Songyun Xu

Stanford Medicine, Stanford, California, United States

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Publications (21)74.7 Total impact

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    ABSTRACT: We have designed and fabricated a polydimethylsiloxane (PDMS) microfluidic device for coupling capillary electrophoresis (CE) and matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). The coupling is advantageous in biological research because CE has the power of separating analytes in a sample based on mobility difference and MALDI-MS provides accurate and sensitive mass analysis of the analytes. The goal is realized by fractionating the separated analytes inside the microfluidic device and pushing the analyte fractions into open reservoirs. Each analyte fraction is then mixed with a matrix solution and deposited on a MALDI target for MALDI-MS. Therefore, a two-step analysis of analytes in the form of CE-MALDI-MS is achieved by using the microfluidic device.
    Journal of the Association for Laboratory Automation 10/2009; 14(5):252-261. · 1.46 Impact Factor
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    ABSTRACT: Alpha-zirconium phosphate nanoplatelets (alpha-ZrPN) were studied as a binding agent for phosphopeptides. Nanoplatelets of alpha-zirconium phosphate were incubated overnight with zirconium oxychloride, followed by centrifugation, and washed twice with water followed by an aqueous solution of 80% acetonitrile to form the binding agent. Alpha-ZrPN were able specifically to capture phosphoserine-containing peptides from a tryptic digest of a complex peptide mixture in which its abundance was only 0.05%. Alpha-ZrPN also bound peptides containing phosphothreonine and phosphotyrosine. The limit of detection for phosphopeptides is approximately 2 fmol, based on using matrix-assisted laser desorption/ionization mass spectrometry. Alpha-ZrPN were applied for the analysis of tryptic digests of mouse liver and leukemia cell phosphoproteomes and succeeded in identifying 158 phosphopeptides (209 phosphorylation sites) from 101 phosphoproteins in mouse liver lysate and 78 phosphopeptides (104 phosphorylation sites) from 59 phosphoproteins in leukemia cell extract. For these two tryptic digests, the alpha-ZrPN approach is able to capture more phosphopeptides than that obtained from TiO2 particles or from Fe(3+)-IMAC beads, but each method is able to bind some phosphopeptides that the others do not.
    Analytical Chemistry 07/2008; 80(14):5542-9. · 5.82 Impact Factor
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    ABSTRACT: This unit contains procedures for analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry with 3,4-diaminobenzophenone (DABP) as a matrix. This new matrix has demonstrated advantages in the analysis of oligonucleotides. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation, and fewer alkali-metal ion adducts compared with results obtained using conventional matrices. Minimal fragmentation and fewer alkali-metal ion adducts were seen even at low oligonucleotide concentrations. It was also found that samples prepared with DABP are highly homogenous, therefore reducing the need to find "sweet spots" in MALDI. Finally, excellent shot-to-shot reproducibility, resolution, and signal-to-noise ratio are observed using the DABP matrix.
    Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 01/2008; Chapter 10:Unit 10.12.
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    Analytical Chemistry - ANAL CHEM. 01/2008; 80(14):5542-5549.
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    ABSTRACT: Large-scale characterization of phosphoproteins requires highly specific methods for the purification of phosphopeptides because of the low abundance of phosphoproteins and substoichiometry of phosphorylation. A phosphopeptide enrichment method using ZrO2 nanoparticles is presented. The high specificity of this approach was demonstrated by the isolation of phosphopeptides from the digests of model phosphoproteins. The strong affinity of ZrO2 nanoparticles to phosphopeptides enables the specific enrichment of phosphopeptides from a complex peptide mixture in which the abundance of phosphopeptides is two orders of magnitude lower than that of nonphosphopeptides. Superior selectivity of ZrO2 nanoparticles for the enrichment of phosphorylated peptides than that of conventional immobilized metal affinity chromatography was observed. Femtomole phosphopeptides from digestion products could be enriched by ZrO2 nanoparticles and can be well detected by MALDI mass spectrometric analysis. ZrO2 nanoparticles were further applied to selectively isolate phosphopeptides from the tryptic digestion of mouse liver lysate for phosphoproteome analysis by nanoliter LC MS/MS (nano-LC-MS/MS) and MS/MS/MS. A total of 248 defining phosphorylation sites and 140 phosphorylated peptides were identified by manual validation using a series of rigid criteria.
