Highly efficient and selective enrichment of peptide subsets combining fluorous chemistry with reversed-phase chromatography.
ABSTRACT The selective capture of target peptides poses a great challenge to modern chemists and biologists, especially when enriching them from proteome samples possessing extremes in concentration dynamic range and sequence diversity. While approaches based on traditional techniques such as biotin-avidin pairing offer versatile tools to design strategies for selective enrichment, problems are still encountered due to sample loss or poor selectivity of enrichment. Here we show that the recently introduced fluorous chemistry approach has attractive properties as an alternative method for selective enrichment. Through appending a perfluorine group to the target peptide, it is possible to dramatically increase the peptide's hydrophobicity and thus enable facile separation of labeled from non-labeled peptides. Use of reversed-phase chromatography allowed for improved peptide recovery in comparison with results obtained using the formerly reported fluorous bonded phase methods. Furthermore, this approach also allowed for on-line separation and identification of both labeled and unlabeled peptides in a single experiment. The net result is an increase in the confidence of protein identification by tandem mass spectrometry (MS2) as all peptides and subsequent information are retained. Successful off-line and on-line enrichment of cysteine-containing peptides was obtained, and high quality MS2 spectra were obtained by tandem mass spectrometry due to the stability of the tag, allowing for facile identification via standard database searching. We believe that this strategy holds great promise for selective enrichment and identification of low abundance target proteins or peptides.
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ABSTRACT: Background Identification of novel genetic risk factors is imperative for a better understanding of B lymphomagenesis and for the development of novel therapeutic strategies. TRAF3, a critical regulator of B cell survival, was recently recognized as a tumor suppressor gene in B lymphocytes. The present study aimed to identify novel oncogenes involved in malignant transformation of TRAF3-deficient B cells.Methods We used microarray analysis to identify genes differentially expressed in TRAF3¿/¿ mouse splenic B lymphomas. We employed lentiviral vector-mediated knockdown or overexpression to manipulate gene expression in human multiple myeloma (MM) cell lines. We analyzed cell apoptosis and proliferation using flow cytometry, and performed biochemical studies to investigate signaling mechanisms. To delineate protein-protein interactions, we applied affinity purification followed by mass spectrometry-based sequencing.ResultsWe identified mutated in colorectal cancer (MCC) as a gene strikingly up-regulated in TRAF3-deficient mouse B lymphomas and human MM cell lines. Aberrant up-regulation of MCC also occurs in a variety of primary human B cell malignancies, including non-Hodgkin lymphoma (NHL) and MM. In contrast, MCC expression was not detected in normal or premalignant TRAF3¿/¿ B cells even after treatment with B cell stimuli, suggesting that aberrant up-regulation of MCC is specifically associated with malignant transformation of B cells. In elucidating the functional roles of MCC in malignant B cells, we found that lentiviral shRNA vector-mediated knockdown of MCC induced apoptosis and inhibited proliferation in human MM cells. Experiments of knockdown and overexpression of MCC allowed us to identify several downstream targets of MCC in human MM cells, including phospho-ERK, c-Myc, p27, cyclin B1, Mcl-1, caspases 8 and 3. Furthermore, we identified 365 proteins (including 326 novel MCC-interactors) in the MCC interactome, among which PARP1 and PHB2 were two hubs of MCC signaling pathways in human MM cells.Conclusions Our results indicate that in sharp contrast to its tumor suppressive role in colorectal cancer, MCC functions as an oncogene in B cells. Our findings suggest that MCC may serve as a diagnostic marker and therapeutic target in B cell malignancies, including NHL and MM.Journal of Hematology & Oncology 09/2014; 7(1):56. DOI:10.1186/s13045-014-0056-6 · 4.93 Impact Factor
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ABSTRACT: We report herein an extraction method for the analysis of perfluorinated compounds in human serum based on magnetic core-mesoporous shell microspheres with decyl-perfluorinated interior pore-walls (Fe3O4@mSiO2-F17). Thanks to the unique properties of the Fe3O4@mSiO2-F17 microspheres, macromolecules like proteins could be easily excluded from the mesoporous channels due to size exclusion effect, and perfluorinated compounds (PFCs) in protein-rich biosamples such as serum could thus be directly extracted with the fluorocarbon modified on the channel wall without any other pretreatment procedure. The PFCs adsorbed Fe3O4@mSiO2-F17 microspheres could then be simply and rapidly isolated by using a magnet, followed by being identified and quantified by LC-MS/MS (high-performance liquid chromatography coupled to tandem mass spectrometry). Five perfluorinatedcarboxylic acids (C6, C8-C11) and perfluorooctane sulfonate (PFOS) were selected as model analytes. In order to achieve the best extraction efficiency, some important factors including the amount of Fe3O4@mSiO2-F17 microspheres added, adsorption time, type of elution solvent, eluting solvent volume and elution time were investigated. The ranges of the LOD were 0.02-0.05ngmL(-1) for the six PFCs. The recovery of the optimized method varies from 83.13% to 92.42% for human serum samples.Analytica Chimica Acta 09/2014; DOI:10.1016/j.aca.2014.07.032 · 4.52 Impact Factor
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ABSTRACT: Perfluoroalkyl-containing compounds have a unique 'fluorous' property that refers to the remarkably specific affinity they share. Fluorous compounds can be easily isolated from non-fluorous species on the perfluoroalkyl-functionalized stationary phases used in fluorous solid-phase extraction and fluorous liquid chromatography by means of fluorous-fluorous interactions (fluorophilicity). Recently, this unique specificity has been applied to the highly selective enrichment and analysis of different classes of biogenic and related compounds in complex samples. Because the biogenic compounds are generally not 'fluorous', they must be derivatized with appropriate perfluoroalkyl group-containing reagent in order to utilize fluorous interaction. In this review, we introduce the application of fluorous affinity techniques including derivatization methods to biogenic sample analysis.Journal of Pharmaceutical and Biomedical Analysis 05/2014; DOI:10.1016/j.jpba.2014.04.035 · 2.83 Impact Factor