Peng-Yuan Yang

Fudan University, Shanghai, Shanghai Shi, China

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Publications (94)277.83 Total impact

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    ABSTRACT: Colorectal cancer (CRC) is the third most common cancer in males and the second in females worldwide with very poor prognosis. Collagen alpha-1(III) (COL3A1) gene, encoding an extracellular matrix protein, is upregulated in human cancers. Here, we revealed that COL3A1 was increased in CRC by analysis of five Oncomine gene expression datasets (n = 496). Immunohistochemistry analysis of a tissue microarray (n = 90) demonstrated that cancer epithelial but not stromal COL3A1 was significantly upregulated comparing with the normal counterparts. High COL3A1 mRNA and/or protein expression was accompanied with high stage, T stage, Dukes stage, grade and older age, as well as smoking and recurrence status. Upregulated COL3A1 predicted poor overall (p = 0.003) and disease-free (p = 0.025) survival. Increased epithelial but not stromal COL3A1 protein predicted worse outcome (p = 0.03). Older patients (age>65) with high COL3A1 had worse survival than younger (age≤65) with high COL3A1. Plasma COL3A1 was increased in CRC patients (n = 86) by 5.4 fold comparing with healthy individuals, enteritis and polyps patients. Plasma COL3A1 had an area under curve (AUC) of 0.92 and the best sensitivity/specificity of 98.8%/69.1%. While plasma CEA had a poorer prediction power (AUC = 0.791, sensitivity/selectivity = 70.2%/73.0%). Older patients (age≥60) had higher plasma COL3A1 than younger patients. The epithelial COL3A1 protein had an AUC of 0.975 and the best sensitivity/specificity of 95.2%/91.1%. Silencing of COL3A1 suppressed CRC cell proliferation in in vitro MTT assay and in in vivo Zebra fish xenograft model by downregulation of PI3K/AKT and WNT signaling. COL3A1 was a novel diagnosis and prognosis marker of CRC.
    Preview · Article · Jan 2016 · Oncotarget
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    ABSTRACT: Tandem MS (MS2) quantification using the series of N- and C-terminal fragment ion pairs generated from isobaric-labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N- and C-terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling (IVTAL) labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64% and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solution for N- and C-terminal fragment ion pairs based isobaric MS2 quantitative methods. This article is protected by copyright. All rights reserved.
    No preview · Article · Sep 2015 · Proteomics
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    ABSTRACT: Colorectal cancer (CRC) represents the third most common cancer in males and second in females worldwide. Here, we performed a quantitative 8-plex iTRAQ proteomics analysis of the secreted proteins from five colonic fibroblast cultures and three colon cancer epithelial cell lines. We identified 1114 proteins at 0% FDR, including 587 potential secreted proteins. We further recognized 116 fibroblast-enriched proteins which were significantly associated with cell movement, angiogenesis, proliferation and wound healing, and 44 epithelial cell-enriched proteins. By interrogation of Oncomine database, we found that 20 and 8 fibroblast-enriched proteins were up- and downregulated in CRC, respectively. Western blots confirmed the fibroblast-specific secretion of filamin C, COL6A3, COL4A1 and spondin-2. Upregulated mRNA and stroma expression of COL6A3 in CRC, which were revealed by Oncomine analyses and tissue-microarray-immunohistochemistry, indicated poor prognosis. COL6A3 expression was significantly associated with Dukes stage, T stage, stage, recurrence and smoking status. Circulating plasma COL6A3 in CRC patients was upregulated significantly comparing with healthy peoples. Receiver operating characteristic curve analysis revealed that COL6A3 has better predictive performance for CRC with an area under the curve of 0.885 and the best sensitivity/specificity of 92.9%/81.3%. Thus we demonstrated that COL6A3 was a potential diagnosis and prognosis marker of CRC.
