1.
Enhanced detection and desalting free protocol for phosphopeptides eluted from immobilized Fe (III) affinity chromatography in direct MALDI TOF analysis.
Zhu, L, Zhang, J, Guo, Y
Journal of proteomics. 2014;:360-5
Abstract
UNLABELLED IMAC strategy is widely used in phosphopeptide enrichment, but most of the current eluents contain large amount of salt, which must be discarded before MS detection. Here, we present techniques to elute phosphopeptides with low ionization efficiency reagents, which could be left in the eluate for direct MS analysis, thus saving desalting and the following steps. Several reagents were studied, including 5-sulfosalicylic acid dihydrate, acetyl acetone and glyphosate. The results show that glyphosate has very outstanding advantages: only monophosphopeptides can be eluted with glyphosate solution, while all phosphopeptides can be eluted with negatively charged glyphosate ions with pH9. Moreover, the high ionic strength can minimize nonspecific electrostatic interactions in elution step and limit the generation of potential phosphopeptide-metal ion adducts such as sodium or Fe(3+) counterparts. S/N of phosphopeptides could be enhanced 3-5 folds in MALDI MS detection and phosphopeptide recovery is greatly improved while compared with its counterparts eluted by commonly used elution buffers. By applying this reagent into IMAC elution, the whole experimental process could be more convenient, time-saving and cost-saving, which is of great importance to the enrichment and detection of phosphopeptides in phosphoproteomics research. BIOLOGICAL SIGNIFICANCE This potent desalting-free and signal enhanced elution method can improve the sensitivity and detection of phosphopeptides in MALDI TOF MS analysis, both time saving and cost saving. With these advantages, it's highly appropriate for the high throughout analysis of phosphoproteomics.
2.
[The application of small molecule bioactive probes in the identification of cellular targets].
Zhang, J, Zhou, HC
Yao xue xue bao = Acta pharmaceutica Sinica. 2012;(3):299-306
Abstract
Identification of the cellular targets of bioactive compounds is a major challenge and a key issue in chemical biology and drug discovery. As an important technology in functional proteomics, small molecule probes play a pivotal role in the identification of cellular targets of bioactive compounds. This review is intended to introduce the application principles and structural design philosophy of chemical probes for the purpose of mechanistic study. Recent cases of successful application were also discussed to further demonstrate the principles and significance ofbioactive small molecule-based probes.
3.
Protein-centric data integration for functional analysis of comparative proteomics data.
McGarvey, PB, Zhang, J, Natale, DA, Wu, CH, Huang, H
Methods in molecular biology (Clifton, N.J.). 2011;:323-39
Abstract
High-throughput proteomic, microarray, protein interaction and other experimental methods all generate long lists of proteins and/or genes that have been identified or have varied in accumulation under the experimental conditions studied. These lists can be difficult to sort through for Biologists to make sense of. Here we describe a next step in data analysis--a bottom-up approach at data integration--starting with protein sequence identifications, mapping them to a common representation of the protein and then bringing in a wide variety of structural, functional, genetic, and disease information related to proteins derived from annotated knowledge bases and then using this information to categorize the lists using Gene Ontology (GO) terms and mappings to biological pathway databases. We illustrate with examples how this can aid in identifying important processes from large complex lists.
4.
A novel strategy for proteome-wide ligand screening using cross-linked phage matrices.
Qian, C, Liu, JN, Tang, F, Yuan, D, Guo, Z, Zhang, J
The Journal of biological chemistry. 2010;(13):9367-9372
Abstract
To find a suitable ligand from a complex antigen system is still a mission to be accomplished. Here we have explored a novel "library against proteome" panning strategy for ligand screening and antigen purification from a complex system using phage-displayed antibody technology. Human plasma proteome was targeted for phage library panning. During the process, the panning was carried out in solution, using a biotin/streptavidin beads separation system, for three rounds. Nine monoclonal phages, bound tightly to a number of unknown plasma proteins, were selected from the last round, six of which were directly employed as cross-linked matrices to purify their corresponding antigens from the plasma. The proteins isolated by G5 and E1 matrices were identified as amyloid protein and apolipoprotein A-I precursor, respectively. The results demonstrated that it was feasible to simultaneously obtain a number of ligand phages for various antigens, including low abundant proteins in a non-comparative proteome-wide system.
5.
Proteome-wide prediction of acetylation substrates.
Basu, A, Rose, KL, Zhang, J, Beavis, RC, Ueberheide, B, Garcia, BA, Chait, B, Zhao, Y, Hunt, DF, Segal, E, et al
Proceedings of the National Academy of Sciences of the United States of America. 2009;(33):13785-90
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Abstract
Acetylation is a well-studied posttranslational modification that has been associated with a broad spectrum of biological processes, notably gene regulation. Many studies have contributed to our knowledge of the enzymology underlying acetylation, including efforts to understand the molecular mechanism of substrate recognition by several acetyltransferases, but traditional experiments to determine intrinsic features of substrate site specificity have proven challenging. Here, we combine experimental methods with clustering analysis of protein sequences to predict protein acetylation based on the sequence characteristics of acetylated lysines within histones with our unique prediction tool PredMod. We define a local amino acid sequence composition that represents potential acetylation sites by implementing a clustering analysis of histone and nonhistone sequences. We show that this sequence composition has predictive power on 2 independent experimental datasets of acetylation marks. Finally, we detect acetylation for selected putative substrates using mass spectrometry, and report several nonhistone acetylated substrates in budding yeast. Our approach, combined with more traditional experimental methods, may be useful for identifying acetylated substrates proteome-wide.