Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

2012 ◽  
Vol 11 (3) ◽  
pp. 1582-1590 ◽  
Author(s):  
Zhou Li ◽  
Rachel M. Adams ◽  
Karuna Chourey ◽  
Gregory B. Hurst ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Metabolic Labeling ◽  
Label Free ◽  
Chemical Labeling ◽  
Systematic Comparison

Relative and Absolute Quantitation in Mass Spectrometry–Based Proteomics

2018 ◽  
Vol 11 (1) ◽  
pp. 49-77 ◽  
Author(s):  
J. Astor Ankney ◽  
Adil Muneer ◽  
Xian Chen
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrum ◽  
Quantitative Proteomics ◽  
Label Free ◽  
Absolute Quantitation ◽  
Chemical Labeling ◽  
Stable Isotope Label ◽  
Proteome Coverage ◽  
Isotope Label ◽  
Quantification Accuracy

Mass spectrometry–based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label–based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling–based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.

Development of Algorithms for Mass Spectrometry-based Label-free Quantitative Proteomics*

2011 ◽  
Vol 38 (6) ◽  
pp. 506-518 ◽  
Author(s):  
Wei ZHANG ◽  
Ji-Yang ZHANG ◽  
Hui LIU ◽  
Han-Chang SUN ◽  
Chang-Ming XU ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Label Free

scholarly journals Temporal Quantitative Proteomics Analysis of Neuroblastoma Cells Treated with Bovine Milk-Derived Extracellular Vesicles Highlights the Anti-Proliferative Properties of Milk-Derived Extracellular Vesicles

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 750
Author(s):  
Pamali Fonseka ◽  
Taeyoung Kang ◽  
Sing Chee ◽  
Sai V. Chitti ◽  
Rahul Sanwlani ◽  
...  
Keyword(s):  
High Risk ◽  
Extracellular Vesicles ◽  
Quantitative Proteomics ◽  
Cell Metabolism ◽  
Bovine Milk ◽  
Neuroblastoma Cells ◽  
Treatment Strategies ◽  
Treatment Resistance ◽  
Label Free ◽  
The Impact

Neuroblastoma (NBL) is a pediatric cancer that accounts for 15% of childhood cancer mortality. Amplification of the oncogene N-Myc occurs in 20% of NBL patients and is considered high risk as it correlates with aggressiveness, treatment resistance and poor prognosis. Even though the treatment strategies have improved in the recent years, the survival rate of high-risk NBL patients remain poor. Hence, it is crucial to explore new therapeutic avenues to sensitise NBL. Recently, bovine milk-derived extracellular vesicles (MEVs) have been proposed to contain anti-cancer properties. However, the impact of MEVs on NBL cells is not understood. In this study, we characterised MEVs using Western blotting, NTA and TEM. Importantly, treatment of NBL cells with MEVs decreased the proliferation and increased the sensitivity of NBL cells to doxorubicin. Temporal label-free quantitative proteomics of NBL cells highlighted the depletion of proteins involved in cell metabolism, cell growth and Wnt signalling upon treatment with MEVs. Furthermore, proteins implicated in cellular senescence and apoptosis were enriched in NBL cells treated with MEVs. For the first time, this study highlights the temporal proteomic profile that occurs in cancer cells upon MEVs treatment.

scholarly journals Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

PROTEOMICS ◽  
2011 ◽  
Vol 11 (8) ◽  
pp. 1508-1516 ◽  
Author(s):  
Dana V. Skarra ◽  
Marilyn Goudreault ◽  
Hyungwon Choi ◽  
Michael Mullin ◽  
Alexey I. Nesvizhskii ◽  
...  
Keyword(s):  
Protein Phosphatase ◽  
Quantitative Proteomics ◽  
Label Free ◽  
Protein Phosphatase 5 ◽  
Interactome Mapping
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