    Electrophoresis 06/2007; 28(13):2201 - 2215. · 3.26 Impact Factor
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    ABSTRACT: Human plasma contains a complex matrix of proteolytically derived peptides (plasma peptidome) that may provide a correlate of biological events occurring in the entire organism. Analyzing these peptides from a small amount of serum/ plasma is difficult due to the complexity of the sample and the low levels of these peptides. Here, we describe a novel peptidome analysis approach using multiwalled carbon nanotubes (MWCNTs) as an alternative adsorbent to capture endogenous peptides from human plasma. Harvested peptides were analyzed by using liquid chromatography-mass spectrometry as a means of detecting and assessing the adsorbed molecules. The improved sensitivity and resolution obtained by using liquid chromatography-mass spectrometry allowed detection of 2521 peptide features (m/z 300-1800 range) in about 50 microL of plasma. 374 unique peptides were identified with high confidence by two-dimensional liquid chromatography system coupled to a nano-spray ionization linear ion trap-mass spectrometer. High recovery of BSA digest peptides enriched with MWCNTs, in both standard buffer and high abundance protein solution, was observed. Comparative studies showed that MWCNTs were superior to C18 and C8 for the capture of the smaller peptides. This approach could hold promise of routine plasma peptidome analysis.
    Journal of Separation Science 05/2007; 30(6):930-43. · 2.59 Impact Factor
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    ABSTRACT: A new approach for the preparation of a biochip on porous silicon and the application of the biochip for detection of small molecule-protein interactions with desorption/ionization on porous silicon (DIOS) was demonstrated. The galvanostatically etched porous silicon substrates were chemically modified firstly to yield carboxylic acid terminated surfaces, and then the protein was covalently attached to the surface through amide bonding. By applying a solution of candidate chemicals to the surface and a subsequent wash step, the masses of captured compounds could be analyzed by DIOS. DIOS has advantages of being a direct detection tool compared to the classic fluorescence or chemiluminescence methods, because the process of labeling molecules employed in the fluorescence or chemiluminescence methods can sometimes alert the properties of the labeled molecule. The recognition between proteins and their binding partners is efficient and selective. A good tolerance to disturbance and high enrichment factor of the biochip to the analytes was observed. As an on-chip-based approach, the demonstrated method has a potential to perform in a high-throughput format.
    Rapid Communications in Mass Spectrometry 02/2007; 21(7):1277-81. · 2.51 Impact Factor
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    ABSTRACT: Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is widely used in a variety of fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range for obtaining molecular weights and for structural characterization of macromolecules. In this article we summarize recent developments in matrix additives, new matrices, and sample-pretreatment methods using off-probe or on-probe techniques or nanomaterials for MALDI-TOF-MS analysis of biological samples.
    Analytical and Bioanalytical Chemistry 02/2007; 387(1):193-204. · 3.66 Impact Factor
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    ABSTRACT: In this study, a gel free chemiproteomic method based on chromatography was developed and applied for the biological fingerprinting analysis of complex biological system. p-Aminobenzamidine (ABA), an inhibitor of trypsin-like serine proteases, was immobilized for characterizing their interacting proteins in human plasma. By the proteomic analysis method, 214 proteins were identified with obvious affinity to the immobilized ABA. By searching the sequences of above proteins with consensus patterns of the two active sites, seven proteins belong to trypsin-like serine protease group were found. Based on the Gene Ontology annotation, the identified trypsin-like serine proteases have the function of catalytic activity and calcium ion binding, and are mainly involved in the biological process of blood coagulation. Eight more other proteins related to calcium ion binding and blood coagulation were found. Nearly all of these proteins cannot be identified by directly analyzing the plasma sample demonstrating the chemiproteomics a useful approach to characterize interacting proteins in the low abundance range.
