Haojie Lu

Fudan University, Shanghai, Shanghai Shi, China

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Publications (85)337.68 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Analysis of oligosaccharides with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) remains challenging due to their low ionization efficiency. The sensitivity achieved by MS for oligosaccharides lags far behind that for proteins/peptides. Here, the hydrazinonicotinic acid (HYNIC) is proposed as a new matrix to realize highly sensitive and selective analysis of oligosaccharides in MALDI-MS. The detection limit of maltoheptaose provided by HYNIC is as low as 1 amol, which is five orders of magnitude lower than that provided by traditional matrix 2,5-dihydroxybenzoic acid (DHB). Interestingly, HYNIC displayed remarkable selectivity for ionization of oligosaccharides, making glycans from glycoprotein become more accessible to be detected even without pre-purification, as demonstrated by the direct detection of the oligosaccharides from human serum without pre-separation of the proteins/peptides. The HYNIC matrix also possessed the virtue of higher homogeneity of crystallization and better salt tolerance (up to 200 mM NaCl, 140 mM urea and 40 mM sulfocarbamide et al.) compared with traditional matrix DHB. Furthermore, HYNIC matrix afforded adequate fragmentation, thus providing rich information for the structure elucidation of oligosaccharide. Therefore, HYNIC as the matrix to directly analyze oligosaccharides is inherently simple and straightforward.
    The Analyst 10/2014; · 4.23 Impact Factor
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    ABSTRACT: Selective extraction of phosphopeptidome from complicated biological samples is of great importance towards the development of diagnostic and prognostic biomarkers, but still remains challenge. In this work, rattle-type mTiO2@P(NIPAM-co-MBA) composite microspheres comprising a mesoporous crystalline mTiO2 core, an intermediate hollow space and a crosslinked P(NIPAM-co-MBA) network shell were elaborately designed and fabricated via two-step reflux-precipitation polymerization followed by a hydrothermal process. Firstly, a non-crosslinked PMAA layer was directly coated onto the surface of TiO2 core without any pretreatment. Then the formed TiO2@PMAA was encapsulated with another crosslinked P(NIPAM-co-MBA) layer with the aid of the strong hydrogen bonding interaction between the two polymer layers. Finally, a hydrothermal process was adopted to convert the TiO2 core into a crystalline and mesoporous counterpart. At the same time, non-crosslinked PMAA layer was selectively removed to form rattle-type structure. The crosslinked P(NIPAM-co-MBA) shell make the rattle-type mTiO2@P(NIPAM-co-MBA) possess great size-exclusion effect against both high-molecular-weight nonphosphoproteins and high-molecular-weight phosphoproteins while the mTiO2 core was in charge of the selective enrichment of low-molecular-weight phosphopeptides. With the help of these unique properties, the rattle-type mTiO2@P(NIPAM-co-MBA) microspheres show excellent potential for one-step selective extraction of phosphopeptidome.
    RSC Advances 08/2014; · 3.71 Impact Factor
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    ABSTRACT: For the highly efficient extraction of the N-glycoproteome, a novel solid-phase extraction method based on oxime click chemistry has been developed. With the use of a newly synthesized aminooxy-functionalized magnetic nanoparticle, the oxidized glycan chains on glycopeptides readily react with the aminooxy groups through oxime click chemistry, resulting in the highly selective extraction of glycopeptides. Compared to the traditional hydrazide chemistry-based method, which takes 12-16 h of coupling time, this new method renders excellent enrichment performance within 1 h. Furthermore, the enrichment sensitivity (fmol level), selectivity (extracting glycopeptides from mixtures of nonglycopeptides at a 1:100 molar ratio), and reproducibility (CVs < 20%) are also dramatically improved. We have successfully profiled the N-glycoproteome from only 1 μL of human colorectal cancer serum using this innovative protocol, which offers a more efficient alternative N-glycoproteome extraction method.
