Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics

Kline, Kelli G.; Finney, Greg L.; Wu, Christine C.

doi:10.1093/bfgp/elp008

Cited by 15 publications

(8 citation statements)

References 69 publications

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“…Peptides from the protein digest were analyzed by the MudPIT approach adopted from Kline and colleagues . Briefly, peptides were identified with a nano‐LC/MS/MS system consisting of an ultra‐performance liquid chromatography (Waters; USA) and a hybrid linear quadrapole ion trap—Fourier transform ICR (LTQ‐FT) MS (ThermoFinnigan; USA) equipped with a nano‐ESI source.…”

Section: Methodsmentioning

confidence: 99%

Differential protein expression and basal lamina remodeling in human heart failure

et al. 2016

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Purpose A goal of this study was to identify and investigate previously unrecognized components of the remodeling process in the progression to heart failure by comparing protein expression in ischemic failing (F) and nonfailing (NF) human hearts. Experimental design Protein expression differences were investigated using multidimensional protein identification and validated by Western analysis. This approach detected basal lamina (BL) remodeling, and further studies analyzed samples for evidence of structural BL remodeling. A rat model of pressure overload (PO) was studied to determine whether nonischemic stressors also produce BL remodeling and impact cellular adhesion. Results Differential protein expression of collagen IV, laminin α2, and nidogen-1 indicated BL remodeling develops in F versus NF hearts Periodic disruption of cardiac myocyte BL accompanied this process in F, but not NF heart. The rat PO myocardium also developed BL remodeling and compromised myocyte adhesion compared to sham controls. Conclusions and clinical relevance Differential protein expression and evidence of structural and functional BL alterations develop during heart failure. The compromised adhesion associated with this remodeling indicates a high potential for dysfunctional cellular integrity and tethering in failing myocytes. Therapeutically targeting BL remodeling could slow or prevent the progression of heart disease.

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Section: Methodsmentioning

confidence: 99%

Differential protein expression and basal lamina remodeling in human heart failure

et al. 2016

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“…However, these approaches only allow for the comparison of one sample pair at a time, in contrast to proteomics labeling techniques such as iTRAQ enabling the comparison of up to eight samples [ 199 ]. Recently, Bowman and Zaia [ 197 ] synthesized different tags on the basis of 2-aminobenzoic acid applicable to reductive amination, which are suitable for the direct comparison of four samples which, based on the incorporation of deuterium versus hydrogen atoms, give rise to an isotopic variety with a mass difference of 4 Da between the glycans from different samples.…”

Section: Separation and Detectionmentioning

confidence: 99%

Glycan labeling strategies and their use in identification and quantification

et al. 2010

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Most methods for the analysis of oligosaccharides from biological sources require a glycan derivatization step: glycans may be derivatized to introduce a chromophore or fluorophore, facilitating detection after chromatographic or electrophoretic separation. Derivatization can also be applied to link charged or hydrophobic groups at the reducing end to enhance glycan separation and mass-spectrometric detection. Moreover, derivatization steps such as permethylation aim at stabilizing sialic acid residues, enhancing mass-spectrometric sensitivity, and supporting detailed structural characterization by (tandem) mass spectrometry. Finally, many glycan labels serve as a linker for oligosaccharide attachment to surfaces or carrier proteins, thereby allowing interaction studies with carbohydrate-binding proteins. In this review, various aspects of glycan labeling, separation, and detection strategies are discussed.FigureMALDI-FTICR-MS of 2AA-labeled total plasma N-glycans

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“…Isotopic labelling or label-free methods have been developed and successfully applied in MudPIT experiments [74]. A simple method for label-free quantification is the spectral counting [76].…”

Section: Methods In Proteomicsmentioning

confidence: 99%

“…The different peptide fractions are eluted from the chromatography columns by alternating salt pulses or organic mobile gradients. They are subsequently stored or, more commonly, directly applied to the mass spectrometer [ 71 , 74 ]. MudPIT approaches commonly use electrospray ionization (ESI) mass spectrometers since the chromatography eluate can be directly “online” analyzed with a connected ESI mass spectrometer [ 75 ].…”

Section: Methods In Proteomicsmentioning

confidence: 99%

Transcriptome and Proteome Research in Veterinary Science: What Is Possible and What Questions Can Be Asked?

Klopfleisch

Gruber

2012

The Scientific World Journal

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In recent years several technologies for the complete analysis of the transcriptome and proteome have reached a technological level which allows their routine application as scientific tools. The principle of these methods is the identification and quantification of up to ten thousands of RNA and proteins species in a tissue, in contrast to the sequential analysis of conventional methods such as PCR and Western blotting. Due to their technical progress transcriptome and proteome analyses are becoming increasingly relevant in all fields of biological research. They are mainly used for the explorative identification of disease associated complex gene expression patterns and thereby set the stage for hypothesis-driven studies. This review gives an overview on the methods currently available for transcriptome analysis, that is, microarrays, Ref-Seq, quantitative PCR arrays and discusses their potentials and limitations. Second, the most powerful current approaches to proteome analysis are introduced, that is, 2D-gel electrophoresis, shotgun proteomics, MudPIT and the diverse technological concepts are reviewed. Finally, experimental strategies for biomarker discovery, experimental settings for the identification of prognostic gene sets and explorative versus hypothesis driven approaches for the elucidation of diseases associated genes and molecular pathways are described and their potential for studies in veterinary research is highlighted.

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Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics

Cited by 15 publications

References 69 publications

Differential protein expression and basal lamina remodeling in human heart failure

Differential protein expression and basal lamina remodeling in human heart failure

Glycan labeling strategies and their use in identification and quantification

Transcriptome and Proteome Research in Veterinary Science: What Is Possible and What Questions Can Be Asked?

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