    Journal of Chromatography A 12/2006; 1134(1-2):134-42. · 4.61 Impact Factor
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    ABSTRACT: A matrix assisted laser desorption/ionization time-of-flight mass spectrometry platform for quantitatively monitoring enzyme activity and screening enzyme inhibitors has been demonstrated. The described method employs a new matrix of oxidized carbon nanotubes. Compared with the traditional fluorescence approach, this label-free method has the advantage of directly identifying the substrates and products in enzymatic reactions. Moreover, the method could be conveniently carried out with any commercial mass spectrometer without modification. We quantitatively monitored the acetylcholinesterase activity and screened acetylcholinesterase inhibitors with a detection rate of about 3.3 s per sample.
    Journal of the American Society for Mass Spectrometry 12/2006; 17(11):1616-9. · 3.59 Impact Factor
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    ABSTRACT: Phosphorylation is one of the most important post-translational modifications of proteins, which modulates a wide range of biological functions and activity of proteins. The analysis of phosphopeptides is still one of the most challenging tasks in proteomics research by mass spectrometry. In this study, a novel phosphopeptide enrichment approach based on the strong interaction of zirconium phosphonate (ZrP) modified surface with phosphopeptides has been developed. ZrP modified porous silicon (ZrP-pSi) wafer was prepared to specifically capture the phosphopeptides from complex peptide mixtures, and then the captured phosphopeptides were analyzed by MALDI-TOF MS by directly placing the wafer on a MALDI target. The phosphopeptide enrichment and MALDI analysis were both performed on the ZrP-pSi wafer which significantly reduced the sample loss and simplified the analytical procedures. The prepared ZrP-pSi wafer has been successfully applied for the enrichment of phosphopeptides from the tryptic digest of standard phosphoproteins beta-casein and alpha-casein. The excellent selectivity of this approach was demonstrated by analyzing phosphopeptides in the digest mixture of beta-casein and bovine serum albumin with molar ratio of 1:100. High detection sensitivity has been achieved for the analysis of the phosphopeptides from tryptic digestion of 2 fmol beta-casein on the ZrP-pSi surface.
    Journal of Proteome Research 10/2006; 5(9):2431-7. · 5.06 Impact Factor
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    ABSTRACT: High concentrations of urea and guanidine hydrochloride are commonly used for the denaturation of protein, which was digested by enzymatic proteolysis for the identification by MS analysis. The presence of these contaminants seriously suppresses the ion signal of analytes in MALDI-TOF MS analysis. Herein, a novel MALDI matrix, 3, 4-diaminobenzophenone (DABP), has been found with high tolerance for these contaminants in MALDI MS analysis. The ion signal of analyte insulin can be detected in the presence of 2 M guanidine hydrochloride and 1.5 M urea using DABP as matrix. The tryptic digest of BSA (400 fmol) in 1 M guanidine hydrochloride or 1 M urea was successfully analyzed without any pretreatment prior to MS analysis. Furthermore, it has been found that this matrix can also effectively suppress the cation ion adduction of the peptides in the presence of high concentrations of metal ions in sample solution.
    Analytical Chemistry 05/2006; 78(8):2593-9. · 5.82 Impact Factor
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    ABSTRACT: Iminodiacetic acid (IDA)-1,2-epoxy-9-decene has been synthesized and covalently linked to the surface of porous silicon wafer through a photochemical reaction. The negatively charged carboxylic acid groups on the porous silicon wafer are capable of binding oppositely charged species from sample solutions through electrostatic interactions. This allows the removal of contaminants prior to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) by simply washing the porous silicon surface. The carboxylic acid end groups on porous silicon can be used to selectively bind and concentrate target species in sample solutions. Furthermore, Fe(3+)-IDA-derivatized porous silicon was prepared to specifically and effectively concentrate phosphopeptides from the tryptic digests of phosphoproteins, followed by MALDI-MS analysis.
