1
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Chen Z, Zhong X, Tie C, Chen B, Zhang X, Li L. Development of a hydrophilic interaction liquid chromatography coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging platform for N-glycan relative quantitation using stable-isotope labeled hydrazide reagents. Anal Bioanal Chem 2017; 409:4437-4447. [PMID: 28540462 DOI: 10.1007/s00216-017-0387-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/21/2022]
Abstract
In this work, the capability of newly developed hydrophilic interaction liquid chromatography (HILIC) coupled with matrix-assisted laser desorption/ionization-mass spectrometric imaging (MALDI-MSI) platform for quantitative analysis of N-glycans has been demonstrated. As a proof-of-principle experiment, heavy and light stable-isotope labeled hydrazide reagents labeled maltodextrin ladder were used to demonstrate the feasibility of the HILIC-MALDI-MSI platform for reliable quantitative analysis of N-glycans. MALDI-MSI analysis by an Orbitrap mass spectrometer enabled high-resolution and high-sensitivity detection of N-glycans eluted from HILIC column, allowing the re-construction of LC chromatograms as well as accurate mass measurements for structural inference. MALDI-MSI analysis of the collected LC traces showed that the chromatographic resolution was preserved. The N-glycans released from human serum was used to demonstrate the utility of this novel platform in quantitative analysis of N-glycans from a complex sample. Benefiting from the minimized ion suppression provided by HILIC separation, comparison between MALDI-MS and the newly developed platform HILIC-MALDI-MSI revealed that HILIC-MALDI-MSI provided higher N-glycan coverage as well as better quantitation accuracy in the quantitative analysis of N-glycans released from human serum. Graphical abstract Reconstructed chromatograms based on HILIC-MALDI-MSI results of heavy and light labeled maltodextrin enabling quantitative glycan analysis.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Cai Tie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Xinxiang Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, WI, 53705, USA.
- School of Life Sciences, Tianjin University, No.92 Weijin Road, Nankai District, Tianjin, 300072, China.
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2
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Wang P, Giese RW. Recommendations for quantitative analysis of small molecules by matrix-assisted laser desorption ionization mass spectrometry. J Chromatogr A 2017; 1486:35-41. [PMID: 28118972 DOI: 10.1016/j.chroma.2017.01.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/21/2016] [Accepted: 01/16/2017] [Indexed: 12/15/2022]
Abstract
Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for quantitative analysis of small molecules for many years. It is usually preceded by an LC separation step when complex samples are tested. With the development several years ago of "modern MALDI" (automation, high repetition laser, high resolution peaks), the ease of use and performance of MALDI as a quantitative technique greatly increased. This review focuses on practical aspects of modern MALDI for quantitation of small molecules conducted in an ordinary way (no special reagents, devices or techniques for the spotting step of MALDI), and includes our ordinary, preferred methods The review is organized as 18 recommendations with accompanying explanations, criticisms and exceptions.
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Affiliation(s)
- Poguang Wang
- Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, Northeastern University, Boston, MA 02115, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences and Barnett Institute, Bouve College, Northeastern University, Boston, MA 02115, USA.
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3
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Wang RQ, Bao K, Croué JP, Ng SC. Hydrophilic interaction chromatography coupled matrix assisted laser desorption/ionization mass spectrometry for molecular analysis of organic compounds in medicines, tea, and coffee. Analyst 2013; 138:6737-41. [DOI: 10.1039/c3an01425h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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4
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Boccardi C, Rocchiccioli S, Cecchettini A, Mercatanti A, Citti L. An automated plasma protein fractionation design: high-throughput perspectives for proteomic analysis. BMC Res Notes 2012; 5:612. [PMID: 23116412 PMCID: PMC3517536 DOI: 10.1186/1756-0500-5-612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/26/2012] [Indexed: 01/17/2023] Open
Abstract
Background Human plasma, representing the most complete record of the individual phenotype, is an appealing sample for proteomics analysis in clinical applications. Up to today, the major obstacle in a proteomics study of plasma is the large dynamic range of protein concentration and the efforts of many researchers focused on the resolution of this important drawback. Findings In this study, proteins from pooled plasma samples were fractionated according to their chemical characteristics on a home-designed SPE automated platform. The resulting fractions were digested and further resolved by reversed-phase liquid chromatography coupled with MALDI TOF/TOF mass spectrometry. A total of 712 proteins were successfully identified until a concentration level of ng/mL. Pearson correlation coefficient was used to test reproducibility. Conclusions Our multidimensional fractionation approach reduced the analysis time (2 days are enough to process 16 plasma samples filling a 96-well plate) over the conventional gel-electrophoresis or multi-LC column based methods. The robotic processing, avoiding contaminants or lack of sample handling skill, promises highly reproducible specimen analyses (more than 85% Pearson correlation). The automated platform here presented is flexible and easily modulated changing fractioning elements or detectors.
