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Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm

Jan M Brauner, Teja W Groemer, Armin Stroebel, Simon Grosse-Holz, Timo Oberstein, Jens Wiltfang, Johannes Kornhuber, Juan Maler
2014 BMC Bioinformatics  
Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images.  ...  We propose a ready-to-use algorithm for spot detection and quantification that uses fitting of two dimensional Gaussian function curves for the extraction of data from two dimensional gel electrophoresis  ...  Acknowledgement We thank Friederike Grosse-Holz for proof-reading of the manuscript.  ... 
doi:10.1186/1471-2105-15-181 pmid:24915860 pmcid:PMC4085234 fatcat:tir2we5qafej7i2iysfvtyriui

2D electrophoresis image brightness correction based on gradient interval histogram

Qiaofeng Ou, Jiabing Xiao, Lei Yu, Kaizhi Wu, Bangshu Xiong
2020 BMC Bioinformatics  
Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics.  ...  To reduce the errors of spot quantification in 2DE images, a novel brightness correction method based on gradient interval histogram (GIH) is proposed in this paper.  ...  Acknowledgements The authors gratefully acknowledge the supports of the sponsors. Availability of data and materials The original 2DE images have been included in the additional files.  ... 
doi:10.1186/s12859-020-3432-y pmid:32192430 fatcat:urlcjondi5cbxhkl7jo2dlcsdy

A Proteomic Analysis of Maize Chloroplast Biogenesis

P. M. Lonosky
2004 Plant Physiology  
proteome that occur during the greening process using techniques of two-dimensional gel electrophoresis and mass spectrometry.  ...  We also evaluate hierarchical and nonhierarchical statistical methods to analyze the patterns of expression of 526 "high-quality," unique spots on the two-dimensional gels.  ...  , Cambridge, MA), and four anonymous reviewers for careful review of this manuscript.  ... 
doi:10.1104/pp.103.032003 pmid:14966246 pmcid:PMC344533 fatcat:lr222tugifd5lo275xhr3ej4im

Proteomic Methods for Biomarker Discovery in Urine

Daniel W. Wilkey, Michael L. Merchant
2007 Seminars in Nephrology  
Thirty protein spots across the high-to-low isoelectric point (pI) and molecular mass (Mr) ranges were selected as seed spots against which a total of 18 gel images (5 gels per two 2-h treatment conditions  ...  The ability to directly compare and quantify proteins from 2 different samples minimizes the problems of gel-to-gel variation, ensures a more accurate alignment of gel images between replicate gels, and  ... 
doi:10.1016/j.semnephrol.2007.09.001 pmid:18061841 fatcat:z7f233outbgnnftmxitqv6ut5a

MALDI-TOF MS as evolving cancer diagnostic tool: A review

Miguel Angel Merlos Rodrigo, Ondrej Zitka, Sona Krizkova, Amitava Moulick, Vojtech Adam, Rene Kizek
2014 Journal of Pharmaceutical and Biomedical Analysis  
MALDI-TOF is a powerful tool for surveying proteins and peptides comprising the realm for clinical analysis.  ...  Recent developments in mass spectrometry have introduced clinical proteomics to the forefront of diseases diagnosis, offering reliable, robust and efficient analytical method for biomarker discovery and  ...  The key regulatory molecules in breast cancer were detected using the Western Blot analysis, two-dimensional (2-D) electrophoresis and MALDI-TOF MS.  ... 
doi:10.1016/j.jpba.2014.03.007 pmid:24699369 fatcat:ok4dllwbcjhbxisgcnbj2ersse

Enhanced detectability in proteome studies

Supawadee Sriyam, Supachok Sinchaikul, Payungsak Tantipaiboonwong, Ching Tzao, Suree Phutrakul, Shui-Tein Chen
2007 Journal of chromatography. B  
This review describes the current development of potential methods to enhance the detection and quantification in proteome studies.  ...  Therefore, we believe that this review provided many proteomic approaches, which would be very potent and useful for proteome studies and for further diagnostic and therapeutic applications.  ...  We also gratefully acknowledge the provision of serum and urine samples from Lampang Regional Cancer Center (Thailand).  ... 
doi:10.1016/j.jchromb.2006.10.065 pmid:17140866 fatcat:fr3glnq5qrbqlo3ejqgwvwh43m

Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis

Yapeng Su, Qihui Shi, Wei Wei
2017 Proteomics  
In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical  ...  The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation.  ...  Acknowledgement The authors acknowledge the following funding agencies and grants for support some of the work  ... 
doi:10.1002/pmic.201600267 pmid:28128880 pmcid:PMC5554115 fatcat:3vd2xx5hdrghbptr63tb3oc5wu

Developing Novel Methods for Protein Analysis and Their Potential Implementation in Diagnosing Neurological Diseases [chapter]

Olgica Trenchevska, Vasko Aleksovski, Dobrin Nedelkov, Kiro Stojanoski
2012 Advanced Topics in Neurological Disorders  
"A novel experimental design for comparative twodimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard." Proteomics 3(1): 36-44.Anderson, N.  ...  By combining IEF with gel electrophoresis, two dimensional gel electrophoresis is created (2D-GE), a technique, which Developing Novel Methods for Protein Analysis and Their Potential  ...  It consists of 9 chapters encompassing a wide range of areas including bioengineering, stem cell transplantation, gene therapy, proteomic analysis, alternative treatment and neuropsychiatry analysis.  ... 
doi:10.5772/31731 fatcat:voeyeumfffa2zhm5xgyyxchmrq

