Gel absorption-based sample preparation for the analysis of membrane proteome by mass spectrometry

Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics

Sample preparation is a key step in proteomics workflows. Tube-gel (TG) is a fast and repeatable sample preparation method that consists in the instantaneous trapping of the sample in a polyacrylamide gel matrix. It takes advantage of in-gel sample preparations by allowing the use of high concentrations of sodium-dodecyl sulfate but avoids the time-consuming step of electrophoresis. Therefore, TG limits the sample handling and is thus particularly suitable for high-throughput quantitative proteomics when large sample numbers have to be processed, as it is often the case in biomarker research and clinical proteomics projects.

Gel Absorption-Based Sample Preparation Method for Shotgun Analysis of Membrane Proteome

Membrane proteins solubilized in a starting buffer containing high concentration of SDS are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion, and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins, especially integral membrane proteins.

A Streamlined Sample Preparation Method for Mass Spectrometric Analysis

Mass spectrometry-based proteomic technology experienced remarkable advancement in the past decades. However, their application was still hampered by the complexity of sample preparation. Conventional strategies for sample preparation incorporate multiple time-consuming steps, including cell lysis, protein extraction, protease cleavage, and desalting. Thus, we explored a simplified method (the cell-absorb method) during which living cells were absorbed into vacuum-dried polyacrylamide gel and directly digested in gel into peptides for subsequent LC-MS/MS analysis. As a consequence, both of the steps for cell lysis and protein extraction involved in traditional protocol were skipped. In addition to the decrease in time, more proteins were identified. Indeed, 3022 proteins were identified by the cell-absorb method. Meanwhile, only 2642 and 2420 proteins were identified by the classical SDS-PAGE based method and the reported gel absorption-based method, respectively. The cell-absorb method exhibited apparent advantage in terms of the depth of proteome coverage. Furthermore, the number of proteins identified show excellent reproducibility with a CV (coefficient of variation) of 0.03 among three replicates using the cell-absorb method. These advantages suggest that cell-absorb method is a promising choice for mapping the whole proteome of cells. © 2018 by John Wiley & Sons, Inc.

Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics

Sample preparation for quantitative proteomics is a crucial step to ensure the repeatability and the accuracy of the results. However, there is no universal method compatible with the wide variety of protein extraction buffers currently used. We have recently demonstrated the compatibility of tube-gel with SDS-based buffers and its efficiency for label-free quantitative proteomics by comparing it to stacking gel and liquid digestion. Here, we investigated the compatibility of tube-gel with alternatives to SDS-based buffers allowing notably the extraction of proteins in various pH conditions. We also explored the use of photopolymerization to extend the number of possibilities, as it is compatible with a wide range of pH and is non-oxidative. To achieve this goal, we compared six extraction buffers in combination with two polymerization conditions to further optimize the tube-gel protocol and evaluate its versatility. Identification and quantitative results demonstrated the compatibility of tube-gel with all tested conditions by overall raising quite comparable results. In conclusion, tube-gel is a versatile and simple sample preparation method for large-scale quantitative proteomics applications. Complete datasets are available via ProteomeXchange with identifier PXD008656.

Direct digestion of living cells via a gel-based strategy for mass spectrometric analysis

A novel sample preparation method was established for proteomic analysis, during which living cells were absorbed into vacuum-dried polyacrylamide gel and directly digested into peptides for subsequent LC-MS/MS assays. As a consequence, both of the steps for cell lysis and protein extraction involved in a conventional digestion method were skipped.