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Affiliation(s)
- Claudia Boccardi
- Institute of Clinical Physiology-CNR, Via Moruzzi 1, 56124 Pisa, Italy
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5
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Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, Jin J, Witkowska HE. Automated Iterative MS/MS Acquisition: A Tool for Improving Efficiency of Protein Identification Using a LC–MALDI MS Workflow. Anal Chem 2011; 83:6286-93. [DOI: 10.1021/ac200911v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Haichuan Liu
- UCSF Sandler-Moore Mass Spectrometry Core Facility and Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94143, United States
| | - Lee Yang
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Ming Dong
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Steven C. Hall
- UCSF Sandler-Moore Mass Spectrometry Core Facility and Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94143, United States
| | - Susan J. Fisher
- UCSF Sandler-Moore Mass Spectrometry Core Facility and Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94143, United States
| | - Mark D. Biggin
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jian Jin
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - H. Ewa Witkowska
- UCSF Sandler-Moore Mass Spectrometry Core Facility and Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94143, United States
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6
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Ishihara T, Fukuda I, Morita A, Takinami Y, Okamoto H, Nishimura SI, Numata Y. Development of quantitative plasma N-glycoproteomics using label-free 2-D LC-MALDI MS and its applicability for biomarker discovery in hepatocellular carcinoma. J Proteomics 2011; 74:2159-68. [PMID: 21704746 DOI: 10.1016/j.jprot.2011.06.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/07/2011] [Accepted: 06/12/2011] [Indexed: 01/04/2023]
Abstract
There has been rapid progress in the development of clinical proteomic methodologies with improvements in mass spectrometric technologies and bioinformatics, leading to many new methodologies for biomarker discovery from human plasma. However, it is not easy to find new biomarkers because of the wide dynamic range of plasma proteins and the need for their quantification. Here, we report a new methodology for relative quantitative proteomic analysis combining large-scale glycoproteomics with label-free 2-D LC-MALDI MS. In this method, enrichment of glycopeptides using hydrazide resin enables focusing on plasma proteins with lower abundance corresponding to the tissue leakage region. On quantitative analysis, signal intensities by 2-D LC-MALDI MS were normalized using a peptide internal control, and the values linked to LC data were treated with DeView™ software. Our proteomic method revealed that the quantitative dynamic ranged from 10² to 10⁶ pg/mL of plasma proteins with good reproducibility, and the limit of detection was of the order of a few ng/mL of proteins in biological samples. To evaluate the applicability of our method for biomarker discovery, we performed a feasibility study using plasma samples from patients with hepatocellular carcinoma, and identified biomarker candidates, including ceruloplasmin, alpha-1 antichymotrypsin, and multimerin-1.
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Affiliation(s)
- Takeshi Ishihara
- Discovery Research Laboratories, Shionogi & Co. Ltd., Fukushima-ku, Osaka 553-0002, Japan
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7
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PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:450290. [PMID: 22084688 PMCID: PMC3200137 DOI: 10.1155/2011/450290] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/10/2011] [Accepted: 02/09/2011] [Indexed: 11/17/2022]
Abstract
We present a versatile user-friendly software tool, PolyAlign, for the alignment of multiple LC-MS signal maps with the option of manual landmark setting or automated alignment. One of the spectral images is selected as a reference map, and after manually setting the landmarks, the program warps the images using either polynomial or Hermite transformation. The software provides an option for automated landmark finding. The software includes a very fast zoom-in function synchronized between the images, which facilitate detecting correspondences between the adjacent images. Such an interactive visual process enables the analyst to decide when the alignment is satisfactory and to correct known irregularities. We demonstrate that the software provides significant improvements in the alignment of LC-MALDI data, with 10-15 landmark pairs, and it is also applicable to correcting electrospray LC-MS data. The results with practical data show substantial improvement in peak alignment compared to MZmine, which was among the best analysis packages in a recent assessment. The PolyAlign software is freely available and easily accessible as an integrated component of the popular MZmine software, and also as a simpler stand-alone Perl implementation to preview data and apply landmark directed polynomial transformation.