    Analytical chemistry. 07/2014;
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    ABSTRACT: In this paper, we demonstrate a rapid and reproducible one-dimensional LC-MS/MS workflow for the fast quantitative proteomic research. We have optimized the LC-MS/MS conditions including digestion and gradient conditions, sample loading amount, and MS parameter settings. As a result, we were able to obtain as twice as many protein identifications comparing with the LC-MS/MS conditions before optimization. More than 4500 protein groups and 50000 peptides were identified in less than 8 hours without any fractionation. This one-dimensional workflow was then applied to analysis of the MLN4924 treated/untreated HUVEC cell samples with label-free quantification. In these experiments, a total of 179 proteins showed statistically significantly expression changed after the MLN4924 treatment. Functional analysis showed that these proteins are associated with cell death and survival, gene expression, cell cycle and DNA replication, recombination and repair.This article is protected by copyright. All rights reserved
    Proteomics 07/2014; · 4.43 Impact Factor
  • Minbo Liu, Haojie Lu
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    ABSTRACT: C-termini of proteins often play an important role in various biological processes, such as the transcription and translation from DNA to protein and also participating in various biological regulations. The determination of protein C-terminus is so crucial because it provides not only distinct functional annotation, but also a way to monitor the proteolysis-modified proteins. Based on the biological mass spectrometry, a series of novel methods and technologies were developed both for qualitative and quantitative analyses of protein C-terminus. These methods or technologies can be applied to accurate and effective protein C-terminus profiling, including the sequences and quantitative information of C-termini, which reveals the biological function of C-termini in life's activities and provides a better understanding of the degradation of mature proteins. Combined with our research, this review highlights the improvements in C-terminal proteomics study in the past decades, including the methodologies for recognition and identification of C-terminus, as well as the enrichment strategies for protein C-terminus.
    07/2014; 30(7):1083-93.
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    ABSTRACT: Magnetic yolk-shell MSP@ZrO2 microspheres consisting of a movable magnetic supraparticle (MSP) core and a crystalline ZrO2 shell were synthesized via two-step controlled "sol-gel" approach for the first time. Firstly, large amount of the generated hydrolyzate Zr(OH)4 was firmly fixed onto the surface of the crosslinked polymethylacrylic acid matrix via strong hydrogen bonding interaction between Zr(OH)4 and the carboxyl groups. Then a calcination process was adopted to convert the Zr(OH)4 into a continuous ZrO2 shell and simultaneously make the ZrO2 shell crystallized. At the same time, the polymer matrix could be selectively removed to form yolk-shell structure, which has better dispersability and higher adsorbing efficiency of phosphopeptides than its solid counterpart. The formation mechanism of such yolk-shell microspheres could be reasonably proved by the results of TEM, TGA, VSM, XRD and FT-IR characterizations. By taking advantage of the unique properties, the yolk-shell MSP@ZrO2 exhibited high specificity and great capability in selective enrichment of phosphopeptides, and a total of 33 unique phosphopeptides mapped to 33 different phosphoproteins had been identified from 1 mL of human saliva. This result clearly demonstrated that the yolk-shell MSP@ZrO2 has great performance in purifying and identifying the low-abundant phosphopeptides from real complex biological samples. Moreover, the synthetic method can be used to produce hybrid yolk-shell MSP@ZrO2-TiO2.
    Langmuir 05/2014; · 4.38 Impact Factor
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    ABSTRACT: Study of site-specific N-glycosylation in complex sample remains a huge analytical challenge, because protein glycosylation is structurally diverse in post translational modifications resulting in an intricacy of N-glycopeptides. Here we have developed a novel approach for high-throughput N-glycopeptide profiling, based on a network-centric algorithm for deciphering glycan fragmentation in mass-spectrometry. We performed an extensive validation and a high-throughput N-glycosylation study on serum and identified thousands of N-glycopeptide spectra with high confidence. The results revealed a similar level of glycan microheterogeneity to that of conventional glycomics approach on individual proteins, and provided the unique in-depth site-specific information that could only be studied through glycopeptide profiling.
