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A New Approach to Protein Identification [chapter]

Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel Pevzner
2006 Lecture Notes in Computer Science  
In addition to speed, our approach provides a new paradigm for identifying post-translational modifications. 1 Hunyadi-Goulyas and Medzihradszky, 2004 [10] give a table of over 30 common chemical adducts  ...  In this paper we introduce a new idea that allows one to perform MS/MS database search . . . without ever comparing a spectrum against a database.  ...  Acknowledgements The authors would like to thank Ebrahim Zandi for providing the MS/MS dataset used to benchmark our algorithm and Vineet Bafna and Stephen Tanner for insightful discussions and help in  ... 
doi:10.1007/11732990_31 fatcat:nt3x4cwo7jfh5ido7vzxhsbome

A proteomic approach to the identification of heterogeneous nuclear ribonucleoproteins as a new family of poly(ADP-ribose)-binding proteins

Jean-Philippe GAGNÉ, Joanna M. HUNTER, Benoît LABRECQUE, Benoît CHABOT, Guy G. POIRIER
2003 Biochemical Journal  
A new class of poly(ADP-ribose) (pADPr)-binding proteins, heterogeneous nuclear ribonucleoproteins (hnRNPs), has been identified by a proteomic approach using matrix-assisted laserdesorption-ionization  ...  Rotofor2 protein fractions were further separated by SDS\ PAGE and then transferred to a PVDF membrane. pADPrbinding proteins were analysed by autoradiography of the protein blot after incubation with  ...  DISCUSSION Using a proteomic approach, we have identified a new family of proteins that bind to pADPr, namely hnRNPs. Prasad et al.  ... 
doi:10.1042/bj20021675 pmid:12517304 pmcid:PMC1223283 fatcat:4abdkapjtvawfjdb4gqj4c4wca

Proteomics: A New Diagnostic Frontier

G. L. Hortin
2006 Clinical Chemistry  
Recent advances in technology and complete identification of the human genome sequence have opened up new opportunities for analysis of proteins for clinical diagnostic purposes.  ...  Results: New analytical methods allow the simultaneous analysis of a large number of proteins in biological fluids such as serum and plasma, offering partial views of the complete set of proteins or proteome  ...  Usually, this has enabled the sequence identification of a larger number of proteins than by the top-down approach, but the bottom-up approach does not identify what molecular form of the parent protein  ... 
doi:10.1373/clinchem.2006.067280 pmid:16675505 fatcat:jeb43zf4szhljfjqs7gwsbnvd4

Genetic and proteomic approaches to identify cancer drug targets

G Roti, K Stegmaier
2011 British Journal of Cancer  
In this review, we discuss the application of genomic (gene expression-based), genetic (short hairpin RNA and open reading frame screening), and proteomic approaches to protein target identification.  ...  In order to address this problem, as well as to identify modulators of biological states in the absence of knowing the protein target of the state switch, alternative phenotypic screening approaches, such  ...  Foundation, Lady Tata Memorial Trust, and Leukemia and Lymphoma Society Special Fellow award (GR); and by the National Cancer Institute, American Cancer Society, Howard Hughes Medical Institute, and Stand-up-to-Cancer  ... 
doi:10.1038/bjc.2011.543 pmid:22166799 pmcid:PMC3262130 fatcat:db5e7p7cizarfj4k5ymkxmhlvi

Current trends in computational inference from mass spectrometry-based proteomics

B.-J. M. Webb-Robertson, W. R. Cannon
2007 Briefings in Bioinformatics  
Mass spectrometry offers a high-throughput approach to quantifying the proteome associated with a biological sample and hence has become the primary approach of proteomic analyses.  ...  Computation is tightly coupled to this advanced technological platform as a required component of not only peptide and protein identification, but quantification and functional inference, such as protein  ...  A second phase of MS allows capture of the MS/MS spectrum of a single peptide. Figure 2 : 2 The two common approaches to peptide identifications.  ... 
doi:10.1093/bib/bbm023 pmid:17584764 fatcat:zqcehyvcbnd6vhhufmvvkjag7y

Inference and Validation of Protein Identifications

Manfred Claassen
2012 Molecular & Cellular Proteomics  
This review aims to survey the different conceptual approaches to the different tasks of inferring and statistically validating protein identifications and to discuss their implications on the scope of  ...  The inherent uncertainty of mass spectrometric data and the complexity of a proteome render protein inference and the statistical validation of protein identifications a non-trivial task, still being a  ...  The more entries the database comprises the more likely the incorrect peptide spectrum match will map to a new, so far unsupported protein entry and thereby give rise to a false positive protein identification  ... 
doi:10.1074/mcp.r111.014795 pmid:22865921 pmcid:PMC3494198 fatcat:jesgfw5ytvgafg2ndogtsbxxpi

A meta-proteogenomic approach to peptide identification incorporating assembly uncertainty and genomic variation

Sujun Li, Haixu Tang, Yuzhen Ye
2019 Molecular & Cellular Proteomics  
Here we developed a software pipeline for identification of peptides and proteins from metaproteomic MS/MS data using proteins derived from matching metagenomic (and metatranscriptomic) data as the search  ...  database, based on two novel approaches Graph2Pro (published) and Var2Pep (new).  ...  A hope to alleviate this limitation is to augment the identification of proteins using variant peptides. Here we use the wastewater data set (SD3-MG) as an example to illustrate this approach.  ... 
doi:10.1074/mcp.tir118.001233 pmid:31142575 pmcid:PMC6692780 fatcat:73fvq7cirzhozn3sy3sx4lqqje