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8
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Toyama A, Nakagawa H, Matsuda K, Ishikawa N, Kohno N, Daigo Y, Sato TA, Nakamura Y, Ueda K. Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer. Proteome Sci 2011; 9:18. [PMID: 21473792 PMCID: PMC3090313 DOI: 10.1186/1477-5956-9-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 04/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Serum is an ideal source of biomarker discovery and proteomic profiling studies are continuously pursued on serum samples. However, serum is featured by high level of protein glycosylations that often cause ionization suppression and confound accurate quantification analysis by mass spectrometry. Here we investigated the effect of N-glycan and sialic acid removal from serum proteins on the performance of label-free quantification results. RESULTS Serum tryptic digests with or without deglycosylation treatment were analyzed by LC-MALDI MS and quantitatively compared on the Expressionist Refiner MS module. As a result, 345 out of 2,984 peaks (11.6%) showed the specific detection or the significantly improved intensities in deglycosylated serum samples (P < 0.01). We then applied this deglycosylation-based sample preparation to the identification of lung cancer biomarkers. In comparison between 10 healthy controls and 20 lung cancer patients, 40 peptides were identified to be differentially presented (P < 0.01). Their quantitative accuracies were further verified by multiple reaction monitoring. The result showed that deglycosylation was needed for the identification of some unique candidates, including previously unreported O-linked glycopeptide of complement component C9. CONCLUSIONS We demonstrated here that sample deglycosylation improves the quantitative performance of shotgun proteomics, which can be effectively applied to any samples with high glycoprotein contents.
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Affiliation(s)
- Atsuhiko Toyama
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Tsurumiku-Suehirocho1-7-22, Yokohama, Japan.
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9
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Rational development of a strategy for modifying the aggregatibility of proteins. Proc Natl Acad Sci U S A 2011; 108:4297-302. [PMID: 21368182 DOI: 10.1073/pnas.1100195108] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The conversion of peptide and proteins from their soluble state into well-organized aggregates, together with the accompanied oxidation of methionine residue, presents a significant challenge to human health, to the manufacture of protein therapeutics, and to the synthesis of proteins and glycoproteins. Despite their fundamental importance, little is known about the molecular basis of these two side reactions and their control. Here, using chemical peptide synthesis, we further confirmed the importance of the balance between hydrophobic interactions and electrostatic repulsive forces in inducing and inhibiting aggregation and methionine oxidation. Most importantly, through extending the established principle, we are able to effectively stabilize the problematic peptide fragment through the attachment of cleavable arginine tags. Future applications of our approach are expected to facilitate the synthesis and study of difficult peptides, proteins, and glycoproteins and will provide more opportunities for the optimization of protein biopharmaceuticals and for the development of cell-permeable biomolecules.
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10
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Getie-Kebtie M, Lazarev A, Eichelberger M, Alterman M. Label-free mass spectrometry-based relative quantification of proteins separated by one-dimensional gel electrophoresis. Anal Biochem 2011; 409:202-12. [DOI: 10.1016/j.ab.2010.10.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 10/15/2010] [Accepted: 10/15/2010] [Indexed: 02/04/2023]
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11
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Cecchettini A, Rocchiccioli S, Boccardi C, Citti L. Vascular smooth-muscle-cell activation: proteomics point of view. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 288:43-99. [PMID: 21482410 DOI: 10.1016/b978-0-12-386041-5.00002-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vascular smooth-muscle cells (VSMCs) are the main component of the artery medial layer. Thanks to their great plasticity, when stimulated by external inputs, VSMCs react by changing morphology and functions and activating new signaling pathways while switching others off. In this way, they are able to increase the cell proliferation, migration, and synthetic capacity significantly in response to vascular injury assuming a more dedifferentiated state. In different states of differentiation, VSMCs are characterized by various repertories of activated pathways and differentially expressed proteins. In this context, great interest is addressed to proteomics technology, in particular to differential proteomics. In recent years, many authors have investigated proteomics in order to identify the molecular factors putatively involved in VSMC phenotypic modulation, focusing on metabolic networks linking the differentially expressed proteins. Some of the identified proteins may be markers of pathology and become useful tools of diagnosis. These proteins could also represent appropriately validated targets and be useful either for prevention, if related to early events of atherosclerosis, or for treatment, if specific of the acute, mid, and late phases of the pathology. RNA-dependent gene silencing, obtained against the putative targets with high selective and specific molecular tools, might be able to reverse a pathological drift and be suitable candidates for innovative therapeutic approaches.
