Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis

Wu, Christine C.; MacCoss, Michael J.; Howell, Kathryn E.; Matthews, Dwight E.; Yates, John R.

doi:10.1021/ac049208j

Cited by 372 publications

(344 citation statements)

References 44 publications

Supporting

Mentioning

340

Contrasting

Unclassified

Order By: Relevance

“…2 for proteome metric equations). We term this ‘within proteome’ because the SILAM approach corrects for different ionization efficiencies and yields among peptides by comparing each to its cognate from the added 15 N‐labeled standard, thereby revealing relative changes in concentration from sample to sample within the measured proteome, but does not reliably quantify true concentrations in the tissue (Wu et al ., 2004). …”

Section: Resultsmentioning

confidence: 99%

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

et al. 2015

View full text Add to dashboard Cite

SummaryCombating the social and economic consequences of a growing elderly population will require the identification of interventions that slow the development of age‐related diseases. Preserved cellular homeostasis and delayed aging have been previously linked to reduced cell proliferation and protein synthesis rates. To determine whether changes in these processes may contribute to or predict delayed aging in mammals, we measured cell proliferation rates and the synthesis and replacement rates (RRs) of over a hundred hepatic proteins in vivo in three different mouse models of extended maximum lifespan (maxLS): Snell Dwarf, calorie‐restricted (CR), and rapamycin (Rapa)‐treated mice. Cell proliferation rates were not consistently reduced across the models. In contrast, reduced hepatic protein RRs (longer half‐lives) were observed in all three models compared to controls. Intriguingly, the degree of mean hepatic protein RR reduction was significantly correlated with the degree of maxLS extension across the models and across different Rapa doses. Absolute rates of hepatic protein synthesis were reduced in Snell Dwarf and CR, but not Rapa‐treated mice. Hepatic chaperone levels were unchanged or reduced and glutathione S‐transferase synthesis was preserved or increased in all three models, suggesting a reduced demand for protein renewal, possibly due to reduced levels of unfolded or damaged proteins. These data demonstrate that maxLS extension in mammals is associated with improved hepatic proteome homeostasis, as reflected by a reduced demand for protein renewal, and that reduced hepatic protein RRs hold promise as an early biomarker and potential target for interventions that delay aging in mammals.

show abstract

Section: Resultsmentioning

confidence: 99%

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Metabolic 15 N Labeling and Preparation of S.cerevisiae Samples-Yeast were grown and labeled using a previously published protocol 9,10 . Unlabeled and 15 N-labeled yeast were mixed in known ratios (i.e., 1:1, 5:1, 10:1, 50:1 and 100:1) as determined by OD 600 /ml.…”

Section: Preparation Of Samplesmentioning

confidence: 99%

Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer

et al. 2007

Self Cite

View full text Add to dashboard Cite

The quantitative analysis of complex biological samples has emerged as a key research area in the field of proteomics. Although quantitative proteomic experiments remain challenging, these strategies have been greatly facilitated by the development of newer high-performance mass spectrometers. In this work, we have evaluated the use of the LTQ-Orbitrap, a hybrid mass spectrometer in which a linear ion trap is coupled to an Orbitrap mass analyzer, for quantitative analyses. By analyzing a range of yeast protein standards, we found that the high mass accuracy, high resolution, large ion capacity, and large dynamic range of the LTQ-Orbitrap led to a significant improvement in the number and quality of the peptide ratio measurements compared to similar analyses done on the LTQ. We also successfully quantified protein expression differences that occur in metabolically labeled rat synapses during brain development to further demonstrate the suitability of the LTQ-Orbitrap for the comparative analysis of complex tissue samples.

show abstract

“…Labeling techniques use isotopic labels as a reference for relative or absolute quantitation. These labels can be introduced into samples in vivo by metabolic labeling (Wu et al, 2004) or SILAC (Ong et al, 2002), and in vitro by iTRAQ (Ross et al, 2004) or TMT tags (Dayon et al, 2008). In particular, iTRAQ is a comprehensive and efficient method for proteomic quantification that provides multiplex capability and can identify lowexpressed proteins with high confidence in complex samples.…”

Section: Proteomic Studies In Micementioning

confidence: 99%

Proteomic Approaches and Identification of Novel Therapeutic Targets for Alcoholism

Gorini

Harris

Mayfield

2013

Neuropsychopharmacol

View full text Add to dashboard Cite

Recent studies have shown that gene regulation is far more complex than previously believed and does not completely explain changes at the protein level. Therefore, the direct study of the proteome, considerably different in both complexity and dynamicity to the genome/transcriptome, has provided unique insights to an increasing number of researchers. During the past decade, extraordinary advances in proteomic techniques have changed the way we can analyze the composition, regulation, and function of protein complexes and pathways underlying altered neurobiological conditions. When combined with complementary approaches, these advances provide the contextual information for decoding large data sets into meaningful biologically adaptive processes. Neuroproteomics offers potential breakthroughs in the field of alcohol research by leading to a deeper understanding of how alcohol globally affects protein structure, function, interactions, and networks. The wealth of information gained from these advances can help pinpoint relevant biomarkers for early diagnosis and improved prognosis of alcoholism and identify future pharmacological targets for the treatment of this addiction.

show abstract

Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis

Cited by 372 publications

References 44 publications

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice

Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer

Proteomic Approaches and Identification of Novel Therapeutic Targets for Alcoholism

Contact Info

Product

Resources

About