Proteomics Applications in Health: Biomarker and Drug Discovery and Food Industry

Nasrin Amiri-Dashatan, Mehdi Koushki, Hojjat-Allah Abbaszadeh, Mohammad Rostami-Nejad, Mostafa Rezaei-Tavirani
2018 Iranian journal of pharmaceutical research  
Proteomics is also used in drug target identification using different approaches such as chemical proteomics and protein interaction networks.  ...  Advances in proteomics methods offer many promising new directions of studying in clinical fields.  ...  These data may help to develop new drug target identification.  ... 
pmid:30568709 pmcid:PMC6269565 fatcat:ldajxjjfpjcipho3bfvvzrijkq

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching

Penghao Wang, Susan R Wilson
2013 BMC Bioinformatics  
Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching.  ...  Results: We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching.  ...  Therefore, we have developed a new integrative method, NovoDB, for protein identification.  ... 
doi:10.1186/1471-2105-14-s2-s24 pmid:23369017 pmcid:PMC3549845 fatcat:chismfze3vgbnhnuym5arh7tz4

Proteomics Approach and Techniques in Identification of Reliable Biomarkers for Diseases

Raed Abdullah Alharbi
2020 Saudi Journal of Biological Sciences  
There are three essential steps of this approach including: extraction and separation of proteins, identification of proteins, and verification of proteins.  ...  Proteins are considered as a type of biomarkers based on their characteristics. Therefore, proteomics approach is one of the most promising approaches in this field.  ...  Acknowledgments The author would like to thank Deanship of Scientific Research at Majmaah University, Al Majmaah, 11952, Saudi Arabia for supporting this work under the Project Number R-1441-65.  ... 
doi:10.1016/j.sjbs.2020.01.020 pmid:32127776 pmcid:PMC7042613 fatcat:hlwg64varzbdznxqki4e4honfu

New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery

Yun Tang, Weiliang Zhu, Kaixian Chen, Hualiang Jiang
2006 Drug Discovery Today : Technologies  
Two new technologies of CADD associated with target identification and new chemical entity discovery will be the focus of this review.:  ...  In the postgenomic era, computer-aided drug design (CADD) has considerably extended its range of applications, spanning almost all stages in the drug discovery pipeline, from target identification to lead  ...  For example, a proteomic approach for identification of binding proteins for a given small molecule involves comparison of the protein expression profiles for a given cell or tissue in the presence or  ... 
doi:10.1016/j.ddtec.2006.09.004 pmid:24980533 pmcid:PMC7185835 fatcat:qddbkqp3ingljngqwndsmbggaa

Research challenges, opportunities and synergism in systems engineering and computational biology

Christodoulos A. Floudas
2005 AIChE Journal  
Global optimization addresses the computation and characterization of global minima and maxima of a nonconvex objective function subject to a nonconvex set of equality and inequality constraints.  ...  greater potential impact in a variety of engineering applications.  ...  The key advances in computational methods for peptide and protein identification are discussed, based on the classification into (a) database-based approaches, and (b) de novo approaches.  ... 
doi:10.1002/aic.10620 fatcat:4hgnhia5lnd5zpraheedpgtbpm

Chemical genetics: exploring and controlling cellular processes with chemical probes

Craig M Crews, Ute Splittgerber
1999 TIBS -Trends in Biochemical Sciences. Regular ed  
Subsequent identification of the underlying genetic change or, in the case of the chemical genetic approach, identification of compound-binding protein(s) poses a new question: how does modification of  ...  Furthermore, in recent years, identification of target proteins has also provided new opportunities for the development of creative approaches for controlling intracellular processes (see, for example,  ... 
doi:10.1016/s0968-0004(99)01425-5 pmid:10431176 fatcat:nafaj3l4ubcu3aoa6teu73wg4a

Three Dimensional Liquid Chromatography Coupling Ion Exchange Chromatography/Hydrophobic Interaction Chromatography/Reverse Phase Chromatography for Effective Protein Separation in Top-Down Proteomics

Santosh G. Valeja, Lichen Xiu, Zachery R. Gregorich, Huseyin Guner, Song Jin, Ying Ge
2015 Analytical Chemistry  
47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications.  ...  For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 non-redundant proteins) as compared to  ...  Gary Valaskovic of New Objective Inc., for providing the PicoFrit™ PLRP-S column.  ... 
doi:10.1021/acs.analchem.5b00657 pmid:25867201 pmcid:PMC4575680 fatcat:t7m27d32a5czxid2xdtg74wlxi

Hitting the Target: Emerging Technologies in the Search for Kinase Substrates

B. D. Manning, L. C. Cantley
2002 Science Signaling  
However, several recent in vitro and in vivo technologies have emerged as promising new avenues toward identification of new substrates of protein kinases.  ...  The first demonstration that this was a viable technique for detecting novel kinase substrates came with the identification of Sip1p as a two-hybrid-interacting protein with the yeast Snf1p kinase (4).  ...  However, several recent in vitro and in vivo technologies have emerged as promising new avenues toward identification of new substrates of protein kinases.  ... 
doi:10.1126/stke.2002.162.pe49 pmid:12475999 fatcat:hyjn4bui7jhm5aqgigqco5ykqm
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