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12
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Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
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13
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Romanova EV, Lee JE, Kelleher NL, Sweedler JV, Gulley JM. Mass spectrometry screening reveals peptides modulated differentially in the medial prefrontal cortex of rats with disparate initial sensitivity to cocaine. AAPS JOURNAL 2010; 12:443-54. [PMID: 20490734 DOI: 10.1208/s12248-010-9204-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Accepted: 05/03/2010] [Indexed: 01/06/2023]
Abstract
To better understand why certain individuals are more vulnerable to cocaine abuse and addiction, we identify peptide markers associated with individual variation in sensitivity to the behavioral effects of cocaine. Previous studies in rats show that low, compared to high, cocaine responders are more sensitive to cocaine-induced behavioral plasticity (sensitization), exhibit enhanced conditioning to cocaine's rewarding effects, and are more motivated to self administer cocaine. In the current study, we combine matrix-assisted laser desorption/ionization mass spectrometry with multivariate statistical methods to analyze tissue extracts from rat dorsal striatum, nucleus accumbens, and medial prefrontal cortex (mPFC) to examine trends in peptide changes that coincide with behavioral phenotype. Peptide profiles of these three regions from individual animals were characterized via mass spectrometry. Resulting mass peaks that were statistically different between these groups were identified using principal component analysis. The mass peaks were then identified in pooled samples via multistage liquid chromatography mass spectrometry. A total of 74 peptides from 28 proteins were sequenced from defined brain regions. Statistically significant changes in peak intensities for seven peptides were found in the mPFC of rats given a single injection of 10 mg/kg cocaine, with low cocaine responders showing approximately 2-fold increase in peak intensities for the acetylated N terminus peptides of stathmin and Hint 1, as well as truncated ATP synthase. These results suggest that distinct peptide profiles in the mPFC are associated with individuals that exhibit reduced sensitivity to the behavioral effects of cocaine.
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Affiliation(s)
- Elena V Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, USA
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14
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Rocchiccioli S, Citti L, Boccardi C, Ucciferri N, Tedeschi L, Lande C, Trivella MG, Cecchettini A. A gel-free approach in vascular smooth muscle cell proteome: perspectives for a better insight into activation. Proteome Sci 2010; 8:15. [PMID: 20334645 PMCID: PMC2858725 DOI: 10.1186/1477-5956-8-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 03/24/2010] [Indexed: 12/31/2022] Open
Abstract
Background The use of chromatography coupled with mass spectrometry (MS) analysis is a powerful approach to identify proteins, owing to its capacity to fractionate molecules according to different chemical features. The first protein expression map of vascular smooth muscle cells (VSMC) was published in 2001 and since then other papers have been produced. The most detailed two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) map was presented by Mayr et al who identified 235 proteins, corresponding to the 154 most abundant unique proteins in mouse aortic VSMC. A chromatographic approach aimed at fractionating the VSMC proteome has never been used before. Results This paper describes a strategy for the study of the VSMC proteome. Our approach was based on pre-fractionation with ion exchange chromatography coupled with matrix assisted laser desorption-time of flight mass spectrometry analysis assisted by a liquid chromatography (LC-MALDI-TOF/TOF). Ion exchange chromatography resulted in a good strategy designed to simplify the complexity of the cellular extract and to identify a large number of proteins. Selectivity based on the ion-exchange chemical features was adequate if evaluated on the basis of protein pI. The LC-MALDI approach proved to be highly reproducible and sensitive since we were able to identify up to 815 proteins with a concentration dynamic range of 7 orders of magnitude. Conclusions In our opinion, the large number of identified proteins and the promising quantitative reproducibility made this approach a powerful method to analyze complex protein mixtures in a high throughput way and to obtain statistical data for the discovery of key factors involved in VSMC activation and to analyze a label-free differential protein expression.
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Affiliation(s)
- Silvia Rocchiccioli
- Department of Human Morphology and Applied Biology, University of Pisa, Via Roma 55, 56126 Pisa, Italy.