    Full-text · Article · Aug 2015 · Oncotarget
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    ABSTRACT: The application of calibration transfer methods has been successful in combination with near-infrared spectroscopy or other tools for prediction of chemical composition. One of the developed methods that can provide accurate performances is the piecewise direct standardization (PDS) method, which in this paper is firstly applied to transfer from one day to another the second-order calibration model based on alternating trilinear decomposition (ATLD) method built for the interference-free resolution and determination of multi-analytes in complex systems by liquid chromatography-mass spectrometry (LC-MS) in full scan mode. This is an example of LC-MS analysis in which interferences have been found, making necessary the use of second-order calibration because of its capacity for modeling this phenomenon, which implies analytes of interest can be resolved and quantified even in the presence of overlapped peaks and unknown interferences. Once the second-order calibration model based on ATLD method was built, the calibration transfer was conducted to compensate for the signal instability of LC-MS instrument over time. This allows one to reduce the volume of the heavy works for complete recalibration which is necessary for later accurate determinations. The root-mean-square error of prediction (RMSEP) and average recovery were used to evaluate the performances of the proposed strategy. Results showed that the number of calibration samples used on the real LC-MS data was reduced by using the PDS method from 11 to 3 while producing comparable RMSEP values and recovery values that were statistically the same (F-test, 95% confidence level) to those obtained with 11 calibration samples. This methodology is in accordance with the highly recommended green analytical chemistry principles, since it can reduce the experimental efforts and cost with regard to the use of a new calibration model built in modified conditions. Copyright © 2015 Elsevier B.V. All rights reserved.
    Full-text · Article · Jun 2015 · Journal of Chromatography A
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    ABSTRACT: Colorectal cancer (CRC) is the third and second most common cancer in males and females worldwide, respectively. Spondin-2 is a conserved secreted extracellular matrix protein and a candidate cancer biomarker. Here we found that Spondin-2 mRNA was upregulated in CRC tissues using quantitative RT-PCR and data-mining of public Oncomine microarray datasets. Spondin-2 protein was increased in CRC tissues, as revealed by immunohistochemistry analyses of two tissue microarrays containing 180 cases. Spondin-2 gene expression was significantly associated with CRC stage, T stage, M stage and Dukes stage, while its protein was associated with age and M stage. Kaplan-Meier analysis revealed that the upregulated Spondin-2 mRNA and protein predicted poor prognosis of CRC patients. Univariate and multivariate Cox regression analyses indicated that grade, recurrence, N stage and high Spondin-2 were independent predictors of overall survival of CRC patients. ELISA revealed that plasma Spondin-2 was upregulated in CRC and dropped after surgery. Receiver operating characteristic curve analysis demonstrated that plasma Spondin-2 has superior predictive performance for CRC with an area under the curve of 0.959 and the best sensitivity/specificity of 100%/90%. Furthermore, ectopic expression of Spondin-2 enhanced colon cancer cell proliferation. Spondin-2 could be an independent diagnostic and prognostic biomarker of colon cancer.
    Full-text · Article · Apr 2015 · Oncotarget
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    ABSTRACT: The tumor cell proliferation, migration and invasion were influenced by the interaction between the cancer cells and their microenvironment. In current study, we established two pairs of the primary fibroblast cultures from colorectal adenocarcinoma tissues and the normal counterparts and identified 227 proteins in the colonic fibroblast secretomes; half of these proteins were novel. The mass spectrometry data and analyzed results presented here provide novel insights into the molecular characteristics and modulatory role of colon cancer associated fibroblasts. The data is related to “Identification of colonic fibroblast secretomes reveals secretory factors regulating colon cancer cell proliferation” by Chen et al. [1].
