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Variable blood processing procedures contribute to plasma proteomic variability Clin. Proteom. (IF 2.568) Pub Date : 2021-01-19 Patrick Halvey; Victor Farutin; Laura Koppes; Nur Sibel Gunay; Dimitrios A. Pappas; Anthony M. Manning; Ishan Capila
Plasma is a potentially rich source of protein biomarkers for disease progression and drug response. Large multi-center studies are often carried out to increase the number of samples analyzed in a given study. This may increase the chances of variation in blood processing and handling, leading to altered proteomic results. This study evaluates the impact of blood processing variation on LC–MS/MS proteomic
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Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics Clin. Proteom. (IF 2.568) Pub Date : 2021-01-07 Kristin L. M. Boylan; Somaieh Afiuni-Zadeh; Melissa A. Geller; Peter A. Argenta; Timothy J. Griffin; Amy P. N. Skubitz
The purpose of this study was to determine whether the residual fixative from a liquid-based Pap test or a swab of the cervix contained proteins that were also found in the primary tumor of a woman with high grade serous ovarian cancer. This study is the first step in determining the feasibility of using the liquid-based Pap test or a cervical swab for the detection of ovarian cancer protein biomarkers
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Global proteome profiling of human livers upon ischemia/reperfusion treatment Clin. Proteom. (IF 2.568) Pub Date : 2021-01-06 Haijian Cai; Shunli Qi; Qi Yan; Jun Ling; Jian Du; Lijian Chen
Hepatic ischemia/reperfusion (I/R) injury represents a major risk factor for liver transplantation and is related to graft dysfunction and acute/chronic rejection. However, a significant part of these processes remain poorly characterized. To reveal differences in the proteome during liver I/R injury, we collected human liver biopsy samples during hepatectomy before and after the Pringle maneuver and
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Identification of differentially expressed proteins and clinicopathological significance of HMGB2 in cervical cancer Clin. Proteom. (IF 2.568) Pub Date : 2021-01-06 Xiao Han; Siyi Zhong; Pengnan Zhang; Yanmei Liu; Sangsang Shi; Congquan Wu; Shujun Gao
To investigate the complexity of proteomics in cervical cancer tissues, we used isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry analysis on a panel of normal cervical tissues (N), high-grade squamous intraepithelial lesion tissues (HSIL) and cervical cancer tissues (CC). Total 72 differentially expressed proteins were identified both in CC vs N and CC vs HSIL. The
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Label-free proteomic analysis of serum exosomes from paroxysmal atrial fibrillation patients Clin. Proteom. (IF 2.568) Pub Date : 2021-01-06 Hanwen Ni; Wenqi Pan; Qi Jin; Yucai Xie; Ning Zhang; Kang Chen; Tianyou Lin; Changjian Lin; Yun Xie; Jiemin Wu; Peihua Ni; Liqun Wu
Atrial fibrillation (AF) is the most common cardiac heterogeneous rhythm disorder. It represents a major cause of mortality and morbidity, mainly related to embolic events and heart failure. Mechanisms of AF are complex and remain incompletely understood. Recent evidence suggests exosomes are membrane-coated objects released by many cell-types. Their presence in body fluids and the variable surface
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Tear proteomic profile in three distinct ocular surface diseases: keratoconus, pterygium, and dry eye related to graft-versus-host disease Clin. Proteom. (IF 2.568) Pub Date : 2020-12-07 Daniel de Almeida Borges; Marcos Rodrigo Alborghetti; Adriana Franco Paes Leme; Romenia Ramos Domingues; Bruna Duarte; Melina Veiga; Marilia Trindade Ferrer; Ana Claudia Viana Wanzeler; Carlos Eduardo Leite Arieta; Monica Alves
Diseases of the anterior segment of the eye may present different mechanisms, intensity of symptoms, and impact on the patients’ quality of life and vision. The tear film is in direct contact with the ocular surface and cornea and can be easily accessed for sample collection, figuring as a promising source of potential biomarkers for diagnosis and treatment control. This study aimed to evaluate tear
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Clinical proteomics for prostate cancer: understanding prostate cancer pathology and protein biomarkers for improved disease management Clin. Proteom. (IF 2.568) Pub Date : 2020-11-20 Claire Tonry; Stephen Finn; John Armstrong; Stephen R. Pennington
Following the introduction of routine Prostate Specific Antigen (PSA) screening in the early 1990′s, Prostate Cancer (PCa) is often detected at an early stage. There are also a growing number of treatment options available and so the associated mortality rate is generally low. However, PCa is an extremely complex and heterogenous disease and many patients suffer disease recurrence following initial