    Journal of Proteome Research 04/2014; · 5.06 Impact Factor
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    ABSTRACT: The efficient isolation of low-abundance phosphopeptides from complicated biological samples containing a significant quantity of nonphosphopeptides and proteins is essential for phosphopeptidome research but remains a great challenge. In this article, magnetic composite microspheres comprising a magnetic colloidal nanocrystal cluster core and a mesoporous titania shell with an average pore diameter of 3.4 nm were modified by directly coating an amorphous titania shell onto the magnetite core, followed by converting the amorphous titania shell into a crystalline structure via a hydrothermal process at 80 °C. The as-prepared magnetic mesoporous titania microspheres possess a remarkable specific surface area that is as high as 603.5 m2/g, which is an appropriate pore size with a narrow size distribution and a high magnetic responsiveness. These outstanding features imply that the composite microspheres exhibit extraordinary performance in phosphopeptidome research, including high specificity toward phosphopeptides, an excellent size-exclusion effect against phosphoproteins, exceptional enrichment capacity and efficient separation from mixtures. Encouraged by the experimental results, we employed this method to investigate the phosphopeptidome of snake venom for the first time. A total of 35 phosphopeptides were identified from the snake venom from the family Viperidae, accounting for 75% of the total identified peptides. This result represents the largest dataset of the phosphopeptidome in snake venom from the family Viperidae.
    ACS Applied Materials & Interfaces 04/2014; · 5.90 Impact Factor
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    ABSTRACT: In view of the biological significance of glycosylation for human health, profiling of glycoproteome from complex biological samples is highly inclined toward the discovery of disease biomarkers and clinical diagnosis. Nevertheless, due to the existence of glycopeptides at relatively low abundances compared with non-glycosylated peptides and glycan microheterogeneity, glycopeptides need to be highly selectively enriched from complex biological samples for mass spectrometry analysis. Herein, a new type of hydrazide functionalized core-shell magnetic nanocomposite has been synthesized for highly specific enrichment of N-glycopeptides. The nanocomposites with both the magnetic core and the polymer shell hanging high density of hydrazide groups were prepared by first functionalization of the magnetic core with polymethacrylic acid by reflux precipitation polymerization to obtain the Fe3O4@poly methylacrylic acid (Fe3O4@PMAA), then modification of the surface of Fe3O4@PMAA with adipic acid dihydrazide (ADH) to obtain Fe3O4@poly methylacrylic hydrazide (Fe3O4@PMAH). The abundant hydrazide groups towards highly specific enrichment of glycopeptides and the magnetic core make it suitable for the large-scale, high-throughput and automated sample processing. In addition, the hydrophilic polymer surface can provide low non-specific adsorption of other peptides. Compared to commercially available hydrazide resin, Fe3O4@PMAH improved more than five times the signal-to-noise ratio of standard glycopeptides. Finally, this nanocomposite was applied in the profiling of N-glycoproteome from the colorectal cancer patient serum. Totally, 175 unique glycopeptides and 181 glycosylation sites corresponding to 63 unique glycoproteins were identified in three repeated experiments, with the specificities of the enriched glycopeptides and corresponding glycoproteins of 69.6% and 80.9% respectively. Because of all these attractive features, we believe that this novel hydrazide functionalized core-shell magnetic nanocomposite will shed new light on the profiling of N-glycoproteome from complex biological samples in high throughput.
    ACS Applied Materials & Interfaces 04/2014; · 5.90 Impact Factor
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    ABSTRACT: We invented a new method for highly efficient and specific enrichment of glycopeptides using two different nanomaterials synergistically. One is boronic-acid functionalized Fe3O4 nanoparticles, enriching glycopeptides through formation of cyclic boronate esters between the boronic-acid groups and the cis-diol groups on glycopeptides. The other nanomaterial is conventional poly(methyl methacrylate) nanobeads, which have strong adsorption towards non-glycopeptides. By optimizing the proportion of these two materials, extremely high sensitivity and selectivity are achieved in analyzing the standard glycopeptides/non-glycopeptides mixture solutions. Since the washing step is not necessary for these conditions, the enrichment process is simplified and the recovery efficiency of target glycopeptides reaches 90%. Finally, this approach is successfully applied to analyze human serum with the sample volume as little as 1 μL, in which 147 different N-glycosylation peptides within 66 unique glycoproteins are identified. All these performances by the synergistic enrichment are much better than employing one specific enrichment agent alone.