    Full-text · Article · Dec 2014
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    ABSTRACT: Gastric cancer (GC) is the fourth and fifth most common cancer in men and women, respectively. We identified 2,750 proteins at false discovery rates of 1.3% (protein) and 0.03% (spectrum) by comparing the proteomic profiles of three GC and a normal gastric cell lines. Nine proteins were significantly dysregulated in all three GC cell lines, including filamin C, a muscle-specific filamin and a large actin-cross-linking protein. Downregulation of filamin C in GC cell lines and tissues were verified using quantitative PCR and immunohistochemistry. Data-mining using public microarray datasets shown that filamin C was significantly reduced in many human primary and metastasis cancers. Transient expression or silencing of filamin C affected the proliferation and colony formation of cancer cells. Silencing of endogenous filamin C enhanced cancer cell migration and invasion, whereas ectopic expression of filamin C had opposing effects. Silencing of filamin C increased the expression of matrix metallopeptidase 2 and improved the metastasis of prostate cancer in a zebrafish model. High filamin C associated with better prognosis of prostate cancer, leukemia and breast cancer patients. These findings establish a functional role of filamin C in human cancers and these data will be valuable for further study of its mechanisms.
    Full-text · Article · Nov 2014 · Oncotarget
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    ABSTRACT: β-blockers are the first-line therapeutic agents for treating cardiovascular diseases and also a class of prohibited substances in athletic competitions. In this work, a smart strategy that combines three-way liquid chromatography-mass spectrometry (LC-MS) data with second-order calibration method based on alternating trilinear decomposition (ATLD) algorithm was developed for simultaneous determination of ten β-blockers in human urine and plasma samples. This flexible strategy proved to be a useful tool to solve the problems of overlapped peaks and uncalibrated interferences encountered in quantitative LC-MS, and made the multi-targeted interference-free qualitative and quantitative analysis of β-blockers in complex matrices possible. The limits of detection were in the range of 2.0×10(-5)-6.2×10(-3)μgmL(-1), and the average recoveries were between 90 and 110% with standard deviations and average relative prediction errors less than 10%, indicating that the strategy could provide satisfactory prediction results for ten β-blockers in human urine and plasma samples only using liquid chromatography hyphenated single-quadrupole mass spectrometer in full scan mode. To further confirm the feasibility and reliability of the proposed method, the same batch samples were analyzed by multiple reaction monitoring (MRM) method. T-test demonstrated that there are no significant differences between the prediction results of the two methods. Considering the advantages of fast, low-cost, high sensitivity, and no need of complicated chromatographic and tandem mass spectrometric conditions optimization, the proposed strategy is expected to be extended as an attractive alternative method to quantify analyte(s) of interest in complex systems such as cells, biological fluids, food, environment, pharmaceuticals and other complex samples.
    Full-text · Article · Oct 2014 · Analytica Chimica Acta
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    ABSTRACT: Unlabelled: Stromal microenvironment influences tumor cell proliferation and migration. Fibroblasts represent the most abundant stromal constituents. Here, we established two pairs of normal fibroblast (NF) and cancer-associated fibroblast (CAF) cultures from colorectal adenocarcinoma tissues and the normal counterparts. The NFs and CAFs were stained positive for typical fibroblast markers and inhibited colon cancer (CC) cell proliferation in in vitro cocultures and in xenograft mouse models. The fibroblast conditioned media were analyzed using LC-MS and 227 proteins were identified at a false discovery rate of 1.3%, including 131 putative secretory and 20 plasma membrane proteins. These proteins were enriched for functional categories of extracellular matrix, adhesion, cell motion, inflammatory response, redox homeostasis and peptidase inhibitor. Secreted protein acidic and rich in cysteine, transgelin, follistatin-related protein 1 (FSTL1) and decorin was abundant in the fibroblast secretome as confirmed by Western blot. Silencing of FSTL1 and transgelin in colonic fibroblast cell line CCD-18Co induced an accelerated proliferation of CC cells in cocultures. Exogenous FSTL1 attenuates CC cell proliferation in a negative fashion. FSTL1 was upregulated in CC patient plasma and cancerous tissues but had no implication in prognosis. Our results provided novel insights into the molecular signatures and modulatory role of CC associated fibroblasts. Biological significance: In this study, a label-free LC-MS was performed to analyze the secretomes of two paired primary fibroblasts, which were isolated from fresh surgical specimen of colorectal adenocarcinoma and adjacent normal colonic tissues and exhibited negative modulatory activity for colon cancer cell growth in in vitro cocultures and in vivo xenograph mouse models. Follistatin-related protein 1 was further revealed to be one of the stroma-derived factors of potential suppression role for colon cancer cell proliferation. Our results provide novel insights into the molecular signatures and the modulatory role of colon cancer associated fibroblasts, and establish a valuable resource for the development of therapeutic agents or novel clinic biomarker.