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Comparative analysis of differentially abundant proteins quantified by LC–MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples Clin. Proteom. (IF 2.568) Pub Date : 2020-11-07 Lori A. Sturtz; Guisong Wang; Punit Shah; Richard Searfoss; Praveen-Kumar Raj-Kumar; Jeffrey A. Hooke; J. Leigh Fantacone-Campbell; Brenda Deyarmin; Mary Lou Cutler; Rangaprasad Sarangarajan; Niven R. Narain; Hai Hu; Michael A. Kiebish; Albert J. Kovatich; Craig D. Shriver
Proteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry (MS). However, FF specimens are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types
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Subclinical effects of remote ischaemic conditioning in human kidney transplants revealed by quantitative proteomics Clin. Proteom. (IF 2.568) Pub Date : 2020-11-02 Adam M. Thorne; Honglei Huang; Darragh P. O‘Brien; Marco Eijken; Nicoline Valentina Krogstrup; Rikke Norregaard; Bjarne Møller; Rutger J. Ploeg; Bente Jespersen; Benedikt M. Kessler
Remote ischaemic conditioning (RIC) is currently being explored as a non-invasive method to attenuate ischaemia/reperfusion injuries in organs. A randomised clinical study (CONTEXT) evaluated the effects of RIC compared to non-RIC controls in human kidney transplants. RIC was induced prior to kidney reperfusion by episodes of obstruction to arterial flow in the leg opposite the transplant using a tourniquet
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Application of SWATH mass spectrometry in the identification of circulating proteins does not predict future weight gain in early psychosis Clin. Proteom. (IF 2.568) Pub Date : 2020-10-27 Adrian Heald; Narges Azadbakht; Bethany Geary; Silke Conen; Helene Fachim; Dave Chi Hoo Lee; Nophar Geifman; Sanam Farman; Oliver Howes; Anthony Whetton; Bill Deakin
Weight gain is a common consequence of treatment with antipsychotic drugs in early psychosis, leading to further morbidity and poor treatment adherence. Identifying tools that can predict weight change in early psychosis may contribute to better-individualised treatment and adherence. Recently we showed that proteomic profiling with sequential window acquisition of all theoretical fragment ion spectra
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A robust multiplex immunoaffinity mass spectrometry assay (PromarkerD) for clinical prediction of diabetic kidney disease Clin. Proteom. (IF 2.568) Pub Date : 2020-10-20 Scott Bringans; Jason Ito; Tammy Casey; Sarah Thomas; Kirsten Peters; Ben Crossett; Orla Coleman; Holger A. Ebhardt; Stephen R. Pennington; Richard Lipscombe
PromarkerD is a novel proteomics derived blood test for predicting diabetic kidney disease (DKD). The test is based on an algorithm that combines the measurement of three plasma protein biomarkers (CD5L, APOA4, and IBP3) with three clinical variables (age, HDL-cholesterol, and eGFR). The initial format of the assay used immunodepletion of plasma samples followed by targeted mass spectrometry (MRM-LCMS)
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Early changes in tear film protein profiles after femtosecond LASIK surgery Clin. Proteom. (IF 2.568) Pub Date : 2020-10-19 Janika Nättinen; Petri Mäkinen; Ulla Aapola; Lasse Orsila; Juhani Pietilä; Hannu Uusitalo
Femtosecond laser-assisted in situ keratomileusis (LASIK) has proven to be an efficacious, predictable, and safe procedure for the correction of refractive errors. We examined the early tear protein changes of patients undergoing LASIK surgery in order to better understand the mechanisms and proteins related to laser corneal surgery and initial recovery. Corneal flaps were created with Ziemer FEMTO
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A proteomic repertoire of autoantigens identified from the classic autoantibody clinical test substrate HEp-2 cells Clin. Proteom. (IF 2.568) Pub Date : 2020-09-21 Julia Y. Wang; Wei Zhang; Jung-hyun Rho; Michael W. Roehrl; Michael H. Roehrl
Autoantibodies are a hallmark of autoimmune diseases. Autoantibody screening by indirect immunofluorescence staining of HEp-2 cells with patient sera is a current standard in clinical practice. Differential diagnosis of autoimmune disorders is based on commonly recognizable nuclear and cytoplasmic staining patterns. In this study, we attempted to identify as many autoantigens as possible from HEp-2
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A nomogram based on glycomic biomarkers in serum and clinicopathological characteristics for evaluating the risk of peritoneal metastasis in gastric cancer. Clin. Proteom. (IF 2.568) Pub Date : 2020-09-19 Junjie Zhao,Ruihuan Qin,Hao Chen,Yupeng Yang,Wenjun Qin,Jing Han,Xuefei Wang,Shifang Ren,Yihong Sun,Jianxin Gu
Peritoneal metastasis (PM) in gastric cancer (GC) remains an untreatable disease, and is difficult to diagnose preoperatively. Here, we aim to establish a novel prediction model. The clinicopathologic characteristics of a cohort that included 86 non-metastatic GC patients and 43 PMGC patients from Zhongshan Hospital were retrospectively analysed to identify PM associated variables. Additionally, mass