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15
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Rocchiccioli S, Congiu E, Boccardi C, Citti L, Callipo L, Laganà A, Capobianco E. A proteomic study of microgravity cardiac effects: feature maps of label-free LC-MALDI data for differential expression analysis. MOLECULAR BIOSYSTEMS 2010; 6:2218-29. [DOI: 10.1039/c0mb00065e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Abstract
Exploiting the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes has currently been receiving a lot of attention. In recent years, most of the effort has been put into demonstrating the possible clinical applications of the various omics fields. The cost-effectiveness analysis has been, so far, rather neglected. The cost of omics-derived applications is still very high, but future technological improvements are likely to overcome this problem. In this chapter, we will give a general background of the main omics fields and try to provide some examples of the most successful applications of omics that might be used in clinical diagnosis and in a therapeutic context.
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Affiliation(s)
- Ewa Gubb
- Bioinformatics, Parque Technológico de Bizkaia, Derio, Spain
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17
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Chi LM, Lee CW, Chang KP, Hao SP, Lee HM, Liang Y, Hsueh C, Yu CJ, Lee IN, Chang YJ, Lee SY, Yeh YM, Chang YS, Chien KY, Yu JS. Enhanced interferon signaling pathway in oral cancer revealed by quantitative proteome analysis of microdissected specimens using 16O/18O labeling and integrated two-dimensional LC-ESI-MALDI tandem MS. Mol Cell Proteomics 2009; 8:1453-74. [PMID: 19297561 PMCID: PMC2709179 DOI: 10.1074/mcp.m800460-mcp200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 03/09/2009] [Indexed: 11/06/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) remains one of the most common cancers worldwide, and the mortality rate of this disease has increased in recent years. No molecular markers are available to assist with the early detection and therapeutic evaluation of OSCC; thus, identification of differentially expressed proteins may assist with the detection of potential disease markers and shed light on the molecular mechanisms of OSCC pathogenesis. We performed a multidimensional (16)O/(18)O proteomics analysis using an integrated ESI-ion trap and MALDI-TOF/TOF MS system and a computational data analysis pipeline to identify proteins that are differentially expressed in microdissected OSCC tumor cells relative to adjacent non-tumor epithelia. We identified 1233 unique proteins in microdissected oral squamous epithelia obtained from three pairs of OSCC specimens with a false discovery rate of <3%. Among these, 977 proteins were quantified between tumor and non-tumor cells. Our data revealed 80 dysregulated proteins (53 up-regulated and 27 down-regulated) when a 2.5-fold change was used as the threshold. Immunohistochemical staining and Western blot analyses were performed to confirm the overexpression of 12 up-regulated proteins in OSCC tissues. When the biological roles of 80 differentially expressed proteins were assessed via MetaCore analysis, the interferon (IFN) signaling pathway emerged as one of the most significantly altered pathways in OSCC. As many as 20% (10 of 53) of the up-regulated proteins belonged to the IFN-stimulated gene (ISG) family, including ubiquitin cross-reactive protein (UCRP)/ISG15. Using head-and-neck cancer tissue microarrays, we determined that UCRP is overexpressed in the majority of cheek and tongue cancers and in several cases of larynx cancer. In addition, we found that IFN-beta stimulates UCRP expression in oral cancer cells and enhances their motility in vitro. Our findings shed new light on OSCC pathogenesis and provide a basis for the future development of novel biomarkers.
