteins from stroke patients with and without endovascular closure of PFO are significantly different and suggest a novel mechanism for cholesterol efflux

The anatomy of PFO suggests that it can allow thrombi and potentially harmful circulatory factors to travel directly from the venous to the arterial circulation – altering circulatory phenotype. Our previous p...

Authors: Mary F Lopez, Bryan Krastins, David A Sarracino, Gregory Byram, Maryann S Vogelsang, Amol Prakash, Scott Peterman, Shadab Ahmad, Gouri Vadali, Wenjun Deng, Ignacio Inglessis, Tom Wickham, Kathleen Feeney, G William Dec, Igor Palacios, Ferdinando S Buonanno…

Quantitative tandem mass-spectrometry of skin tissue reveals putative psoriatic arthritis biomarkers

Psoriatic arthritis (PsA) is a distinct inflammatory arthritis occurring in 30% of psoriasis patients. There is a high prevalence of undiagnosed PsA in psoriasis patients; therefore, identifying soluble biomar...

Authors: Daniela Cretu, Kun Liang, Punit Saraon, Ihor Batruch, Eleftherios P Diamandis and Vinod Chandran

Integration of omics sciences to advance biology and medicine

In the past two decades, our ability to study cellular and molecular systems has been transformed through the development of omics sciences. While unlimited potential lies within massive omics datasets, the su...

Authors: Emily S Boja, Christopher R Kinsinger, Henry Rodriguez and Pothur Srinivas

LecT-Hepa facilitates estimating treatment outcome during interferon therapy in chronic hepatitis C patients

A combination treatment of interferon and ribavirin is the standard and the commonly used treatment for chronic hepatitis C (CHC). Developing noninvasive tests like serum indicators that can predict treatment ...

Authors: Xia Zou, Xiumei Chi, Yu Pan, Dongning Du, Haibo Sun, Atsushi Matsuda, Wei Li, Atsushi Kuno, Xinxin Zhang, Hisashi Narimatsu, Junqi Niu and Yan Zhang

Quantifying CD4 receptor protein in two human CD4+ lymphocyte preparations for quantitative flow cytometry

In our previous study that characterized different human CD4+ lymphocyte preparations, it was found that both commercially available cryopreserved peripheral blood mononuclear cells (PBMC) and a commercially a...

Authors: Meiyao Wang, Martin Misakian, Hua-Jun He, Peter Bajcsy, Fatima Abbasi, Jeffrey M Davis, Kenneth D Cole, Illarion V Turko and Lili Wang

Differentiation of mucinous from non-mucinous pancreatic cyst fluid using dual-stained, 1 dimensional polyacrylamide gel electrophoresis

Pancreatic cysts are being increasingly identified in patients. Mucinous cysts have malignant potential whereas non-mucinous cysts do not. Distinguishing potentially malignant cysts from harmless ones by the c...

Authors: John M Streitz, Michael T Madden, Wilmar Salo, Kirk P Bernadino, Joseph L Deutsch and John C Deutsch

Plasticity of fibroblasts demonstrated by tissue-specific and function-related proteome profiling

Fibroblasts are mesenchymal stromal cells which occur in all tissue types. While their main function is related to ECM production and physical support, they are also important players in wound healing, and hav...

Authors: Astrid Slany, Anastasia Meshcheryakova, Agnes Beer, Hendrik Jan Ankersmit, Verena Paulitschke and Christopher Gerner

Proteomic analysis of human placental syncytiotrophoblast microvesicles in preeclampsia

Placental syncytiotrophoblast microvesicles (STBM) are shed into the maternal circulation during normal pregnancy. STBM circulate in significantly increased amounts in preeclampsia (PE) and are considered to b...

Authors: Sonia Baig, Narasimhan Kothandaraman, Jayapal Manikandan, Li Rong, Kim Huey EE, Jeffrey Hill, Chin Wee Lai, Wan Yu Tan, Felicia Yeoh, Anita Kale, Lin Lin Su, Arijit Biswas, Sheila Vasoo and Mahesh Choolani

Assessment of the influence of the patient’s inflammatory state on the accuracy of a haptoglobin selected reaction monitoring assay

The use of targeted LC-MS/MS methods for protein quantitation in clinical laboratories implies a careful evaluation of potential sources of analytical interference. In this study, we investigated whether infla...

Authors: Olivier Lassout, Denis Hochstrasser and Pierre Lescuyer