    Analytical Chemistry 01/2014; · 5.82 Impact Factor
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    ABSTRACT: Mitotic clonal expansion (MCE) is one of the important events taking place at the early stage during 3T3-L1 adipocyte differentiation. To investigate the mechanism underlying this process, we carried out a temporal proteomic analysis to profile the dynamic changes in MCE. Using 8-plex-iTRAQ-2DLC-MS/MS analysis, 3152 proteins were quantified during the initial 28 h of 3T3-L1 adipogenesis. Functional analysis was performed on 595 proteins with maximum or minimum quantities at 20 h of adipogenic induction that were potentially involved in MCE, which identified PI3K/AKT/mTOR as the most relevant pathway. Among the 595 proteins, PKM2 (Pyruvate kinase M2), a patterned protein identified as a potential target gene of C/EBPβ in our previous work, was selected for further investigation. Network analysis suggested positive correlations among C/EBPβ, PIN1 and PKM2, which may be related with the PI3K-AKT pathway. Knockdown of PKM2 with siRNA inhibited both MCE and adipocyte differentiation of 3T3-L1 cells. Moreover, PKM2 was down-regulated at both mRNA level and protein level upon the knockdown of C/EBPβ. And over-expressed PKM2 can partially restored MCE, although did not restore terminal adipocyte differentiation which were inhibited by siC/EBPβ. Thus, PKM2, potentially regulated by C/EBPβ, is involved in MCE during adipocyte differentiation. The dynamic proteome changes quantified here provide a promising basis for revealing molecular mechanism regulating adipogenesis.
    Journal of Proteome Research 01/2014; · 5.06 Impact Factor
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    ABSTRACT: Glycosylation is estimated to be found in over 50% of human proteins. Aberrant protein glycosylation and alteration of glycans are closely related to many diseases. More than half of the cancer biomarkers are glycosylated-proteins, and specific glycoforms of glycosylated-proteins may serve as biomarkers for either the early detection of disease or the evaluation of therapeutic efficacy for treatment of diseases. Glycoproteomics, therefore, becomes an emerging field that can make unique contributions to the discovery of biomarkers of cancers. The recent advances in mass spectrometry (MS)-based glycoproteomics, which can analyze thousands of glycosylated-proteins in a single experiment, have shown great promise for this purpose. Herein, we described the MS-based strategies that are available for glycoproteomics, and discussed the sensitivity and high throughput in both qualitative and quantitative manners. The discovery of glycosylated-proteins as biomarkers in some representative diseases by employing glycoproteomics was also summarized.
    Clinical proteomics. 01/2014; 11(1):18.
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    ABSTRACT: In this work, for the first time, hydrazide functionalized PAMAM was designed and synthesized for efficient and selective enrichment of N-linked glycopeptides from complex biological samples using FASP (filter-aided sample preparation) mode.
    Chemical Communications 12/2013; · 6.38 Impact Factor
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    ABSTRACT: Cancer genomics unveils many cancer-related mutations, including some Chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs, however, whether it could be translated to proteins is still required more evidence. Herein, we proposed a transomics strategy to profile the expression status of human Chr.20 genes (555 in Ensembl v72). The data of transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that approximately 80% of the coding genes on Chr.20 were detected with mRNA signals in three liver cancer cell lines, whereas of the proteome identified only about 45% of the Chr.20 coding genes. The high overlapping of identified genes in mRNA and RNC-mRNA (Ribosome Nascent-chain Complex-bound mRNAs, translating mRNAs), and the consistent distribution of the abundance averages of mRNA and RNC-mRNA along the Chr.20 sub-regions in three live cancer cell lines indicating that the mRNA information is efficiently transmitted from transcription to translational stage, qualitatively and quantitatively. Of the 457 genes identified in mRNAs and RNC-mRNA, 136 were found containing SNVs with 213 sites, and over 40% of these SNVs existed only in metastatic cell lines, suggesting them as the metastasis-related SNVs. Proteomics analysis showed that 16 genes with 20 SNV sites were detected with reliable MS/MS signals, and some SNVs were further validated by the MRM approach. With the integration of the omics data at the three expression phases, therefore, we are able to achieve the overall view to the gene expression of Chr.20, which is constructive in understanding of the potential trend of encoding genes in a cell line and exploration of new type of markers related with cancers.
