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Advances in Proteome Analysis by Mass Spectrometry

Timothy J. Griffin, Ruedi Aebersold
2001 Journal of Biological Chemistry  
The interpretation of the information contained in the genomic sequence of a species with respect to the structure, function, and control of biological processes is a technical and conceptual challenge  ...  Mass spectrometry has become the analytical technology of choice for many of the aspects of proteome analyses that are reflected by the covalent structure of proteins.  ...  Wright and R. Aebersold, manuscript in preparation. FIG. 1. Global, quantitative mass spectrometric analysis of protein expression. A, the structure of the ICAT reagent.  ... 
doi:10.1074/jbc.r100014200 pmid:11585843 fatcat:t3wlcwhswvdwvjsifvdezs4qpm

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling

Argyris Politis, Carla Schmidt
2018 Journal of Proteomics  
In this review we summarise recent advances and challenges in structural mass spectrometric techniques.  ...  These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease.  ...  Notably, entire proteomes can nowadays be explored in very short time spans [30, 31] . As such several proteomes and their interactomes have been described to a high standard.  ... 
doi:10.1016/j.jprot.2017.04.019 pmid:28461040 fatcat:46ocsvaqwjhwbncx3nzpa4wx2m

Lipoproteomics: using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins

Andrew N. Hoofnagle, Jay W. Heinecke
2009 Journal of Lipid Research  
Lipoproteomics: using mass spectrometry-based proteomics to explore the assembly, structure, and function of lipoproteins. J.  ...  Proteomics, a global approach to understanding protein expression, regulation, and function, transcends analysis of individual components.  ...  In addition, the lipids in lipoproteins make protein digestion and mass spectrometric analysis challenging.  ... 
doi:10.1194/jlr.r900015-jlr200 pmid:19738003 pmcid:PMC2739765 fatcat:cwxi6isjkzeyzbwng32rvk3m4e

Proteomics Identification of Proteins in Human Cortex Using Multidimensional Separations and MALDI Tandem Mass Spectrometer

Sheng Pan, Min Shi, Jinghua Jin, Roger L. Albin, Andy Lieberman, Marla Gearing, Biaoyang Lin, Catherine Pan, Xiaowei Yan, Daniel T. Kashima, Jing Zhang
2007 Molecular & Cellular Proteomics  
The integrated proteomics analytical flow consisted of biochemical fractionation, strong cation exchange chromatography, reverse phase liquid chromatography, and MALDI-TOF/TOF mass spectrometric analysis  ...  These proteins demonstrated diverse isoelectric points and molecular weights and are involved in several molecular functions, including protein binding, catalytic activity, transport, structure, and signal  ...  mass spectrometric analysis.  ... 
doi:10.1074/mcp.m700158-mcp200 pmid:17644759 fatcat:pvpzfln6tngdpjyspqhr5n3lga

The Origins of Organellar Mapping by Protein Correlation profiling

Matthias Mann
2020 Proteomics  
Now, classical biochemical methods that break apart the cells and fractionate them along a gradient have gotten a new lease on life through modern methods of mass spectrometry-based proteomics.  ...  Cells have a rich inner structure that is commonly explored by microscopy.  ...  specific mass spectrometric read out.  ... 
doi:10.1002/pmic.201900330 pmid:32744740 fatcat:4n5aa2gzevbwxnqzlzql7riaue

Mass Spectrometry-Based Technologies for Probing the Three-Dimensional World of Plant Proteins

Matthew R Blackburn, Benjamin B Minkoff, Michael R Sussman
2022 Plant Physiology  
the molecular underpinnings of plant structure and function.  ...  Over the past two decades, mass spectrometric (MS) based proteomics technologies have facilitated the study of signaling pathways throughout biology.  ...  structure and function.  ... 
doi:10.1093/plphys/kiac039 pmid:35139210 pmcid:PMC9070838 fatcat:wylbf347hbalrgi5fakwtyewjy

Mass Spectrometric Characterization of Protein Structure Details Refines the Proteome Signature for Invasive Ductal Breast Carcinoma

Claudia Röwer, Cornelia Koy, Michael Hecker, Toralf Reimer, Bernd Gerber, Hans-Jürgen Thiesen, Michael O. Glocker
2011 Journal of the American Society for Mass Spectrometry  
In addition, detailed protein structure investigations enabled refining our proteome signature for invasive ductal breast carcinoma, opening the way to structure-/function studies with respect to disease  ...  In-depth MS/MS measurements enabled analyses of protein structure details of selected proteins.  ...  Mass Spectrometric Protein Structure Characterization For protein structure analysis of 2D gel separated proteins, we applied mass spectrometric peptide mapping, focusing on the four proteins mentioned  ... 
doi:10.1007/s13361-010-0031-6 pmid:21472563 fatcat:bigpb4mjhfg4baq4xtb75qo57y

A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium [article]

