Facile synthesis of a graphene/nickel-cobalt hydroxide ternary hydrogel for high-performance supercapacitors.

In this paper, a graphene/nickel-cobalt hydroxide ternary hydrogel (G-Ni-Co) with superior electrochemical performances was prepared by a simple hydrothermal method using Ni(NO)·6HO, Co(NO)·6HO, and graphene oxide as the starting materials. The mass fraction and the pH value of the reaction system were optimized. The prepared G-Ni-Co was assembled into a symmetric supercapacitor and its electrochemical performance was estimated.

Procedures for the biochemical enrichment and proteomic analysis of the cytoskeletome.

The cell cytoskeleton is composed of microtubules, intermediate filaments, and actin that provide a rigid support structure important for cell shape. However, it is also a dynamic signaling scaffold that receives and transmits complex mechanosensing stimuli that regulate normal physiological and aberrant pathophysiological processes. Studying cytoskeletal functions in the cytoskeleton's native state is inherently difficult due to its rigid and insoluble nature.

Proteomic and biochemical methods to study the cytoskeletome.

The cytoskeleton is fundamental to many cellular functions including cell proliferation, differentiation, adhesion, and migration. It is composed of actin, microtubules, intermediate filaments, and integrin cell surface receptors, which form focal adhesions with the extracellular matrix. These elements are highly integrated in the cell providing a rigid network of interconnected cables and protein scaffolds, which generate force and mechanical support to maintain cell shape and movement.

Proteome-wide discovery and characterizations of nucleotide-binding proteins with affinity-labeled chemical probes.

Nucleotide-binding proteins play pivotal roles in many cellular processes including cell signaling. However, targeted studies of the subproteome of nucleotide-binding proteins, especially protein kinases and GTP-binding proteins, remain challenging. Here, we report a general strategy in using affinity-labeled chemical probes to enrich, identify, and quantify ATP- and GTP-binding proteins in the entire human proteome.

Systematic analysis of protein phosphorylation networks from phosphoproteomic data.

In eukaryotes, hundreds of protein kinases (PKs) specifically and precisely modify thousands of substrates at specific amino acid residues to faithfully orchestrate numerous biological processes, and reversibly determine the cellular dynamics and plasticity. Although over 100,000 phosphorylation sites (p-sites) have been experimentally identified from phosphoproteomic studies, the regulatory PKs for most of these sites still remain to be characterized. Here, we present a novel software package of iGPS for the prediction of in vivo site-specific kinase-substrate relations mainly from the phosphoproteomic data.

Quantitative proteomic analysis revealed lovastatin-induced perturbation of cellular pathways in HL-60 cells.

Lovastatin, a member of the statin family of drugs, is widely prescribed for treating hypercholesterolemia. The statin family of drugs, however, also shows promise for cancer treatment and prevention. Although lovastatin is known to be an inhibitor for HMG-CoA reductase, the precise mechanisms underlying the drug's antiproliferative activity remain unclearly defined.

Perspectives of comprehensive phosphoproteome analysis using shotgun strategy.

Protein phosphorylation is a ubiquitous post-translational modification that regulates almost all cellular processes. The analysis of protein phosphorylation is challenging due to the high dynamic range and low abundance natures of the analyte. Shotgun based proteomics has emerged as a very useful platform to achieve a comprehensive phosphoproteome analysis in considerable depth.

Enrichment of peptides containing consensus sequence by an enzymatic approach for targeted analysis of proteins.

Multiple residues with consensus sequence, i.e. motif, on proteins are closely related to protein function.

Spatial phosphoprotein profiling reveals a compartmentalized extracellular signal-regulated kinase switch governing neurite growth and retraction.

Brain development and spinal cord regeneration require neurite sprouting and growth cone navigation in response to extension and collapsing factors present in the extracellular environment. These external guidance cues control neurite growth cone extension and retraction processes through intracellular protein phosphorylation of numerous cytoskeletal, adhesion, and polarity complex signaling proteins. However, the complex kinase/substrate signaling networks that mediate neuritogenesis have not been investigated.

The proteome analysis of oleaginous yeast Lipomyces starkeyi.

Oleaginous yeast Lipomyces starkeyi, a species in the Saccharomycetales order, has the capability to accumulate over 70% of its cell biomass as lipid under defined culture conditions. In this study, analysis of L. starkeyi AS 2.

Global proteome quantification for discovering imatinib-induced perturbation of multiple biological pathways in K562 human chronic myeloid leukemia cells.

Imatinib mesylate, currently marketed by Novartis as Gleevec in the U.S., has emerged as the leading compound to treat the chronic phase of chronic myeloid leukemia (CML), through its inhibition of Bcr-Abl tyrosine kinases, and other cancers.

Quantitative proteomic analysis reveals the perturbation of multiple cellular pathways in jurkat-T cells induced by doxorubicin.

Doxorubicin remains an important part of chemotherapy regimens in the clinic and is considered an effective agent in the treatment of acute lymphoblastic leukemia (ALL). Although the cellular responses induced by doxorubicin treatment have been investigated for years, the precise mechanisms underlying its cytotoxicity and therapeutic activity remain unclear. Here we utilized mass spectrometry, together with stable isotope labeling by amino acids in cell culture (SILAC), to analyze comparatively the protein expression in Jurkat-T cells before and after treatment with a clinically relevant concentration of doxorubicin.

Classification filtering strategy to improve the coverage and sensitivity of phosphoproteome analysis.