    Journal of Proteome Research 11/2013; · 5.06 Impact Factor
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    ABSTRACT: C-termini of proteins often play an important role in various biological processes. The determination of protein C-terminus is crucial since it provides not only distinct functional annotation, but also a way to monitor the proteolysis-modified proteins. In this study, an isotopic labeling approach based on oxazolone chemistry was developed to achieve the identification and quantification of C-termini. Aminolysis reagent such as arginine selectively reacts with the α-carboxyl group at peptide C-terminus via oxazolone-like intermediate. Side chain carboxyl groups does not participate this reaction. When an isotopic mixture consisting of 50% arginine (0Arg) and 50% C6-arginine (6Arg) was introduced to react with C-terminus of protein and followed by proteolysis, C-terminal peptide could be directly recognized in the mass spectrum due to its unique isotopic paired peaks, and the sequence could be interpreted in MS2. Besides, the incorporation of an additional basic amino acid in C-terminal peptide greatly enhanced the signal intensity for C-termini detection. Moreover, the isotopic arginine labeling strategy could be applied for relative C-termini quantitation. Our method showed an excellent correlation of the measured ratios to theoretical ratios and high reproducibility within 2 order of magnitude of dynamic range. The correlation coefficients (R2) were higher than 0.99, with the coefficients of variation (CVs) ranging from 1.16% to 10.91%. Finally, the approach was used to analyze the C-termini from Thermoanaerobacter tengcongensis which was cultured under different temperature. As a result, 68 C-termini have been identified and 53 of them were quantified in total using our strategy, and 24 neo-C-terminal peptides have also been discovered.
    Analytical Chemistry 10/2013; · 5.82 Impact Factor
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    ABSTRACT: The site-specific characterization of N-glycans in glycoproteins with the potential of clinical application is important. In our previous report, the overall N-glycans of sera haptoglobin (Hp) β chain were found to be different in liver diseases. Hp β chain contains four potential sites of N-glycosylation. In this study, we investigated the potential change of N-glycans on Hp β chain in a site-specific fashion. Sera Hp β chain in healthy individuals as well as patients with hepatitis B virus (HBV), liver cirrhosis (LC) and hepatocellular carcinoma (HCC) were purified, digested and subjected to liquid chromatography-electrospray ionization-higher energy collision dissociation mass spectrometry, which allowed identification and structure determination of the glycopeptide, as well as the relative quantification of glycans present on each glycopeptide. The quantitative results revealed that the sialylation of NLFLN(207)HSEN(211)ATAK and the fucosylated structure at all glycopeptides increased significantly in LC and HCC patients compared with those in HBV patients and healthy individuals. A set of different N-glycan patterns of Hp β chain in various liver diseases has been determined. Thus, the sialylated and fucosylated glycoforms of Hp β chain might be related to early hepatocarcinogenesis and also might be useful as novel differential markers for LC and HCC patients.
    Acta Biochimica et Biophysica Sinica 10/2013; · 1.81 Impact Factor
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    ABSTRACT: Proteasome complexes play essential roles in maintaining cellular protein homeostasis, and serve fundamental roles in cardiac function under normal and pathological conditions. A functional detriment in proteasomal activities has been recognized as a major contributor to the progression of cardiovascular diseases. Therefore, approaches to restore proteolytic function within the setting of the diseased myocardium would be of great clinical significance. In this study, we discovered that the cardiac proteasomal activity could be regulated by acetylation. Histone deacetylase (HDAC) inhibitors (suberoylanilide hydroxamic acid and sodium valproate) enhanced acetylation of 20S proteasome subunits in the myocardium and led to an elevation of proteolytic capacity. This regulatory paradigm was present in both healthy and acutely ischemia/reperfusion (I/R) injured murine hearts, and HDAC inhibition in vitro restored proteolytic capacities to baseline SHAM levels in injured hearts. This mechanism of regulation was also viable in failing human myocardium. With 20S proteasomal complexes purified from murine myocardium treated with HDAC inhibitors in vivo, we confirmed that acetylation of 20S subunits directly, at least in part, presents a molecular explanation for the improvement in function. Furthermore, using high resolution LC-MS/MS, we unraveled the first cardiac 20S acetylome, which identified the acetylation of nine N-termini and seven internal lysine residues. Acetylation on four lysine residues and four N-termini on cardiac proteasomes were novel discoveries of this study. In addition, acetylation of five lysine residues was inducible by HDAC inhibition, which correlated with the enhancement of 20S proteasomal activity. Taken together, our investigation unveiled a novel mechanism of regulating proteasomal function in vivo and established a new strategy to potentially rescue compromised proteolytic function in the failing heart using HDAC inhibitors.