Martin Pabst, Denis Grouzdev, Christopher Lawson, Hugo B.C. Kleikamp, Carol de Ram, Rogier Louwen, Yuemei Lin, Sebastian Lucker, Mark van Loosdrecht, Michele Laureni
2020 bioRxiv   pre-print
Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides  ...  Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures  ...  care, and Ben Abbas for the support with DNA extraction.  ... 
doi:10.1101/2020.12.03.409086 fatcat:mpdqw2l47baypga4pz6hahpfbi

Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms

Olgica Trenchevska, Randall Nelson, Dobrin Nedelkov
2016 Proteomes  
This mini review offers an overview of the development and application of mass spectrometric immunoassays for clinical and population proteomics studies.  ...  Mass spectrometric immunoassays (MSIA) have been devised for studying structural diversity in human proteins.  ...  Numerous methods used in proteomics, from gel electrophoresis and affinity-based analytical methods to structural interaction analyses and protein crystallography, can be applicable for analysis of PTMs  ... 
doi:10.3390/proteomes4010013 pmid:28248223 pmcid:PMC5217360 fatcat:yrbfbyeurnbr3laulripemjrse

Literature Survey on Framework for Generating MS-MS Spectra for MS Spectrometry Data

Xylia Lamisa Nazareth, Shetty Mamatha Gopal
2017 IJARCCE  
Current mass spectrometers are capable of a tremendous throughput, and can survey thousands of proteins from complex sample mixtures.  ...  The most commonly applied mass spectrometry techniques is Tandem-MS. This high-throughput technology generates huge amounts of data.  ...  Several groups have used mass spectrometry to catalogue complete proteomes of unicellular organisms and to explore proteomes of higher organisms, including mouse andhuman.  ... 
doi:10.17148/ijarcce.2017.6437 fatcat:as6y5htmbzc5lpo6rau662mnie

Grand challenges in analytical chemistry: towards more bright eyes for scientific research, social events and human health

Huangxian Ju
2013 Frontiers in Chemistry  
New ambient mass spectrometric techniques and the intelligentialized, miniaturized, and multi-functional mass spectrometers with high sensitivity, simple manipulation, fast response, and good specificity  ...  Fast two-dimensional infrared spectroscopy has been developed for probing biomolecule structure and function (Hunt, 2009) .  ... 
doi:10.3389/fchem.2013.00005 pmid:24790934 pmcid:PMC3982555 fatcat:hijvicwqprgn3bw6qgqp3nb2aq

News in Brief

2005 Nature Methods  
Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry. Nat.  ...  to biotinbased reagents, such as their inertness and possession of a mass defect.  ...  cells with radiolabeled amino acids to generate a standard for mass spectrometric analysis of protein expression in cells growing under different conditions.  ... 
doi:10.1038/nmeth0605-407 fatcat:bztuclpvhrcjdcrh5gvip2ox3a

Proteomics-Based Discovery of Koranimine, a Cyclic Imine Natural Product

Bradley S. Evans, Ioanna Ntai, Yunqiu Chen, Sarah J. Robinson, Neil L. Kelleher
2011 Journal of the American Chemical Society  
Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are large enzymes responsible for the biosynthesis of medically and ecologically important secondary metabolites.  ...  Here we use this proteome mining approach to discover a novel natural product arising from rare adenylation (A) and reductase (Red) domains in its biosynthetic machinery.  ...  Carver Charitable Trust, the University of Illinois and the National Institutes of Health (GM R01 067725 and GM P01 077596) which have supported the development of PrISM.  ... 
doi:10.1021/ja2015795 pmid:21520944 pmcid:PMC3103991 fatcat:tboads4oczfk3c2ygna25i4vnq

Applications of Surface-Enhanced Laser Desorption/Ionization Time-Of- Flight (SELDI-TOF) Mass Spectrometry in Defining Salivary Proteomic Profiles

Sandra K. Al-Tarawneh, Sompop Bencharit
2009 Open Dentistry Journal  
Here we review the development of proteomic analyses for human saliva and focus on the use of a new mass spectrometric technology known as surface-enhanced laser desorption/ionization time-of-flight mass  ...  Recent advancement in mass spectrometry leads us to a new era of proteomic analysis.  ...  Proteomic analysis can be viewed as an experimental approach to explain the information contained in genomic sequences in terms of the structure, function, and control of biological processes and pathways  ... 
doi:10.2174/1874210600903010074 pmid:19543543 pmcid:PMC2697056 fatcat:iff6ylxrwjhh7pisxovgdjiznu

The Role of Mass Spectrometry in Chromatin Biology

Alan J Tackett
2013 Journal of Proteomics & Bioinformatics  
Tackett would like to acknowledge support from NIH grants R01GM106024, R33CA173264, UL1RR029884, P30GM103450, and P20GM103429.  ...  Mass spectrometry has played a vital role in defining what we understand about mechanisms regulating chromatin structure and function.  ...  The immediate future of this field is to explore various types of DNA targeting affinity reagents to purify short stretches of chromosomes for mass spectrometric analysis, while in the long run these approaches  ... 
doi:10.4172/jpb.s2-e001 fatcat:sjcps3dvfbh43lthiqknwavgq4
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