Quantification of Proteins and Metabolites by Mass Spectrometry Without Isotopic Labeling

2007 ◽  
pp. 87-105 ◽  
Author(s):  
Sushmita Mimi Roy ◽  
Christopher H. Becker
Keyword(s):  
Mass Spectrometry ◽  
Isotopic Labeling

Detection of glycation sites in proteins by high-resolution mass spectrometry combined with isotopic labeling

2010 ◽  
Vol 400 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Piotr Stefanowicz ◽  
Monika Kijewska ◽  
Alicja Kluczyk ◽  
Zbigniew Szewczuk
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
High Resolution Mass Spectrometry ◽  
Isotopic Labeling ◽  
High Resolution Mass ◽  
Resolution Mass

Probing Protein/Protein Interactions with Mass Spectrometry and Isotopic Labeling:  Analysis of the p21/Cdk2 Complex

1996 ◽  
Vol 118 (22) ◽  
pp. 5320-5321 ◽  
Author(s):  
Richard W. Kriwacki ◽  
Jiang Wu ◽  
Gary Siuzdak ◽  
Peter E. Wright
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Isotopic Labeling ◽  
Protein Protein Interactions ◽  
Cdk2 Complex

scholarly journals A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria

2020 ◽  
Vol 19 (7) ◽  
pp. 1161-1178 ◽  
Author(s):  
Andreas Linden ◽  
Markus Deckers ◽  
Iwan Parfentev ◽  
Ralf Pflanz ◽  
Bettina Homberg ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Isotopic Labeling ◽  
Growth Conditions ◽  
Cross Linking ◽  
Nadh:Ubiquinone Oxidoreductase ◽  
Protein Protein Interactions ◽  
Copy Numbers ◽  
Transport Chain ◽  
Quantitative Changes

Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase.

Latest developments in sample treatment for 18O-isotopic labeling for proteomics mass spectrometry-based approaches: A critical review

Talanta ◽  
2010 ◽  
Vol 80 (4) ◽  
pp. 1476-1486 ◽  
Author(s):  
J.L. Capelo ◽  
R.J. Carreira ◽  
L. Fernandes ◽  
C. Lodeiro ◽  
H.M. Santos ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Critical Review ◽  
Isotopic Labeling ◽  
Sample Treatment

scholarly journals Altered Retinoic Acid Metabolism in Diabetic Mouse Kidney Identified by 18O Isotopic Labeling and 2D Mass Spectrometry

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e11095 ◽  
Author(s):  
Jonathan M. Starkey ◽  
Yingxin Zhao ◽  
Rovshan G. Sadygov ◽  
Sigmund J. Haidacher ◽  
Wanda S. LeJeune ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Retinoic Acid ◽  
Acid Metabolism ◽  
Isotopic Labeling ◽  
Diabetic Mouse ◽  
Mouse Kidney

scholarly journals Global discovery of high-NaCl-induced changes of protein phosphorylation

2014 ◽  
Vol 307 (5) ◽  
pp. C442-C454 ◽  
Author(s):  
Rong Wang ◽  
Joan D. Ferraris ◽  
Yuichiro Izumi ◽  
Natalia Dmitrieva ◽  
Kevin Ramkissoon ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Renal Medulla ◽  
Isotopic Labeling ◽  
Dna Double Strand Breaks ◽  
Hek 293 ◽  
Strand Breaks ◽  
293 Cells ◽  
And Function ◽  
Induced Changes

High extracellular NaCl, such as in the renal medulla, can perturb and even kill cells, but cells mount protective responses that enable them to survive and function. Many high-NaCl-induced perturbations and protective responses are known, but the signaling pathways involved are less clear. Change in protein phosphorylation is a common mode of cell signaling, but there was no unbiased survey of protein phosphorylation in response to high NaCl. We used stable isotopic labeling of amino acids in cell culture coupled to mass spectrometry to identify changes in protein phosphorylation in human embryonic kidney (HEK 293) cells exposed to high NaCl. We reproducibly identify >8,000 unique phosphopeptides in 4 biological replicate samples with a 1% false discovery rate. High NaCl significantly changed phosphorylation of 253 proteins. Western analysis and targeted ion selection mass spectrometry confirm a representative sample of the phosphorylation events. We analyze the affected proteins by functional category to infer how altered protein phosphorylation might signal cellular responses to high NaCl, including alteration of cell cycle, cyto/nucleoskeletal organization, DNA double-strand breaks, transcription, proteostasis, metabolism of mRNA, and cell death.

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