Characterization of the Human Myocardial Proteome in Inflammatory Dilated Cardiomyopathy by Label-free Quantitative Shotgun Proteomics of Heart Biopsies

Hammer, Elke; Goritzka, Michelle; Ameling, Sabine; Darm, Katrin; Steil, Leif; Klingel, Karin; Trimpert, Christiane; Herda, Lars R.; Dörr, Marcus; Kroemer, Heyo K.; Kandolf, Reinhard; Staudt, Alexander; Felix, Stephan B.; Völker, Uwe

doi:10.1021/pr1008042

Cited by 65 publications

(51 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…We identified over 1,310 unique protein species across FFPE tissues from five patients. This number is comparable to those observed in global, whole-tissue proteomic studies in other tumor samples using similar methodologies (46)(47)(48)(49). In addition, the peptide sequence coverage of up to 88% was a reflection of sufficient protein digestion and reliable protein identification in our study (50).…”

Section: Discussionsupporting

confidence: 88%

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

Azimi

Kaufman

Ali

et al. 2016

CGP

View full text Add to dashboard Cite

Section: Discussionsupporting

confidence: 88%

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

Azimi

Kaufman

Ali

et al. 2016

CGP

View full text Add to dashboard Cite

“…Mass spectrometric analysis of tryptic peptide lysates was performed on an Orbitrap Velos Mass Spectrometer (Thermo Electron, Bremen, Germany) after prefractionation by RP-HPLC as described [5]. The obtained raw data were analyzed using the Refiner MS software version 7.6.6 (GeneData, Basel, Switzerland).…”

Section: Methodsmentioning

confidence: 99%

Effect of Experimental Thyrotoxicosis onto Blood Coagulation: A Proteomics Study

Engelmann¹,

Bischof²,

Dirk³

et al. 2015

Eur Thyroid J

Self Cite

View full text Add to dashboard Cite

Background: Hyperthyroidism is known toinduce a hypercoagulable state. It stimulates plasma levels of procoagulative factors and reduces fibrinolytic activity. So far most of the data have been derived from patients with endogenous hyperthyroidism with a wide variability in the underlying pathogenesis and severity of the disease. Objectives: In this study we experimentally induced thyrotoxicosis in healthy volunteers to explore the effects of thyroxine excess on the plasma proteome. Using a shotgun proteomics approach, the abundance of plasma proteins was monitored before, during and after thyrotoxicosis. Methods: Sixteen healthy male subjects were sampled at baseline, 4 and 8 weeks under 250 µg/day thyroxine p.o., as well as 4 and 8 weeks after stopping the application. Plasma proteins were analyzed after depletion of 6 high-abundance proteins (MARS6) by LC-ESI-MS/MS mass spectrometry. Mass spectrometric raw data were processed using a label-free, intensity-based workflow. Subsequently, the linear dependence between protein abundances and fT₄ levels were calculated using a Pearson correlation. Results: All subjects developed biochemical thyrotoxicosis, and this effect was reversed within the first 4 weeks of follow-up. None of the volunteers noticed any subjective symptoms. Levels of 10 proteins involved in the coagulation cascade specifically correlated with fT₄, supporting an influence of thyroid hormone levels on blood coagulation even at nonpathological levels. Conclusions: The results suggest that experimental thyrotoxicosis exerts selective and specific thyroxine-induced effects on coagulation markers. Our study design allows assessment of thyroid hormone effects on plasma protein levels without secondary effects of other diseases or therapies.

show abstract

“…48 The label-free quantification approach has been used to analyze proteomes from endomyocardial biopsies to identify differential protein expression in inflammatory dilated cardiomyopathy. 49 The study includes identification of 485 proteins, of which 174 were found to be differentially expressed, with at least 1.3-fold changes in intensity (P<0.05). Owing to the versatility of the method, this approach has also been used for quantification of phosphopeptides.…”

Section: Mirza Quantitative Ms-based Methods O5mentioning

confidence: 99%

Quantitative Mass Spectrometry-Based Approaches in Cardiovascular Research

Mirza¹

2012

Circ Cardiovasc Genet

View full text Add to dashboard Cite

ProteomicsC ardiovascular proteomics is a rapidly growing field, especially with the emergence of high-throughput mass spectrometry-based techniques. After the identification of proteins in a given sample, researchers are keen to find out how much of the protein is present, especially in a disease or a given state. Though challenging, over the past few years, several approaches have been established to quantify proteins from cells or tissues at a given state. In this review, we focus on mass spectrometry -based quantitative approaches for both large-scale and targeted proteomic analyses, which can be used in cardiovascular research. Several strategies using labeling and label-free approaches for both relative and absolute quantification (AQUA) have been established to meet the requirements of the researcher. Each of these methods has its own merits and limitations. We will discuss the methods that researchers can opt for to address the biological questions related to cardiovascular research.Cardiovascular proteomics is the branch of proteomics specifically applied to heart and vasculature. The field of proteomics has recently gained greater importance based on its potential to unravel the complex physiological and biochemical mechanisms and pathways in organisms and cells at the molecular level. The goal is to identify proteins that generate/mediate disease process, thereby, opening avenues to new diagnostics and therapeutic strategies. Proteins are much closer to the actual disease process, in most cases, than parent genes. They are the ultimate regulators of cell functions, and the vast majorities serve as drug targets. Differential protein expression analysis, by measuring the upregulated or downregulated proteins in disease state as compared with the normal healthy condition, is vital to understand the disease mechanism.In conjunction with various separation techniques, mass spectrometry (MS)-based methods evolved as the best techniques for the comprehensive characterization of proteins. 1,2After the initial protein identification, a more challenging approach in proteomics is the quantification of the proteins identified.3 Various methods of quantification by MS have been developed recently, for both relative and absolute measurements (Figure 1), and the technology is still expanding to find better and more efficient quantification approaches. This, in turn, is facilitated by the advancements in the MS instrumentation, including powerful analyzers and fragmentation technology. Most of the quantification methods are based on measurements at peptide level and fall under the bottom-up proteomics approach. In this review article, we will outline various MS-based approaches available for measuring the variation in protein abundances and how these techniques are playing a key role in cardiovascular research. Gel-Based QuantificationSeparation of proteins by polyacrylamide gel electrophoresis, followed by MS analysis, has been a common practice in proteomics. With the advent of 2D gel electrophoresis, quantificatio...

show abstract

Characterization of the Human Myocardial Proteome in Inflammatory Dilated Cardiomyopathy by Label-free Quantitative Shotgun Proteomics of Heart Biopsies

Cited by 65 publications

References 47 publications

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue

Effect of Experimental Thyrotoxicosis onto Blood Coagulation: A Proteomics Study

Quantitative Mass Spectrometry-Based Approaches in Cardiovascular Research

Contact Info

Product

Resources

About