Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis

Fléron, Maximilien; Greffe, Yannick; Musmeci, Davide; Massart, Anne-Cécile; Hennequière, Vincent; Mazzucchelli, Gabriel; Waltregny, David; Pauw-Gillet, M. C. De; Castronovo, Vincent; Pauw, Edwin De; Turtoï, Andrei

doi:10.1016/j.jprot.2010.06.003

Cited by 26 publications

(15 citation statements)

References 52 publications

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“…From the ratios of the ion intensities of these sister peptide pairs, the relative abundance of their parent proteins in the original samples can be determined [68]. Recently, a detailed experimental protocol called postdigest ICPL was published highlighting a better protein identification and quantification [69, 70] and when compared to iTRAQ, both techniques have shown comparable number of identified and quantified proteins in the endosperm of castor bean seeds at three developmental stages [71]. So far, the latter study is the unique reported quantitative proteomic investigation on plants using ICPL (Table 2).…”

Section: Overview Of Label-based Proteomic Approachesmentioning

confidence: 99%

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Abdallah

Dumas‐Gaudot

Renaut³

et al. 2012

International Journal of Plant Genomics

172

175

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Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.

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Section: Overview Of Label-based Proteomic Approachesmentioning

confidence: 99%

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Abdallah

Dumas‐Gaudot

Renaut³

et al. 2012

International Journal of Plant Genomics

172

175

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“…Proteomic methods are widely employed for a variety of applications, including disease biomarker discovery, [1]–[4], elucidation of physiological processes [5], and localization of post-translational modifications [6], [7]. For example, malignant cells yield unique “protein profiles” when total protein extracts from such cells are analyzed by 2-D gel electrophoresis or mass spectrometry (MS) methods.…”

Section: Introductionmentioning

confidence: 99%

Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates

et al. 2010

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BackgroundProteomic studies of formalin-fixed paraffin-embedded (FFPE) tissues are frustrated by the inability to extract proteins from archival tissue in a form suitable for analysis by 2-D gel electrophoresis or mass spectrometry. This inability arises from the difficulty of reversing formaldehyde-induced protein adducts and cross-links within FFPE tissues. We previously reported the use of elevated hydrostatic pressure as a method for efficient protein recovery from a hen egg-white lysozyme tissue surrogate, a model system developed to study formalin fixation and histochemical processing.Principal FindingsIn this study, we demonstrate the utility of elevated hydrostatic pressure as a method for efficient protein recovery from FFPE mouse liver tissue and a complex multi-protein FFPE tissue surrogate comprised of hen egg-white lysozyme, bovine carbonic anhydrase, bovine ribonuclease A, bovine serum albumin, and equine myoglobin (55∶15∶15∶10∶5 wt%). Mass spectrometry of the FFPE tissue surrogates retrieved under elevated pressure showed that both the low and high-abundance proteins were identified with sequence coverage comparable to that of the surrogate mixture prior to formaldehyde treatment. In contrast, non-pressure-extracted tissue surrogate samples yielded few positive and many false peptide identifications. Studies with soluble formalin-treated bovine ribonuclease A demonstrated that pressure modestly inhibited the rate of reversal (hydrolysis) of formaldehyde-induced protein cross-links. Dynamic light scattering studies suggest that elevated hydrostatic pressure and heat facilitate the recovery of proteins free of formaldehyde adducts and cross-links by promoting protein unfolding and hydration with a concomitant reduction in the average size of the protein aggregates.ConclusionsThese studies demonstrate that elevated hydrostatic pressure treatment is a promising approach for improving the recovery of proteins from FFPE tissues in a form suitable for proteomic analysis.

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“…This post-digest ICPL can be combined with other fractionation methods such as IEF prior to LC-MS [81] or even with enrichment of peptides with specific PTM's as phosphorylation or glycosylation [82].…”

Section: Chemical Labeling Approaches: Isotope Techniquesmentioning

confidence: 99%

Neuroproteomics — LC-MS Quantitative Approaches

Santa¹,

Anjo²,

Mendes³

et al. 2015

Recent Advances in Proteomics Research

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Neuroproteomics is a scientific field that aims to study all the proteins of the central nervous system, their expression, function, and interactions. The central nervous system is intricate and heterogeneous, and the study of its proteome is consequently complex, with many biological questions still requiring deep investigation. For this, mass spectrometry approaches, most often coupled with liquid chromatography (LC-MS), have been the number one choice in proteomics, and over the years it has added many important findings to the field. At this point it is important that proteomics turns to the quantitative expression of proteins instead of only identifying which proteins are present in a given sample, much because the most important alterations may be slight alterations in the quantity of a protein in a given situation. Therefore, many LC-MS quantitative approaches have been developed relying on the labeling of the proteins or even by using label-free techniques.In this chapter, a brief description of the principles and procedures of several approaches used for relative and absolute, targeted and untargeted quantification of proteins is presented, complemented with a literature revision of their application in the neurosciences field.

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Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis

Cited by 26 publications

References 52 publications

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates

Neuroproteomics — LC-MS Quantitative Approaches

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