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Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. Clin. Proteom. (IF 2.568) Pub Date : 2020-09-18 Astrid Guldbrandsen,Ragnhild Reehorst Lereim,Mari Jacobsen,Hilde Garberg,Ann Cathrine Kroksveen,Harald Barsnes,Frode S Berven
Verification of cerebrospinal fluid (CSF) biomarkers for multiple sclerosis and other neurological diseases is a major challenge due to a large number of candidates, limited sample material availability, disease and biological heterogeneity, and the lack of standardized assays. Furthermore, verification studies are often based on a low number of proteins from a single discovery experiment in medium-sized
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Chloride intracellular channel 4 participate in the protective effect of Ginkgolide B in MPP+ injured MN9D cells: insight from proteomic analysis. Clin. Proteom. (IF 2.568) Pub Date : 2020-09-05 Zili Feng,Zhibin Zhu,Wang Chen,Yu Bai,Daihua Hu,Jia Cheng
Ginkgolide B (GB), the extract of G. biloba leaves, has been shown to be protective against many neurological disorders, including Parkinson’s disease (PD). Efforts have been made to synthesized ginkgolides analogs and derivatives with more targeted and smaller molecular weight. In the present study, four GB derivatives (GBHC-1-GBHC-4) were synthesized, and their protective roles in N-methyl-4-phenylpyridinium
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CSF extracellular vesicle proteomics demonstrates altered protein homeostasis in amyotrophic lateral sclerosis. Clin. Proteom. (IF 2.568) Pub Date : 2020-08-17 Alexander G Thompson,Elizabeth Gray,Imre Mäger,Marie-Laëtitia Thézénas,Philip D Charles,Kevin Talbot,Roman Fischer,Benedikt M Kessler,Mathew Wood,Martin R Turner
Extracellular vesicles (EVs) released by neurons and glia reach the cerebrospinal fluid (CSF). Studying the proteome of CSF-derived EVs offers a novel perspective on the key intracellular processes associated with the pathogenesis of the neurodegenerative disease amyotrophic lateral sclerosis (ALS) and a potential source from which to develop biomarkers. CSF EVs were extracted using ultrafiltration
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Quantitative analysis of differentially expressed proteins in psoriasis vulgaris using tandem mass tags and parallel reaction monitoring. Clin. Proteom. (IF 2.568) Pub Date : 2020-08-12 Yu Li,Peng Lin,Siyao Wang,Shuang Li,Rui Wang,Lin Yang,Hongmei Wang
Psoriasis vulgaris (PV) is a chronic autoimmune inflammatory disease with epidermal hyperkeratosis and parakeratosis. The study was to elucidate the pathogenesis of PV by quantitative proteomic analysis of skin lesion biopsies of PV and healthy tissues with tandem mass tags (TMTs) coupled with liquid chromatography–mass spectrometry (LC–MS)/MS. A total of 4562 differentially expressed proteins (DEPs)
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Proteomic analysis of synovial fluid from rheumatic arthritis and spondyloarthritis patients. Clin. Proteom. (IF 2.568) Pub Date : 2020-08-06 Svend Birkelund,Tue Bjerg Bennike,Kenneth Kastaniegaard,Mads Lausen,Thomas Bouet Guldbæk Poulsen,Tue Wenzel Kragstrup,Bent Winding Deleuran,Gunna Christiansen,Allan Stensballe
The aetiologies and pathogeneses of the joint diseases rheumatoid arthritis (RA) and spondyloarthritis (SpA) are still not fully elucidated. To increase our understanding of the molecular pathogenesis, we analysed the protein composition of synovial fluid (SF) from rheumatoid arthritis (RA) and spondyloarthritis (SpA) patients. Fifty-six synovial fluid samples (RA, n = 32; SpA, n = 24) were digested
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Proteomic approaches for characterizing renal cell carcinoma. Clin. Proteom. (IF 2.568) Pub Date : 2020-07-29 David J Clark,Hui Zhang
Renal cell carcinoma is among the top 15 most commonly diagnosed cancers worldwide, comprising multiple sub-histologies with distinct genomic, proteomic, and clinicopathological features. Proteomic methodologies enable the detection and quantitation of protein profiles associated with the disease state and have been explored to delineate the dysregulated cellular processes associated with renal cell
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Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin. Proteom. (IF 2.568) Pub Date : 2020-07-11 Sara R Savage,Bing Zhang
Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources are available to facilitate the translation of phosphopeptide identification and quantification results into novel biological and clinical insights, a critical step in phosphoproteomics data analysis. These resources include knowledge bases of
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The plasma peptides of sepsis. Clin. Proteom. (IF 2.568) Pub Date : 2020-07-02 Thanusi Thavarajah,Claudia C Dos Santos,Arthur S Slutsky,John C Marshall,Pete Bowden,Alexander Romaschin,John G Marshall