    Full-text · Article · Aug 2014 · Journal of Proteomics
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    Li-Qi Xie · Ai-Ying Nie · Shu-Jun Yang · Chao Zhao · Lei Zhang · Peng-Yuan Yang · Hao-Jie Lu
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    ABSTRACT: Taking advantage of reliable metabolic labeling and accurate isobaric MS2 quantification, we developed a global in vivo terminal amino acid labeling (G-IVTAL) strategy by combining metabolic labeling and isotopic dimethyl labeling for quantifying tryptic peptides. With G-IVTAL, the scale of qualitative and quantitative data can be increased twofold compared with in vivo termini amino acid labeling (IVTAL) in which Lys-N and Arg-C are used for digestion. As a result, up to 81.78% of the identified proteins have been confidently quantified in G-IVTAL-labeled HepG2 cells. Dialyzed serum has been used in most SILAC studies to ensure complete labeling. However, dialysis requires the removal of low molecular weight hormones, cytokines, and cellular growth factors, which are essential for the cell growth of certain cell lines. To address the influence of dialyzed serum in HepG2 growth, the G-IVTAL strategy was applied to quantify the expression differences between dialyzed serum- and normal serum-cultured HepG2 cells. Finally, we discovered 111 differentially expressed proteins, which could be used as references to improve the reliability of the SILAC quantification. Among these, by using western blotting, the differential expressions of MTDH, BCAP31, and GPC3 were confirmed as being influenced by dialyzed serum. The experimental results demonstrate that the G-IVTAL strategy is a powerful tool to achieve accurate and reliable protein quantification.
    Preview · Article · Jul 2014 · The Analyst
  • Hong LIU · Jun YAO · Peng-Yuan YANG · Hui-Zhi FAN
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    ABSTRACT: Due to the complexity of the biological sample, it is important to develop an effective pre-separation method for the liquid chromatography-mass spectrometer (LC-MS) analysis of biological samples. In this experiment, enzymatic hydrolysate of rat liver protein was pre-separated by peptide immobilized pH gradient isoelectric focusing (IPG-IEF) method, and the pre-separated components were further separated by reversed physe liquid chromatography (RPLC) and then identified by LTQ-Orbitrap MS. A total of 2039 kinds of proteins were identified, including 18 kinds of acetylated proteins, 4 kinds of proteins which were never reported before. Next, bioinformatic analysis was carried out for these proteins. The results showed that peptide IPG-IEF coupled with LC-MS/MS is an effective technique for proteomics analysis and this method is suitable for large-scale protein identification.
    No preview · Article · Feb 2014 · Chinese Journal of Analytical Chemistry
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    ABSTRACT: The chromatin remodeling gene AT-rich interactive domain-containing protein 1A (ARID1A) encodes the protein BAF250a, a subunit of human SWI/SNF-related complexes. Recent studies have identified ARID1A as a tumor suppressor. Here, we show that ARID1A expression is reduced in gastric cancer (GC) tissues, which are significantly associated with local lymph node metastasis, tumor infiltration and poor patient prognosis. ARID1A silencing enforces the migration and invasion of GC cells, whereas ectopic expression of ARID1A inhibits migration. The adhesive protein E-cadherin is remarkably downregulated in response to ARID1A silencing, but it is upregulated by ARID1A overexpression. E-cadherin overexpression significantly inhibits GC cell migration and invasion, whereas CDH1 (coded E-cadherin) silencing promotes migration. Restored expression of CDH1 in ARID1A-silenced cell lines restores the inhibition of cell migration. Luciferase reporter assays and chromatin immunoprecipitation indicate that the ARID1A-associated SWI/SNF complex binds to the CDH1 promoter and modulates CDH1 transcription. ARID1A knockdown induces evident morphological changes of GC cells with increased expression of mesenchymal markers, indicating an epithelial–mesenchymal transition. ARID1A silencing does not alter the level of β-catenin but induces a subcellular redistribution of β-catenin from the plasma membrane to the cytoplasm and nucleus. Immunohistochemical studies demonstrate that reduced expression of E-cadherin is associated with local lymph node metastasis, tumor infiltration and poor clinical prognosis. ARID1A and E-cadherin expression show a strong correlation in 75.4% of the analyzed GC tissues. They are synergistically downregulated in 23.5% of analyzed GC tissues. In conclusion, ARID1A targets E-cadherin during the modulation of GC cell migration and invasion.