    Rapid Communications in Mass Spectrometry 02/2006; 20(11):1769-75. · 2.51 Impact Factor
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    ABSTRACT: A new matrix of 3,4-diaminobenzophenone (DABP) was demonstrated to be advantageous in the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. With DABP as a matrix, intact oligonucleotide ions can be readily produced with lower laser powers, resulting in better detection limits, less fragmentation and fewer alkali metal ion adducts compared with the results obtained with conventional matrices. Importantly, minimal fragmentation and fewer alkali metal ion adducts were seen even at low concentrations of oligonucleotides. It was also found that samples prepared with DABP are highly homogenous and therefore reducing the need for finding 'sweet' spots in MALDI. In addition, excellent shot-to-shot reproducibility, resolution and signal-to-noise ratio were seen with DABP as the matrix.
    Nucleic Acids Research 02/2006; 34(13):e94. · 8.81 Impact Factor
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    ABSTRACT: The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for environmental analysis has been mainlyfocused on qualitative analysis of high-mass molecules, such as toxins, humic acid, and microorganisms. Herein,we describe a novel MALDI-TOF-MS method with a matrix of oxidized carbon nanotubes for analysis of low-mass compounds in environmental samples. A number of chemicals in the environment were qualitatively analyzed by the present method, and it was found that most of them, especiallythe highly polar chemicals, were measurable with high sensitivity. With the intrinsic ability to measure high-mass chemicals, this method can compensate for the current shortage of methods for environmental analysis for the measurement of highly polar or high-mass chemicals. For sample analysis, arsenic speciation in Chinese traditional medicines was qualified and diphenylolpropane in water samples was quantified. With the relatively high tolerance of the method to interfering molecules, a simple pretreatment or even no pretreatment could be employed before MS detection. Furthermore, this method can be employed in a high-throughput format.
    Environmental Science and Technology 12/2005; 39(21):8442-7. · 5.48 Impact Factor
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    ABSTRACT: Oxidized carbon nanotubes are tested as a matrix for analysis of small molecules by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). Compared with nonoxidized carbon nanotubes, oxidized carbon nanotubes facilitate sample preparation because of their higher solubility in water. The matrix layer of oxidized carbon nanotubes is much more homogeneous and compact than that of nonoxidized carbon nanotubes. The efficiency of desorption/ionization for analytes and the reproducibility of peak intensities within and between sample spots are greatly enhanced on the surface of oxidized carbon nanotubes. The advantage of the oxidized carbon nanotubes in comparison with alpha-cyano-4-hydroxycinnamic acid (CCA) and carbon nanotubes is demonstrated by MALDI-TOF-MS analysis of an amino acid mixture. The matrix is successfully used for analysis of synthetic hydroxypropyl beta-cyclodextrin, suggesting a great potential for monitoring reactions and for product quality control. Reliable quantitative analysis of jatrorrhizine and palmatine with a wide linear range (1-100 ng/mL) and good reproducibility of relative peak areas (RSD less than 10%) is achieved using this matrix. Concentrations of jatrorrhizine (8.65 mg/mL) and palmatine (10.4 mg/mL) in an extract of Coptis chinensis Franch are determined simultaneously using the matrix and a standard addition method.
    Journal of the American Society for Mass Spectrometry 07/2005; 16(6):883-92. · 3.59 Impact Factor
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    ABSTRACT: A method with carbon nanotubes functioning both as the adsorbent of solid-phase extraction (SPE) and the matrix for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) to analyze small molecules in solution has been developed. In this method, 10 microL suspensions of carbon nanotubes in 50% (vol/vol) methanol were added to the sample solution to extract analytes onto surface of carbon nanotubes because of their dramatic hydrophobicity. Carbon nanotubes in solution are deposited onto the bottom of tube with centrifugation. After removing the supernatant fluid, carbon nanotubes are suspended again with dispersant and pipetted directly onto the sample target of the MALDI-MS to perform a mass spectrometric analysis. It was demonstrated by analysis of a variety of small molecules that the resolution of peaks and the efficiency of desorption/ionization on the carbon nanotubes are better than those on the activated carbon. It is found that with the addition of glycerol and sucrose to the dispersant, the intensity, the ratio of signal to noise (S/N), and the resolution of peaks for analytes by mass spectrometry increased greatly. Compared with the previously reported method by depositing sample solution onto thin layer of carbon nanotubes, it is observed that the detection limit for analytes can be enhanced about 10 to 100 times due to solid-phase extraction of analytes in solution by carbon nanotubes. An acceptable result of simultaneously quantitative analysis of three analytes in solution has been achieved. The application in determining drugs spiked into urine has also been realized.