A practical strategy to discover sepsis specific proteins may be to compare the plasma peptides and proteins from patients in the intensive care unit with and without sepsis. The aim was to discover proteins and/or peptides that show greater observation frequency and/or precursor intensity in sepsis. The endogenous tryptic peptides of ICU-Sepsis were compared to ICU Control, ovarian cancer, breast
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Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry. Clin. Proteom. (IF 2.568) Pub Date : 2020-06-23 Damir Oros,Marina Ceprnja,Jurica Zucko,Mario Cindric,Amela Hozic,Jasenka Skrlin,Karmela Barisic,Ena Melvan,Ksenija Uroic,Blazenka Kos,Antonio Starcevic
Reliable high-throughput microbial pathogen identification in human urine samples is crucial for patients with cystitis symptoms. Currently employed methods are time-consuming and could lead to unnecessary or inadequate antibiotic treatment. Purpose of this study was to assess the potential of mass spectrometry for uropathogen identification from a native urine sample. In total, 16 urine samples having
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Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. Clin. Proteom. (IF 2.568) Pub Date : 2020-06-17 Jeremy A Herrera,Venkatesh Mallikarjun,Silvia Rosini,Maria Angeles Montero,Craig Lawless,Stacey Warwood,Ronan O'Cualain,David Knight,Martin A Schwartz,Joe Swift
Haematoxylin and eosin (H&E)—which respectively stain nuclei blue and other cellular and stromal material pink—are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the
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Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation. Clin. Proteom. (IF 2.568) Pub Date : 2020-06-16 Mario Navarrete,Brice Korkmaz,Carla Guarino,Adam Lesner,Ying Lao,Julie Ho,Peter Nickerson,John A Wilkins
The pathophysiology of subclinical versus clinical rejection remains incompletely understood given their equivalent histological severity but discordant graft function. The goal was to evaluate serine hydrolase enzyme activities to explore if there were any underlying differences in activities during subclinical versus clinical rejection. Serine hydrolase activity-based protein profiling (ABPP) was
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Human follicular fluid proteome reveals association between overweight status and oocyte maturation abnormality. Clin. Proteom. (IF 2.568) Pub Date : 2020-06-08 Xin Liu,Yanhua Wang,Peng Zhu,Jiahui Wang,Juan Liu,Ning Li,Wenting Wang,Wendi Zhang,Chengli Zhang,Yanwei Wang,Xiaofang Shen,Fujun Liu
Human follicular fluid (HFF), which is composed by essential proteins required for the follicle development, provides an important microenvironment for oocyte maturation. Recently, overweight status has been considered as a detrimental impact factor on oocyte maturation, but whether HFF proteome could provide protein markers for assessing overweight-based oocyte maturation deficiency is still unknown
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A comprehensive systematic review of CSF proteins and peptides that define Alzheimer's disease. Clin. Proteom. (IF 2.568) Pub Date : 2020-06-05 Cristina M Pedrero-Prieto,Sonia García-Carpintero,Javier Frontiñán-Rubio,Emilio Llanos-González,Cristina Aguilera García,Francisco J Alcaín,Iris Lindberg,Mario Durán-Prado,Juan R Peinado,Yoana Rabanal-Ruiz
During the last two decades, over 100 proteomics studies have identified a variety of potential biomarkers in CSF of Alzheimer’s (AD) patients. Although several reviews have proposed specific biomarkers, to date, the statistical relevance of these proteins has not been investigated and no peptidomic analyses have been generated on the basis of specific up- or down- regulation. Herein, we perform an
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Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis. Clin. Proteom. (IF 2.568) Pub Date : 2020-06-01 Ji-Hyun Lee,Jae Hun Jung,Jeesoo Kim,Won-Ki Baek,Jinseol Rhee,Tae-Hwan Kim,Sang-Hyon Kim,Kwang Pyo Kim,Chang-Nam Son,Jong-Seo Kim
Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease affecting the axial skeleton and peripheral joints. The etiology of this disease remains poorly understood, but interactions between genetic and environmental factors have been implicated. The present study identified differentially expressed proteins in the synovial fluid (SF) of AS patients to elucidate the underlying cause of
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Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer's disease. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-29 Maotian Zhou,Rafi U Haque,Eric B Dammer,Duc M Duong,Lingyan Ping,Erik C B Johnson,James J Lah,Allan I Levey,Nicholas T Seyfried