    Full-text · Article · Nov 2013 · Carcinogenesis
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    ABSTRACT: Histological differentiation is a major pathological parameter associated with poor prognosis in patients with pancreatic adenocarcinoma (PAC) and the molecular signature underlying PAC differentiation may involve key proteins potentially affecting the malignant characters of PAC. We aimed to identify the proteins which could be implicated in PAC prognosis. We used isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry to compare protein expression in PAC tissues with different degree of histological differentiation. A total of 1623 proteins were repeatedly identified by performing the iTRAQ-based experiments twice. Of these, 15 proteins were differentially expressed according to our defined criteria. Myoferlin(MYOF) was selected to validate the proteomic results by western blotting. Immunohistochemistry in a further 154 PAC cases revealed that myoferlin significantly correlated with the degree of histological differentiation (P=0.004), and univariate and multivariate analyses indicated that MYOF is an independent prognostic factor for survival (hazard ratio, 1.540; 95% confidence interval, 1.061-2.234; P=0.023) of patients with PAC after curative surgery. RNA interference-mediated knockdown of MYOF alleviated malignant phenotypes of both primary and metastatic PAC cell lines in vitro and in vivo. Thus, ITRAQ-based quantitative proteomics revealed the prognostic value of MYOF in PAC. our results provide the possibility of novel strategies for pancreatic adenocarcinoma management.
    No preview · Article · Jul 2013 · Journal of proteomics
  • Lei Nie · Guo-Bin Xu · Xiao-Yan Wang · Yun Liu · Peng-Yuan Yang
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    ABSTRACT: A freezing technique protocol was proposed for coupling microchip electrophoresis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The microfluidic flow was frozen immediately after electrophoresis on microfluidic chip and the separated analyte molecules were kept in their zone pattern in the electrophoresis. Then, the frozen-chip was lyophilized and sent into TOF-MS instrument as a MALDI target, and the analyte molecules in the microfluidic channels were subjected to analysis by mass spectrometry. This approach could eliminate sample cross-contamination, providing a new interface for microchip electrophoresis and MALDI-MS.
    No preview · Article · Jun 2013 · Chinese Chemical Letters
  • Jiang Qing · Zhengxu Huang · Yan Zhang · Hui Zhu · Guobin Tan · Wei Gao · Peng-Yuan Yang
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    ABSTRACT: A miniaturised reflectron time-of-flight mass spectrometer combined with an electron ionisation ion source has been developed for the analysis of gases. An entirely new helium ion removal pulsing technique in this mass spectrometer is used to achieve an improved performance for the first time. The helium carrier gas, which enters into the source along with the gaseous sample, is simultaneously ionised and then orthogonally introduced into the time-of-fight mass analyser. Once the relatively light helium ions in the ion packet become extremely close to the reflectron plate (B-plate for short in this article), a modulated pulse is instantaneously applied on the B-plate and a negative reflectron voltage is set to the B-plate and lasts for a very short period, during which all the helium ions are directly bumped into the B-plate and subsequently removed. The helium ion removal pulsing technique can efficiently avoid saturation of the micro-channel plate caused by too many helium ions. A compact and durable instrument is designed, which has a mass resolving resolution greater than 400 FWHM for online gas analysis. The technology may also be further developed to remove other ions for TOF mass spectrometry.