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MESH Headings
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/chemistry
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Chromatography, Liquid/methods
- Databases, Protein
- Gene Expression Regulation, Neoplastic
- Humans
- Immunohistochemistry
- Interferons/metabolism
- Male
- Microdissection
- Molecular Sequence Data
- Mouth Neoplasms/chemistry
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/pathology
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oxygen Isotopes/metabolism
- Proteome/analysis
- Signal Transduction/physiology
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Tandem Mass Spectrometry/methods
- Tissue Array Analysis
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Affiliation(s)
- Lang-Ming Chi
- From the ‡Molecular Medicine Research Center
- Departments of §Medical Research and Development
| | | | | | | | | | - Ying Liang
- From the ‡Molecular Medicine Research Center
| | - Chuen Hsueh
- From the ‡Molecular Medicine Research Center
- ‖Pathology, Chang Gung Memorial Hospital, Tao-Yuan 333, Taiwan
| | - Chia-Jung Yu
- From the ‡Molecular Medicine Research Center
- **Department of Biochemistry and Molecular Biology, and
| | - I-Neng Lee
- From the ‡Molecular Medicine Research Center
| | | | | | - Yuan-Ming Yeh
- ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University and
| | - Yu-Sun Chang
- From the ‡Molecular Medicine Research Center
- ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University and
| | - Kun-Yi Chien
- From the ‡Molecular Medicine Research Center
- **Department of Biochemistry and Molecular Biology, and
| | - Jau-Song Yu
- From the ‡Molecular Medicine Research Center
- **Department of Biochemistry and Molecular Biology, and
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18
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Parker KC, Walsh RJ, Salajegheh M, Amato AA, Krastins B, Sarracino DA, Greenberg SA. Characterization of Human Skeletal Muscle Biopsy Samples Using Shotgun Proteomics. J Proteome Res 2009; 8:3265-77. [DOI: 10.1021/pr800873q] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kenneth C. Parker
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
| | - Ronan J. Walsh
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
| | - Mohammad Salajegheh
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
| | - Anthony A. Amato
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
| | - Bryan Krastins
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
| | - David A. Sarracino
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
| | - Steven A. Greenberg
- Harvard Partners Center for Genetics and Genomics, Cambridge, MA, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, and Informatics Program, Children’s Hospital Boston, Harvard Medical School, Boston, MA
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19
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Rapp E, Charvát A, Beinsen A, Plessmann U, Reichl U, Seidel-Morgenstern A, Urlaub H, Abel B. Atmospheric pressure free liquid infrared MALDI mass spectrometry: toward a combined ESI/ MALDI-liquid chromatography interface. Anal Chem 2009; 81:443-52. [PMID: 19125446 DOI: 10.1021/ac801863p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new atmospheric pressure (AP)-MALDI-type interface has been developed based on a free liquid (FL) microbeam/microdroplets and a mid-infrared optical parametric oscillator (mid-IR OPO). The device is integrated into a standard on-line nanoESI interface. The generation of molecular ions in the gas phase is believed to be the result of a fast (explosive) laser-induced evaporative dispersion(not desorption) of the microbeam into statistically charged nanodroplets. Only the lowest charge states appear insignificant abundance in this type of experiment. Mass spectra of some common peptides have been acquired in positive ion mode, and the limit-of-detection of this first prototype (liquid microbeam setup) was evaluated to be 17 fmol per second. To improve the duty cycle and to reduce the sample consumption, a droplet-on-demand system was implemented (generating 100 pL droplets).With this setup, about 20 attomole of bradykinin were sufficient to achieve a signal-to-noise ratio better than five.This setup can be operated at flow rates down to 100 nL/min and represents a liquid MALDI alternative to the nanoESI. Our particular interest was the application of the developed ion source for on-line coupling of liquid chromatography with mass spectrometry. The flow rates(>100 microL/min), required for stable operation of the ion source in continuous liquid microbeam mode, matches perfectly the flow rate range of micro HPLC. Therefore, online LC/MS experiments have been realized, employing a microbore C18 reversed-phase column to separate an artificial peptide mixture and tryptic peptides of bovine serum albumin (performing a peptide mass fingerprint). In the latter case, sequence coverage of more than 90%has been achieved.
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Affiliation(s)
- Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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20
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Abstract
Liquid chromatography (LC) can be combined with matrix-assisted laser-desorption ionization (MALDI) mass-spectrometry (MS) by using automated off-line fraction collection of eluates onto a MALDI plate. Commercial tandem MS systems are available for generating product ion spectra of MALDI-produced peptide ions. The MALDI MS/MS spectra can be searched against a proteome database for protein identification. In this chapter, a protocol of sequential solubilization and digestion of membrane proteins involving methanol- and SDS-assisted trypsin digestion and microwave-assisted acid hydrolysis is presented. The process of LC eluate deposition onto a MALDI plate along with practical considerations for achieving optimal performance of eluate deposition is described. Issues related to MALDI MS and MS/MS spectral acquisition are discussed. Database searching and manual inspection of MS/MS spectra of singly charged MALDI-produced peptide ions for positive protein identification are also addressed.