Alzheimer’s disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline. Protein biomarkers of AD brain pathology, including β-amyloid and Tau, are reflected in cerebrospinal fluid (CSF), yet the identification of additional biomarkers linked to other brain pathophysiologies remains elusive. We recently reported a multiplex tandem-mass tag (TMT) CSF proteomic analysis
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New risk score for predicting steroid resistance in patients with focal segmental glomerulosclerosis or minimal change disease. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-29 Qinjie Weng,Qiongxiu Zhou,Jun Tong,Yuanmeng Jin,Yunzi Liu,Xialian Yu,Xiaoxia Pan,Hong Ren,Weiming Wang,Jingyuan Xie,Nan Chen
Glucocorticosteroid is used for patients with primary nephrotic syndrome. This study aims to identify and validate that biomarkers can be used to predict steroid resistance. Our study contained two stages, discovery and validation stage. In discovery stage, we enrolled 51 minimal change disease (MCD) or focal segmental glomerulosclerosis (FSGS) patients treated with full dose steroid. Five urinary
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Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-24 Andrew Macklin,Shahbaz Khan,Thomas Kislinger
Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect
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Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-24 Dongyoon Shin,Joonho Park,Dohyun Han,Ji Hye Moon,Han Suk Ryu,Youngsoo Kim
Metastasis of breast cancer to distal organs is fatal. However, few studies have identified biomarkers that are associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers, such as HER2, ER, and PR, to differentiate between distant and nondistant metastatic breast cancers accurately has necessitated the development of novel biomarker candidates. An integrated
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Effects of cryopreservation and long-term culture on biological characteristics and proteomic profiles of human umbilical cord-derived mesenchymal stem cells. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-24 Xufeng Fu,Bo Xu,Jiang Jiang,Xing Du,Xiaoli Yu,Yaping Yan,Shanshan Li,Briauna Marie Inglis,Huiming Ma,Hongyan Wang,Xiuying Pei,Wei Si
Human umbilical cord-derived MSCs (hUC-MSCs) have been identified as promising seeding cells in tissue engineering and clinical applications of regenerative medicine due to their advantages of simple acquisition procedure and the capability to come from a young tissue donor over the other MSCs sources. In clinical applications, large scale production is required and optimal cryopreservation and culture
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Mass spectrometry-based microbiological testing for blood stream infection. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-13 Fumio Nomura,Sachio Tsuchida,Syota Murata,Mamoru Satoh,Kazuyuki Matsushita
Background The most successful application of mass spectrometry (MS) in laboratory medicine is identification (ID) of microorganisms using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in blood stream infection. We describe MALDI-TOF MS-based bacterial ID with particular emphasis on the methods so far developed to directly identify microorganisms from positive
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Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid. Clin. Proteom. (IF 2.568) Pub Date : 2020-05-04 Chan Hyun Na,Gajanan Sathe,Liana S Rosenthal,Abhay R Moghekar,Valina L Dawson,Ted M Dawson,Akhilesh Pandey
Background Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. Biomarkers that can help monitor the progression of PD or response to disease-modifying agents will be invaluable in making appropriate therapeutic decisions. Further, biomarkers that could be used to distinguish PD from other related disorders with PD-like symptoms will be useful for accurate diagnosis and
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A comprehensive analysis of sialolith proteins and the clinical implications. Clin. Proteom. (IF 2.568) Pub Date : 2020-03-31 Carlos S Busso,Jessie J Guidry,Jhanis J Gonzalez,Vassilia Zorba,Leslie S Son,Peter J Winsauer,Rohan R Walvekar
Background Sialolithiasis or salivary gland stones are associated with high clinical morbidity. The advances in the treatment of sialolithiasis has been limited, however, by our understanding of their composition. More specifically, there is little information regarding the formation and composition of the protein matrix, the role of mineralogical deposition, or the contributions of cell epithelium
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Early detection of Ebola virus proteins in peripheral blood mononuclear cells from infected mice Clin. Proteom. (IF 2.568) Pub Date : 2020-03-17 Michael D. Ward; Tara Kenny; Ernie Bruggeman; Christopher D. Kane; Courtney L. Morrell; Molly M. Kane; Sandra Bixler; Sarah L. Grady; Rachel S. Quizon; Mekbib Astatke; Lisa H. Cazares