    No preview · Article · May 2013 · The Analyst
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    ABSTRACT: Unlabelled: Cystic hydatid disease is an important zoonosis caused by Echinococcus granulosus infection. The expression profiles of its parasitic life stages and host-Echinococcus interactions remain to be elucidated. Here, we identified 157 adult and 1588 protoscolex proteins (1610 in all), including 1290 novel identifications. Paramyosins and an antigen B (AgB) were the dominant adult proteins. Dog proteins (30) identified in adults indicated diminished local inflammation caused by adult infection. The protoscolex expresses proteins that have been reported to be antigens in other parasites, such as 6-phosphofructokinase and calcineurin B. Pathway analyses suggested that E. granulosus uses both aerobic and anaerobic carbohydrate metabolisms to generate ATP. E. granulosus expresses proteins involved in synthesis and metabolism of lipids or steroids. At least 339 of 390 sheep proteins identified in protoscolex were novel identifications not seen in previous analyses. IgGs and lambda light chains were the most abundant antibody species. Sheep proteins were enriched for detoxification pathways, implying that host detoxification effects play a central role during host-parasite interactions. Our study provides valuable data on E. granulosus expression characteristics, allowing novel insights into the molecular mechanisms involved in host-parasite interactions. Biological significance: In this study, the Echinococcus granulosus adult worm proteome was analyzed for the first time. The protein identification of E. granulosus protoscoleces was extended dramatically. We also identified the most abundant host proteins co-purified with Echinococcus. The results provide useful information pertaining to the molecular mechanisms behind host-Echinococcus interaction and Echinococcus biology. This data also increases the potential for identifying vaccine candidates and new therapeutic targets, and may aid in the development of protein probes for selective and sensitive diagnosis of echinococcosis infection. In addition, the data collected here represents a valuable proteomic resource for subsequent genome annotation.
    Full-text · Article · Apr 2013 · Journal of proteomics
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    ABSTRACT: Unlabelled: Studies have revealed that pancreatic cancer (PC) may lead to diabetes mellitus (DM). We aimed to identify the proteins implicated in the development of PC-associated DM in PC tissues with DM. We used isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry to compare protein expression in PC tissues with DM with that in PC tissues without DM and in adjacent nontumor tissues with or without DM. A total of 80 surgically resected fresh tissues from 40 PC patients were included to identify differential protein expression. Western blotting and immunohistochemistry were then applied to evaluate the differential expression of selected proteins. A total of 1611 proteins were repeatedly identified and quantified by performing the iTRAQ-based experiments twice. Of these, 23 proteins were differentially expressed according to our defined criteria (12 upregulated and 11 downregulated). The S100 calcium binding protein A9 and aldehyde dehydrogenase 2 family were selected to validate the proteomic results by western blotting and immunohistochemistry. The identification of key proteins implicated in the development of PC-associated DM could serve as a foundation to better understand and further explore the etiology and pathogenesis of PC-associated DM. Biological significance: The identification of key proteins implicated in the development of PC-associated DM could serve as a foundation to better understand and further explore the etiology and pathogenesis of PC-associated DM.