Biomarker Discovery for Early Detection of Hepatocellular Carcinoma in Hepatitis C–infected Patients

Mehnaz G. Mustafa, John R. Petersen, Hyunsu Ju, Luca Cicalese, Ned Snyder, Sigmund J. Haidacher, Larry Denner, Cornelis Elferink
2013 Molecular & Cellular Proteomics  
difference gel electrophoresis.  ...  Differential expression quantified via two-dimensional difference gel electrophoresis was confirmed by means of 18 O/ 16 O stable isotope differential labeling with LC-MS/MS zoom scans.  ...  A, gel images for HCV and HCC samples in boxed area in FIG. 3 . 3 Preparative two-dimensional gel analysis of differentially expressed proteins.  ... 
doi:10.1074/mcp.m113.031252 pmid:24008390 pmcid:PMC3861713 fatcat:nde5k5wbdvbnlaqhr6gumrtfi4

Image Analysis in Microbiology: A Review

Evgeny Puchkov
2016 Journal of Computer and Communications  
Examples of using image analysis in the studies of both the macroscopic and the microscopic microbiological objects obtained by various imaging techniques are presented and discussed.  ...  This review is focused on using computer image analysis as a means of objective and quantitative characterizing optical images of the macroscopic (e.g. microbial colonies) and the microscopic (e.g. single  ...  Computer image analysis may be helpful in such cases. Examples of application of this approach are presented below.  ... 
doi:10.4236/jcc.2016.415002 fatcat:ncebjjpzzjaetmq42gw5qk5fze

Proteomic technologies in modern biomedical science

V M Govorun, A I Archakov
2002 Biochemistry (Moscow)  
The review also describes approaches of functional proteomics, i.e., interactomics, and also bioinformatic resources used in proteomics for image analysis of 2D-gel-electrophoresis and for identification  ...  Methods of solubilization, electrophoresis, chromatographic protein separation, and visualization of protein spots in gels are described.  ...  Corresponding algorithms for gel matching can be subdivided into two groups: 1) algorithms based on char acteristics of spot image on gel; 2) algorithms based on direct comparison of images by distribution  ... 
pmid:12460109 fatcat:oncpnnuzjvdi5agswao6vq3qzm

Pharmacoproteomic Study of Three Different Chondroitin Sulfate Compounds on Intracellular and Extracellular Human Chondrocyte Proteomes

Valentina Calamia, Patricia Fernández-Puente, Jesús Mateos, Lucía Lourido, Beatriz Rocha, Eulália Montell, Josep Vergés, Cristina Ruiz-Romero, Francisco J. Blanco
2011 Molecular & Cellular Proteomics  
Each of the studied compounds induces a characteristic protein profile in OA chondrocytes.  ...  or purity, by two complementary proteomic approaches.  ...  One-dimensional Gel Electrophoresis and In-gel Digestion of Secreted Proteins-Prior to LC-MS analysis, heavy and light samples were mixed 1:1, and 5 g of each mixed sample were separated on a 10% SDS-PAGE  ... 
doi:10.1074/mcp.m111.013417 pmid:22203690 pmcid:PMC3433908 fatcat:3mizl4btejfojkfzeuzs7k4h7a

Metabolomic Analysis of Natural Products [chapter]

David M. Pereira M. Pereira, Patricia Valentao, Federico Ferreres, Paula B. Andrade
2012 Reviews in Pharmaceutical & Biomedical Analysis  
ACKNOWLEDGEMENTS We gratefully acknowledge the support of Science Foundation Ireland (CSET Grant no. 05/CE3/B754), the Irish Research Council for Science, Engineering and Technology (IRCSET) Embark Scholarship  ...  ACKNOWLEDGEMENTS Support by joint grants from Fondazione CARIPLO (Proteomic platform Operational Network for Biomedicine Excellence in Lombardy project) is gratefully acknowledged.  ...  Algorithms and Softwares for Proteomics In proteomics analysis by means of gel electrophoresis several software for the comprehensive visualization exploration and analysis of 2DE gel data have been developed  ... 
doi:10.2174/978160805190811001010001 fatcat:qtp6ltjyxzh5lor3ke7sxivp7y

Quantification of Gene Expression Based on Microarray Experiment [chapter]

Samane F., Mahmood A.
2011 Bioinformatics - Trends and Methodologies  
Two dimensional loess (twoDloess) method fits a smooth two-dimensional surface to the data which is a function of overall row position r and column position c of the spot on the array.  ...  Since competitor molecule differs in size from the target one, the two PCR products can be separated by gel electrophoresis.  ...  Bioinformatics -Trends and Methodologies is a collection of different views on most recent topics and basic concepts in bioinformatics.  ... 
doi:10.5772/18439 fatcat:pkdph4ilwvd57ayew7765jv3xm

Proteomics: taking over where genomics leaves off

R. Mahajan, P. Gupta
2010 Czech Journal of Genetics and Plant Breeding  
Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life  ...  cycle and in different environmental conditions as every individual has one genome and many proteomes.  ...  Due to a difference in the masses of peptides from two or three populations a direct comparison of MS peak intensities can be made for the two samples. In vitro labelling.  ... 
doi:10.17221/34/2009-cjgpb fatcat:zpcjk3mrgvhdzh73jgudknhfxu
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