    Molecular &amp Cellular Proteomics 09/2013; · 7.25 Impact Factor
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    ABSTRACT: Analysis of oligosaccharides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is often limited by their low ionization efficiency and inadequate fragmentation information. Derivatizations of oligosaccharides to enhance their ionization in MS are widely used, but most of these methods require tedious cleanup steps that may cause sample losses. Here, aminopyrazine is developed as the derivatization reagent as well as the co-matrix to improve the detection of oligosaccharides by MALDI-TOF MS. The purification step is eliminated because aminopyrazine acts as the co-matrix after nonreductive amination derivatization of oligosaccharides. Under optimal conditions, nearly complete derivatization (>95%) is obtained and S/N ratios of oligosaccharide are increased by about 2-6 fold with good signal reproducibility (RSD = 7%). Improved analysis of glycans is also achieved without any prior separation from the mixture of glycans and deglycosylated tryptic digest of glycoproteins. In addition, enhancement of MS/MS fragmentation of derivatized oligosaccharides facilitates their structural elucidation. The proposed derivatization technique is successfully applied to the profiling of N-linked glycans derived from chicken ovalbumin.
    The Analyst 09/2013; · 4.23 Impact Factor
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    ABSTRACT: We describe a novel method for rapid and ultrasensitive detection of intact glycoproteins without enzymatic pretreatment which was commonly used in proteomic research. This method is based on using gold nanoparticle (AuNP) as signal tag in laser desorption/ionization mass spectrometry (LDI-MS) analysis combined with boronic acid assisted isolation strategy. Briefly speaking, target glycoproteins were firstly isolated from sample solution with boronic acid functionalized magnetic microparticles, and then the surface modified gold nanoparticles were added to covalently bind to the glycoproteins. After that, these AuNP tagged glycoproteins were eluted from magnetic microparticles and applied to LDI-MS analysis. The mass signal of AuNP rather than that of glycoprotein was detected and recorded in this strategy. Through data processing of different standard glycoproteins, we have demonstrated that the signal of AuNP could be used to quantitatively represent glycoprotein. This method allows femtomolar detection of intact glycoproteins. We believe that the successful validation of this method on three different kinds of glycoproteins suggests the potential use for tracking trace amount of target glycoproteins in real biological samples in the near future.
    Analytica chimica acta 07/2013; 788C:129-134. · 4.31 Impact Factor
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    ABSTRACT: As a branch of proteomics, peptidome has been extensively applied in biomarker discovery, early diagnosis and pharmacy. In the research of peptidome, sample pretreatment plays a vital role. Here, we review the pretreatment approaches and techniques of peptidome, mainly including ultrafiltration, organic solvent precipitation, solid phase extraction and so on. The biggest challenge of the development of peptidome is the large number of high-abundance proteins in the sample. Therefore, there is an urgent need to develop the fast, efficient, high-throughput and automated sample preparation methods and techniques.
    Se pu = Chinese journal of chromatography / Zhongguo hua xue hui 07/2013; 31(7):603-12.

Publication Stats

812 Citations
337.68 Total Impact Points

Institutions

  • 2006–2014
    • Fudan University
      • • Department of Macromolecular Science
      • • Department of Chemistry
      Shanghai, Shanghai Shi, China
  • 2008–2013
    • University of California, Los Angeles
      • • Division of Cardiology
      • • Department of Medicine
      Los Angeles, California, United States
  • 2012
    • Beijing Proteome Research Center
      Peping, Beijing, China
  • 2009
    • Shanghai Institutes for Biological Sciences
      Shanghai, Shanghai Shi, China
  • 2003–2004
    • Shanghai Research Institute of Chemical Industry
      Shanghai, Shanghai Shi, China