    Journal of the American Society for Mass Spectrometry 03/2005; 16(2):263-70. · 3.59 Impact Factor
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    ABSTRACT: The interactions between small molecules and biomacromolecules constitute one of the most important parts of interconnected biological networks. To understand the recognition mechanisms of these interactions is of vital importance for characterizing the expression and the function of related biomacromolecules and further discovering drug candidates for the pharmaceutical industry and biomarkers for clinical diagnosis. Here, we summarize the general methodology used in these studies, mainly including chromatographic, electromigration and mass spectrometric methods. We present the latest applications of these methods for elucidating simple binding of plasma protein, enzyme, receptor and DNA/RNA with small molecules. We also present recognition studies based on multi-component systems (e.g., phage display, oligonucleotides, chemiproteomics and traditional Chinese medicines), which should be more challenging in both analytical tools and methodology and the function of biological systems.
    TrAC Trends in Analytical Chemistry. 01/2005;
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    ABSTRACT: Desorption/ionization on silicon mass spectrometry (DIOS-MS) is a matrix-free technique that allows for the direct desorption/ionization of low-molecular-weight compounds with little or no fragmentation of analytes. This technique has a relatively high tolerance for contaminants commonly found in biological samples. DIOS-MS has been applied to determine the activity of immobilized enzymes on the porous silicon surface. Enzyme activities were also monitored with the addition of a competitive inhibitor in the substrate solution. It is demonstrated that this method can be applied to the screening of enzyme inhibitors. Furthermore, a method for peptide mapping analysis by in situ digestion of proteins on the porous silicon surface modified by trypsin, combined with matrix-assisted laser desorption/ionization-time of flight-MS has been developed.
    Electrophoresis 12/2004; 25(21-22):3669-76. · 3.26 Impact Factor
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    ABSTRACT: Peptide mass mapping analysis, utilizing a regenerable enzyme microreactor with metal-ion chelated adsorption of enzyme, combined with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was developed. Different procedures from the conventional approaches were adopted to immobilize the chelator onto the silica supports, that is, the metal chelating agent of iminodiacetic acid (IDA) was reacted with glycidoxypropyltrimethoxysilane (GLYMO) before its immobilization onto the inner wall of the fused-silica capillary pretreated with NH(4)HF(2). The metal ion of copper and subsequently enzyme was specifically adsorbed onto the surface to form the immobilized enzyme capillary microreactor, which was combined with MALDI-TOF-MS to apply for the mass mapping analysis of nL amounts of protein samples. The results revealed that the peptide mapping could routinely be generated from 0.5 pmol protein sample in 15 min at 50 degrees C, even 20 fmol cytochrome c could be well digested and detected.
    Electrophoresis 12/2003; 24(21):3633-9. · 3.26 Impact Factor

Publication Stats

524 Citations
74.70 Total Impact Points

Institutions

  • 2009
    • Stanford Medicine
      • Department of Pediatrics
      Stanford, California, United States
  • 2008
    • Dalian Institute of Chemical Physics
      Lü-ta-shih, Liaoning, China
    • Stanford University
      • Department of Pediatrics
      Stanford, CA, United States
  • 2003–2007
    • Northeast Institute of Geography and Agroecology
      • Laboratory of Analytical Chemistry for Life Science
      Beijing, Beijing Shi, China
  • 2003–2006
    • Chinese Academy of Sciences
      • Dalian Institute of Chemical Physics
      Peping, Beijing, China