Detection of viral ribo-nucleic acid (RNA) via real-time polymerase chain reaction (RT-PCR) is the gold standard for the detection of Ebola virus (EBOV) during acute infection. However, the earliest window for viral RNA detection in blood samples is 48–72 h post-onset of symptoms. Therefore, efforts to develop additional orthogonal assays using complementary immunological and serological technologies
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Urinary proteomics of Henoch-Schönlein purpura nephritis in children using liquid chromatography-tandem mass spectrometry Clin. Proteom. (IF 2.568) Pub Date : 2020-03-12 Xiang Fang; Heyan Wu; Mei Lu; Yan Cao; Ren Wang; Meiqiu Wang; Chunlin Gao; Zhengkun Xia
Henoch-Schönlein purpura nephritis (HSPN) is the principal cause of morbidity and mortality in children with Henoch-Schönlein purpura (HSP). However, the criteria for risk assessment currently used is not satisfactory. The urine proteome may provide important clues to indicate the development of HSPN. Here, we detected and compared the urine proteome of patients with HSPN and healthy controls by liquid
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The impact of ultraviolet- and infrared-based laser microdissection technology on phosphoprotein detection in the laser microdissection-reverse phase protein array workflow. Clin. Proteom. (IF 2.568) Pub Date : 2020-03-09 Allison L Hunt,Mariaelena Pierobon,Elisa Baldelli,Julie Oliver,Dave Mitchell,Glenn Gist,Nicholas W Bateman,G Larry Maxwell,Emanuel F Petricoin,Thomas P Conrads
Reversible protein phosphorylation represents a key mechanism by which signals are transduced in eukaryotic cells. Dysregulated phosphorylation is also a hallmark of carcinogenesis and represents key drug targets in the precision medicine space. Thus, methods that preserve phosphoprotein integrity in the context of clinical tissue analyses are crucially important in cancer research. Here we investigated
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The different expression of glycogen phosphorylases in renal clear cell renal carcinoma and chromophobe renal carcinoma. Clin. Proteom. (IF 2.568) Pub Date : 2020-02-26 Yang Lu,Guangda Luo,Songbiao Zhu,Xu Wang,Yuling Chen,ZhouHuan Dong,Shiyu Wang,Jie Ma,Haiteng Deng,Di Wu,Jun Dong
Background The various pathogenesis between Clear cell renal carcinoma (CCRCC) and Chromophobe renal carcinoma (CHRCC) contributes to the different tumor growth rate and metastasis. In this study, we explored the distinct proteomic profiles between these two cancers and found different expression of glycogen phosphorylases in two cancers. Methods We explored novel targets by proteomics. Five CCRCC
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Correction to: Proteomic analysis of degradation ubiquitin signaling by ubiquitin occupancy changes responding to 26S proteasome inhibition. Clin. Proteom. (IF 2.568) Pub Date : 2020-02-21 Ventzislava Hristova,Shisheng Sun,Hui Zhang,Daniel W Chan
[This corrects the article DOI: 10.1186/s12014-020-9265-x.].
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Discovery of a putative blood-based protein signature associated with response to ALK tyrosine kinase inhibition. Clin. Proteom. (IF 2.568) Pub Date : 2020-02-07 Mathilde Couëtoux du Tertre,Maud Marques,Suzan McNamara,Karen Gambaro,Cyrla Hoffert,Lise Tremblay,Nicole Bouchard,Razvan Diaconescu,Normand Blais,Christian Couture,Vincent Pelsser,Hangjun Wang,Laura McIntosh,Valérie Hindie,Stephane Parent,Laetitia Cortes,Yannick-André Breton,Gwenael Pottiez,Pascal Croteau,Valerie Higenell,Luisa Izzi,Alan Spatz,Victor Cohen,Gerald Batist,Jason Agulnik
Background ALK tyrosine kinase inhibition has become a mainstay in the clinical management of ALK fusion positive NSCLC patients. Although ALK mutations can reliably predict the likelihood of response to ALK tyrosine kinase inhibitors (TKIs) such as crizotinib, they cannot reliably predict response duration or intrinsic/extrinsic therapeutic resistance. To further refine the application of personalized
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Prediction of neoadjuvant chemotherapeutic efficacy in patients with locally advanced gastric cancer by serum IgG glycomics profiling. Clin. Proteom. (IF 2.568) Pub Date : 2020-02-06 Ruihuan Qin,Yupeng Yang,Hao Chen,Wenjun Qin,Jing Han,Yong Gu,Yiqing Pan,Xi Cheng,Junjie Zhao,Xuefei Wang,Shifang Ren,Yihong Sun,Jianxin Gu
Background Neoadjuvant chemotherapy (NACT) could improve prognosis and survival quality of patients with local advanced gastric cancer (LAGC) by providing an opportunity of radical operation for them. However, no effective method could predict the efficacy of NACT before surgery to avoid the potential toxicity, time-consuming and economic burden of ineffective chemotherapy. Some research has been investigated
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Quantitative site- and structure-specific N-glycoproteomics characterization of differential N-glycosylation in MCF-7/ADR cancer stem cells. Clin. Proteom. (IF 2.568) Pub Date : 2020-02-05 Feifei Xu,Yue Wang,Kaijie Xiao,Yechen Hu,Zhixin Tian,Yun Chen