Data dependent neutral loss triggered MS3 methodology (NLMS3) is often applied to acquire MS data for the analysis of phosphopeptides. Some phosphopeptides tend to seriously lose the phosphate and result in MS2 spectra with poor fragments and fragment-rich MS3 spectra, while some phosphopeptides do not lose phosphate and result in nice MS2 spectra. Since different phosphopeptides have fragment spectra with different characteristics, filtering all of the phosphopeptide identifications by setting a global filter criteria may be inappropriate and result in low sensitivity.

Fractionation of phosphopeptides on strong anion-exchange capillary trap column for large-scale phosphoproteome analysis of microgram samples.

It is one of the key issues to develop powerful fractionating method to increase the identification of the low-abundance phosphopeptides. In this study, a semi-online 2-D LC separation strategy based on three-step fractionation of the enriched peptides on strong anion-exchange trap column was developed. It was demonstrated that the sensitivity and phosphoproteome coverage obtained by this fractionating method with strong anion-exchange trap column is much higher than those by the conventional methods based on C18 trap column.

ArMone: a software suite specially designed for processing and analysis of phosphoproteome data.

The development of new phosphoproteomic technologies has led to a rapid increase in the number of phosphoprotein identifications. Managing and extracting valuable information from the phosphoproteome data sets and generating output information in user-friendly formats require special data management and process platform. Even though a few proteome pipelines have been developed, they are mainly designed for processing data set of unmodified peptide/protein identifications.

Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.

Reversible protein phosphorylation plays a critical role in liver development and function. Comprehensively cataloging the phosphoproteins and their phosphorylation sites in human liver tissue will facilitate the understanding of physiological and pathological mechanisms of liver. Owing to lacking of efficient approach to fractionate phosphopeptides, nanoflow-RPLC with long-gradient elution was applied to reduce the complexity of the phosphopeptides in this study.

Reversed-phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides.

Protein phosphorylation regulates a series of important biological processes in eukaryotes. However, the phosphorylation sites found up to now are far below than that actually exists in proteins due to the extreme complexity of the proteome sample. Here a new reversed-phase-reversed-phase liquid chromatography (RP-RPLC) approach was developed for multidimensional separation of phosphopeptides.

Instance based algorithm for posterior probability calculation by target-decoy strategy to improve protein identifications.

The target-decoy database search strategy is often applied to determine the global false-discovery rate (FDR) of peptide identifications in proteome research. However, the confidence of individual peptide identification is typically not determined. In this study, we introduced an approach for the calculation of posterior probability of individual peptide identification from the "local false-discovery rate" (local FDR), which is also determined based on a target-decoy database search.

Comprehensive and reliable phosphorylation site mapping of individual phosphoproteins by combination of multiple stage mass spectrometric analysis with a target-decoy database search.

Since the emergence of proteomics, much attention has been paid to the development of new technologies for phosphoproteomcis analysis. Compared with large scale phosphorylation analysis at the proteome level, comprehensive and reliable phosphorylation site mapping of individual phosphoprotein is equally important. Here, we present a modified target-decoy database search strategy for confident phosphorylation site analysis of individual phosphoproteins without manual interpretation of spectra.

Preparation of monodisperse immobilized Ti(4+) affinity chromatography microspheres for specific enrichment of phosphopeptides.

This study presented an approach to prepare monodisperse immobilized Ti(4+) affinity chromatography (Ti(4+)-IMAC) microspheres for specific enrichment of phosphopeptides in phosphoproteome analysis. Monodisperse polystyrene seed microspheres with a diameter of ca. 4.

Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.

The study of protein glycosylation has lagged far behind the progress of current proteomics because of the enormous complexity, wide dynamic range distribution and low stoichiometric modification of glycoprotein. Solid phase extraction of tryptic N-glycopeptides by hydrazide chemistry is becoming a popular protocol for the analysis of N-glycoproteome. However, in silico digestion of proteins in human proteome database by trypsin indicates that a significant percentage of tryptic N-glycopeptides is not in the preferred detection mass range of shotgun proteomics approach, that is, from 800 to 3500 Da.

Improvement of performance in label-free quantitative proteome analysis with monolithic electrospray ionization emitter.

The postcolumn void volume, which is introduced by the connecting tubing and void ESI emitter in the nanoflow LC coupled with MS/MS system (microLC-MS/MS), is harmful for the analysis of peptides in shotgun proteome analysis. A new type of porous C12 monolithic ESI emitter was prepared to eliminate the disruption and mixing effects occurring in the connecting tubing and void emitter. It was demonstrated that the porous hydrophobic monolith inside the emitter played a key role in retaining the good peak profile, and the average peak capacity of the whole separation system increased 12.

Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis.

The elucidation of protein post-translational modifications, such as phosphorylation, remains a challenging analytical task for proteomic studies. Since many of the proteins targeted for phosphorylation are low in abundance and phosphorylation is typically substoichiometric, a prerequisite for their identification is the specific enrichment of phosphopeptide prior to mass spectrometric analysis. Here, we presented a new method termed as immobilized titanium ion affinity chromatography (Ti (4+)-IMAC) for enriching phosphopeptides.

[Identification and relative quantification of peptides by capillary reversed-phase liquid chromatography-tandem mass spectrometry].

A method for the identification and relative quantification of peptides by capillary liquid chromatography ion-trap tandem mass spectrometry (LC-IT-MS/MS) was established. At first, the peptides were automatically identified by correlating the tandem mass spectra with the peptide sequences from a database. After the quantitative information of peptide ions were extracted from the full-scan MS according to the results of database searching, the peak intensities of the identified peptide ions with different charge states were summed together to define the total intensity of the peptide.

Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography.

The mixture of phosphopeptides enriched from proteome samples are very complex. To reduce the complexity it is necessary to fractionate the phosphopeptides. However, conventional enrichment methods typically only enrich phosphopeptides but not fractionate phosphopeptides.