    No preview · Article · Apr 2013 · Journal of proteomics
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    Jun Zhang · Wenhai Wang · Fengying Yang · Xinwen Zhou · Hong Jin · Peng-yuan Yang
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    ABSTRACT: The human hepatoma 3B cell line was chosen as an experimental model for in vitro test of drug screening. The drugs included chlorophyllin and its derivatives such as fluo-chlorophyllin, sodium copper chlorophyllin, and sodium iron chlorophyllin. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) method was used in this study to obtain the primary screening results. The results showed that sodium iron chlorophyllin had the best LC(50) value. Proteomic analysis was then performed for further investigation of the effect of sodium iron chlorophyllin addition to the Hep 3B cell line. The proteins identified from a total protein extract of Hep 3B before and after the drug addition were compared by two-dimensional-gel-electrophoresis. Then 32 three-fold differentially expressed proteins were successfully identified by MALDI-TOF-TOF-MS. There are 29 unique proteins among those identified proteins. These proteins include proliferating cell nuclear antigen (PCNA), T-complex protein, heterogeneous nuclear protein, nucleophosmin, heat shock protein A5 (HspA5) and peroxiredoxin. HspA5 is one of the proteins which are involved in protecting cancer cells against stress-induced apoptosis in cultured cells, protecting them against apoptosis through various mechanisms. Peroxiredoxin has anti-oxidant function and is related to cell proliferation, and signal transduction. It can protect the oxidation of other proteins. Peroxiredoxin has a close relationship with cancer and can eventually become a disease biomarker. This might help to develop a novel treatment method for carcinoma cancer.
    Preview · Article · Aug 2012 · The Analyst
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    ABSTRACT: Electron transfer dissociation (ETD) is a useful and complementary activation method for peptide fragmentation in mass spectrometry. However, ETD spectra typically receive a relatively low score in the identifications of 2+ ions. To overcome this challenge, we, for the first time, systematically interrogated the benefits of combining ion charge enhancing methods (dimethylation, guanidination, m-nitrobenzyl alcohol (m-NBA) or Lys-C digestion) and differential search algorithms (Mascot, Sequest, OMSSA, pFind and X!Tandem). A simple sample (BSA) and a complex sample (AMJ2 cell lysate) were selected in benchmark tests. Clearly distinct outcomes were observed through different experimental protocol. In the analysis of AMJ2 cell lines, X!Tandem and pFind revealed 92.65% of identified spectra; m-NBA adduction led to a 5-10% increase in average charge state and the most significant increase in the number of successful identifications, and Lys-C treatment generated peptides carrying mostly triple charges. Based on the complementary identification results, we suggest that a combination of m-NBA and Lys-C strategies accompanied by X!Tandem and pFind can greatly improve ETD identification.
    No preview · Article · Jul 2012 · Molecular BioSystems
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    ABSTRACT: Quantification by series of b, y fragment ion pairs generated from isobaric-labeled peptides in MS2 spectra has recently been considered an accurate strategy in quantitative proteomics. Here we developed a novel MS2 quantification approach named quantitation by isobaric terminal labeling (QITL) by coupling (18)O labeling with dimethylation. Trypsin-digested peptides were labeled with two (16)O or (18)O atoms at their C-termini in H(2)(16)O or H(2)(18)O. After blocking all ε-amino groups of lysines through guanidination, the N-termini of the peptides were accordingly labeled with formaldehyde-d(2) or formaldehyde. These indistinguishable, isobaric-labeled peptides in MS1 spectra produce b, y fragment ion pairs in the whole mass range of MS2 spectra that can be used for quantification. In this study, the feasibility of QITL was first demonstrated using standard proteins. An accurate and reproducible quantification over a wide dynamic range was achieved. Then, complex rat liver samples were used to verify the applicability of QITL for large-scale quantitative analysis. Finally, QITL was applied to profile the quantitative proteome of hepatocellular carcinoma (HCC) and adjacent non-tumor liver tissues. Given its simplicity, low-cost, and accuracy, QITL can be widely applied in biological samples (cell lines, tissues, and body fluids, etc.) for quantitative proteomic research.
    No preview · Article · Jul 2012 · Journal of proteomics

Publication Stats

2k Citations
277.83 Total Impact Points

Institutions

  • 2004-2015
    • Fudan University
      • • Department of Chemistry
      • • Institutes of Biomedical Sciences
      Shanghai, Shanghai Shi, China
  • 2002-2009
    • Second Military Medical University, Shanghai
      • International Cooperation Laboratory on Signal Transduction
      Shanghai, Shanghai Shi, China
  • 2007
    • Chinese National Human Genome Center at Shanghai
      Shanghai, Shanghai Shi, China
  • 2006
    • Chinese Academy of Sciences
      Peping, Beijing, China