Background Cancer stem cells (CSCs) are reported to be responsible for tumor initiation, progression, metastasis, and therapy resistance where P-glycoprotein (P-gp) as well as other glycoproteins are involved. Identification of these glycoprotein markers is critical for understanding the resistance mechanism and developing therapeutics. Methods In this study, we report our comparative and quantitative
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Proteomic analysis of degradation ubiquitin signaling by ubiquitin occupancy changes responding to 26S proteasome inhibition. Clin. Proteom. (IF 2.568) Pub Date : 2020-01-25 Ventzislava Hristova,Shisheng Sun,Hui Zhang,Daniel W Chan
Background Ubiquitination is a post-translational modification where ubiquitin is covalently attached to lysine residues on substrate proteins to signal their degradation by the 26S proteasome or initiate other non-degradation functions such as cellular trafficking. The diversity of ubiquitin modifications can be attributed to the variable number of ubiquitin molecules attached to a lysine residue
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The omics revolution: beyond genomics. A meeting report. Clin. Proteom. (IF 2.568) Pub Date : 2020-01-24 E C Nice
The "omics revolution: beyond genomics" satellite meeting, run under the auspices of the Australian Peptide Association, The Human Proteome Organisation (HUPO) and the HUPO Australia/New Zealand Chromosome 7 initiative, was held at the Oaks Resort, Port Douglas, Queensland, Australia, on 8th September 2019, immediately prior to the 13th Australian Peptide Conference. The meeting, which had over 100
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Proteomics analysis of colon cancer progression Clin. Proteom. (IF 2.568) Pub Date : 2019-12-28 Saira Saleem; Sahrish Tariq; Iffat Aleem; Sadr-ul Shaheed; Muhammad Tahseen; Aribah Atiq; Sadia Hassan; Muhammad Abu Bakar; Shahid Khattak; Aamir Ali Syed; Asad Hayat Ahmad; Mudassar Hussain; Muhammed Aasim Yusuf; Chris Sutton
The aim of this pilot study was to identify proteins associated with advancement of colon cancer (CC). A quantitative proteomics approach was used to determine the global changes in the proteome of primary colon cancer from patients with non-cancer normal colon (NC), non-adenomatous colon polyp (NAP), non-metastatic tumor (CC NM) and metastatic tumor (CC M) tissues, to identify up- and down-regulated
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The plasma peptides of breast versus ovarian cancer Clin. Proteom. (IF 2.568) Pub Date : 2019-12-23 Jaimie Dufresne; Pete Bowden; Thanusi Thavarajah; Angelique Florentinus-Mefailoski; Zhuo Zhen Chen; Monika Tucholska; Tenzin Norzin; Margaret Truc Ho; Morla Phan; Nargiz Mohamed; Amir Ravandi; Eric Stanton; Arthur S. Slutsky; Claudia C. dos Santos; Alexander Romaschin; John C. Marshall; Christina Addison; Shawn Malone; Daren Heyland; Philip Scheltens; Joep Killestein; Charlotte Teunissen; Eleftherios
There is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous
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Quantitative proteome analysis of Merkel cell carcinoma cell lines using SILAC Clin. Proteom. (IF 2.568) Pub Date : 2019-12-19 Ulana Kotowski; Boban M. Erović; Julia Schnöll; Victoria Stanek; Stefan Janik; Martin Steurer; Goran Mitulović
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine tumour of the skin with growing incidence. To better understand the biology of this malignant disease, immortalized cell lines are used in research for in vitro experiments. However, a comprehensive quantitative proteome analysis of these cell lines has not been performed so far. Stable isotope labelling by amino acids in cell culture (SILAC)
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Clinical method evaluation of hemoglobin S and C identification by top-down selected reaction monitoring and electron transfer dissociation Clin. Proteom. (IF 2.568) Pub Date : 2019-12-17 Olivier Lassout; Ralf Hartmer; Wolfgang Jabs; Lorella Clerici; Yury O. Tsybin; Kaveh Samii; Nicolas Vuilleumier; Denis Hochstrasser; Alexander Scherl; Pierre Lescuyer; Didia Coelho Graça
Biological diagnosis of hemoglobin disorders is a complex process relying on the combination of several analytical techniques to identify Hb variants in a particular sample. Currently, hematology laboratories usually use high-performance liquid chromatography (HPLC), capillary electrophoresis and gel-based methods to characterize Hb variants. Co-elution and co-migration may represent major issues for
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The associations of self-rated health with cardiovascular risk proteins: a proteomics approach. Clin. Proteom. (IF 2.568) Pub Date : 2019-11-18 Xue Bao,Yan Borné,Songjiang Yin,Kaijun Niu,Marju Orho-Melander,Jan Nilsson,Olle Melander,Gunnar Engström