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21
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Hattan SJ, Vestal ML. Novel Three-Dimensional MALDI Plate for Interfacing High-Capacity LC Separations with MALDI-TOF. Anal Chem 2008; 80:9115-23. [DOI: 10.1021/ac8017108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hattan
- Virgin Instruments Corporation, 60 Union Avenue (Suite 1-R), Sudbury, Massachusetts 01776
| | - Marvin L. Vestal
- Virgin Instruments Corporation, 60 Union Avenue (Suite 1-R), Sudbury, Massachusetts 01776
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22
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Neubert H, Bonnert TP, Rumpel K, Hunt BT, Henle ES, James IT. Label-free detection of differential protein expression by LC/MALDI mass spectrometry. J Proteome Res 2008; 7:2270-9. [PMID: 18412385 DOI: 10.1021/pr700705u] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein abundance changes during disease or experimental perturbation are increasingly analyzed by label-free LC/MS approaches. Here we demonstrate the use of LC/MALDI MS for label-free detection of protein expression differences using Escherichia coli cultures grown on arabinose, fructose or glucose as a carbon source. The advantages of MALDI, such as detection of only singly charged ions, and MALDI plate archiving to facilitate retrospective MS/MS data collection are illustrated. MALDI spectra from RP chromatography of tryptic digests of the E. coli lysates were aligned and quantitated using the Rosetta Elucidator system. Approximately 5000 peptide signals were detected in all LC/MALDI runs spanning over 3 orders of magnitude of signal intensity. The average coefficients of variation for all signals across the entire intensity range in all technical replicates were found to be <25%. Pearson correlation coefficients from 0.93 to 0.98 for pairwise comparisons illustrate high replicate reproducibility. Expression differences determined by Analysis of Variance highlighted over 500 isotope clusters ( p < 0.01), which represented candidates for targeted peptide identification using MS/MS. Biologically interpretable protein identifications that could be derived underpin the general utility of this label-free LC/MALDI strategy.
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Affiliation(s)
- Hendrik Neubert
- Pfizer Global Research and Development, Sandwich, Kent CT13 9NJ, United Kingdom.
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23
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Zhang Y, Go EP, Desaire H. Maximizing Coverage of Glycosylation Heterogeneity in MALDI-MS Analysis of Glycoproteins with Up to 27 Glycosylation Sites. Anal Chem 2008; 80:3144-58. [DOI: 10.1021/ac702081a] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ying Zhang
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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24
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Automated normal phase nano high performance liquid chromatography/matrix assisted laser desorption/ionization mass spectrometry for analysis of neutral and acidic glycosphingolipids. Anal Bioanal Chem 2008; 391:289-97. [DOI: 10.1007/s00216-008-1932-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 01/28/2008] [Accepted: 02/01/2008] [Indexed: 10/22/2022]
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25
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Kim BY, Swearingen CB, Ho JAA, Romanova EV, Bohn PW, Sweedler JV. Direct Immobilization of Fab‘ in Nanocapillaries for Manipulating Mass-Limited Samples. J Am Chem Soc 2007; 129:7620-6. [PMID: 17530757 DOI: 10.1021/ja070041w] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interfacing nanoscale elements into a microfluidic device enables a new range of fluidic manipulations. Nanocapillary array membranes (NCAMs), consisting of thin (5 microm < d < 20 microm) membranes containing arrays of nanometer diameter (10 nm < a < 500 nm) pores, are a convenient method of interfacing vertically separated microchannels in microfluidic devices that allow the external control of analyte transport between microfluidic channels. To add functionality to these nanopores beyond simple fluid transport, here we incorporate an antibody-based molecular recognition element onto the pore surface that allows selective capture, purification, and release of specific analytes from a mixture. The pores are fabricated by electroless plating of gold into the nanopores of an NCAM (Au-NCAM). An antibody is then immobilized on the Au-NCAM via gold-thiol chemistry as a thiolated fragment of antigen-binding (Fab') prepared by direct digestion of the antibody followed by reduction of the disulfide linkage on the hinge region. The successful immobilization and biological activity of the resultant Fab' through this protocol is verified on planar gold by fluorescence microscopy, scanning electron microscopy, and atomic force microscopy. Selective capture and release of human insulin is verified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The relative mass spectral peak intensities for insulin versus nonantigenic peptides increase more than 20-fold after passing through the Fab'-Au-NCAM relative to the control Au-NCAM. The affinity-tagged Au-NCAM can be incorporated into microfluidic devices to allow the concentration, capture, and characterization of analytes in complex mixtures with high specificity.
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Affiliation(s)
- Bo Young Kim
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 600 South Mathews, Urbana, Illinois 61801, USA
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26
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Smith JC, Lambert JP, Elisma F, Figeys D. Proteomics in 2005/2006: developments, applications and challenges. Anal Chem 2007; 79:4325-43. [PMID: 17477510 DOI: 10.1021/ac070741j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jeffrey C Smith
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, Canada K1H 8M5
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