Proteomic analysis reveals energy metabolic dysfunction and neurogenesis in the prefrontal cortex of a lipopolysaccharide-induced mouse model of depression

Substantial evidence from previous studies has suggested an association between major depressive disorder (MDD) and inflammation, and previous studies have associated prefrontal cortex (PFC) dysfunction with MDD. Systemic administration of bacterial lipopolysaccharide has been used to study inflammation-associated behavioral changes in rodents. However, proteomic studies investigating PFC protein expression in an LPS-induced mouse model of depression have yet to be conducted. Using two-dimensional electrophoresis coupled with matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry, PFC proteomes were comparatively assessed in LPS-induced acute inflammation reaction mice, LPS-induced depressive-like behavior mice (Dep), and control mice. A total of 26 differentially expressed proteins were identified, two of which were selected for western blot analysis, the results of which revealed a significant increase in the expression levels of creatine kinase B and dihydropyrimidinase-like 3 in Dep mice, suggesting that changes in energy metabolism and neuro-genesis occur in the PFC of Dep mice. Further investigation on these processes and on the proteins of the PFC are required in order to elucidate the pathophysiological mechanism underlying MDD.

Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry

Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.

Enzymatic protein digestion using a dissolvable polyacrylamide gel and its application to mass spectrometry-based proteomics

Enzymatic protein digestion in polyacrylamide gel has been used for sample pretreatment in mass spectrometry-based proteomics due to its effectiveness in removing contaminants that interfere with sample ionization. However, the difficulty of recovering the digested peptides from the solid gel matrix has been a drawback of this method. Here we have developed a novel in-gel digestion method to enhance peptide recovery using a dissolvable, bis-acrylylcystamine (BAC)-crosslinked polyacrylamide gel. After enzymatic protein digestion in BAC gel, we completely dissolved the gel by reductive treatment with tris-(2-carboxyethyl) phosphine to release the digested peptides from the gel. Our analysis revealed that the reductive dissolution of the BAC gel enhances the peptide recovery, which has a significantly higher protein identification capability than the conventional method, using an insoluble polyacrylamide gel. In addition, protein samples trapped in dehydrated BAC gel were stable at room temperature and reproducible sample recovery was obtained after storage for one week. These results indicate that the proposed method could be an effective tool for conducting sample pretreatment for mass spectrometry-based protein analysis.

Sample preparation for the analysis of membrane proteomes by mass spectrometry

The low abundance and highly hydrophobic nature of most membrane proteins make their analysis more difficult than that for common soluble proteins. Successful membrane protein identification is largely dependent on the sample preparation including the enrichment and dissolution of the membrane proteins. A series of conventional and newly developed methods has been applied to the enrichment of low-abundance membrane proteins at membrane and/or protein levels and to the dissolution of hydrophobic membrane proteins. However, all the existing methods have inherent advantages and limitations. Up to now, there has been no unique method that can universally be employed to solve all the problems and more efforts are needed in improving sample preparation for the analysis of membrane proteomes.

Gel-absorption-based sample preparation method for shotgun analysis of membrane proteome

Membrane proteins solubilized in a starting buffer containing high concentration of sodium dodecyl sulfate (SDS) are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly the hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins especially the integral membrane proteins.

Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes

Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.

Shotgun proteomics and network analysis of ubiquitin-related proteins from human breast carcinoma epithelial cells

Protein ubiquitination via the covalent attachment of ubiquitin (Ub) plays an important role in the regulation of the stability, function or localization of multiple proteins in eukaryotic cells. Comprehensive investigation of the proteomics related to ubiquitination will gain the insight into the Ub-mediated regulatory mechanism. In the present study, the combination of polyUb affinity purification, SDS-PAGE separation, and liquid chromatography-tandem mass spectrometry analysis (GeLC-MS/MS) was employed to analyze the Ub-related proteins in human MDA-MB-231 breast carcinoma epithelial cells after treatment with the proteasome inhibitor MG132. A total of 260 non-redundant Ub-related proteins were identified from the cells. These proteins were shown to be involved in a host of critical cellular functions and processes, including transcription, translation, Ub-proteasome pathway, cell cycle, heat shock response, transport, etc. The interaction network analysis by STRING indicated that the identified Ub-related proteins formed eleven clusters, the three most highly ranked network clusters were mainly involved in protein translation, RNA transcription and processing, and Ub-proteasome pathway, suggesting that there were obvious ubiquitination-mediated alternations in gene expression of human MDA-MB-231 cells. The proteomic profiling and their interaction network analysis in this study would help to our systematic understanding of the Ub-related cellular protein functions and the related biological processes in human disease tissue cells.