Background Though subjective, poor self-rated health (SRH) has consistently been shown to predict cardiovascular disease (CVD). The underlying mechanism is unclear. This study evaluates the associations of SRH with biomarkers for CVD, aiming to explore potential pathways between poor SRH and CVD. Methods Based on the Malmö Diet and Cancer Cardiovascular Cohort study, a targeted proteomics approach
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Quantitative analysis of Mycobacterium avium subsp. hominissuis proteome in response to antibiotics and during exposure to different environmental conditions. Clin. Proteom. (IF 2.568) Pub Date : 2019-11-13 Rajoana Rojony,Matthew Martin,Anaamika Campeau,Jacob M Wozniak,David J Gonzalez,Pankaj Jaiswal,L Danelishvili,Luiz E Bermudez
Mycobacterium avium subsp. hominissuis (MAH) belongs to the clinically important non-tuberculous mycobacterial group that infects immunocompromised patients and individuals with underling lung conditions. The need for prolonged therapy is a major challenge of MAH treatment, influencing the development of persistent and drug-resistant infections. The reason why bactericidal drugs take several months
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iTRAQ-based quantitative proteomic analysis provides insight for molecular mechanism of neuroticism. Clin. Proteom. (IF 2.568) Pub Date : 2019-11-08 Lei Tian,Hong-Zhao You,Hao Wu,Yu Wei,Min Zheng,Lei He,Jin-Ying Liu,Shu-Zhen Guo,Yan Zhao,Ren-Lai Zhou,Xingang Hu
Background Neuroticism is a core personality trait and a major risk factor for several mental and physical diseases, particularly in females, who score higher on neuroticism than men, on average. However, a better understanding of the expression profiles of proteins in the circulating blood of different neurotic female populations may help elucidate the intrinsic mechanism of neurotic personality and
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Matrisome analysis of intrahepatic cholangiocarcinoma unveils a peculiar cancer-associated extracellular matrix structure. Clin. Proteom. (IF 2.568) Pub Date : 2019-10-30 Guido Carpino,Diletta Overi,Fabio Melandro,Alessio Grimaldi,Vincenzo Cardinale,Sabina Di Matteo,Gianluca Mennini,Massimo Rossi,Domenico Alvaro,Vincenzo Barnaba,Eugenio Gaudio,Carmine Mancone
Background Intrahepatic cholangiocarcinoma (iCCA) is a malignancy that arises from the intrahepatic biliary tree, showing high mortality rates due to its late clinical presentation and limited treatment options. iCCA is characterized by a dense, reactive desmoplastic stroma marked by a dramatic accumulation of extracellular matrix (ECM). Although recent results strongly suggest a relationship between
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iTRAQ and PRM-based quantitative proteomics in early recurrent spontaneous abortion: biomarkers discovery. Clin. Proteom. (IF 2.568) Pub Date : 2019-10-18 Ying Cui,Ling He,Chun-Yan Yang,Qian Ye
Background Early recurrent spontaneous abortion (ERSA) is a common condition in pregnant women. To prevent ERSA is necessary to look for abortion indicators, such as hormones and proteins, in an early stage. Methods Thirty patients with ERSA were enrolled in the case group. In the control group, we recruited 30 healthy women without a history of miscarriage undergoing voluntary pregnancy termination
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N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clin. Proteom. (IF 2.568) Pub Date : 2019-09-07 Shisheng Sun,Yingwei Hu,Minghui Ao,Punit Shah,Jing Chen,Weiming Yang,Xingwang Jia,Yuan Tian,Stefani Thomas,Hui Zhang
Background N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample
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Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel. Clin. Proteom. (IF 2.568) Pub Date : 2019-08-28 Seong Beom Ahn,Samridhi Sharma,Abidali Mohamedali,Sadia Mahboob,William J Redmond,Dana Pascovici,Jemma X Wu,Thiri Zaw,Subash Adhikari,Vineet Vaibhav,Edouard C Nice,Mark S Baker
Background One of the most significant challenges in colorectal cancer (CRC) management is the use of compliant early stage population-based diagnostic tests as adjuncts to confirmatory colonoscopy. Despite the near curative nature of early clinical stage surgical resection, mortality remains unacceptably high-as the majority of patients diagnosed by faecal haemoglobin followed by colonoscopy occur
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iTRAQ plasma proteomics analysis for candidate biomarkers of type 2 incipient diabetic nephropathy. Clin. Proteom. (IF 2.568) Pub Date : 2019-07-31 Hongmei Lu,Shaodong Deng,Minghui Zheng,Kunhua Hu
Background Diabetic nephropathy is the most frequent cause of end-stage renal disease worldwide. Identification of biomarkers for diabetic nephropathy for early diagnosis may be the key to avoiding damage from this condition. Methods Proteomic iTRAQ technology was first used to identify differentially expressed plasma proteins in type 2 incipient diabetic nephropathy (IDN) using a Q-Exactive mass spectrometer
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