1
|
Hussaarts L, Kaisar MMM, Guler AT, Dalebout H, Everts B, Deelder AM, Palmblad M, Yazdanbakhsh M. Human Dendritic Cells with Th2-Polarizing Capacity: Analysis Using Label-Free Quantitative Proteomics. Int Arch Allergy Immunol 2017; 174:170-182. [PMID: 29130972 DOI: 10.1159/000479512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Dendritic cells (DCs) are the sentinels of the immune system. Upon recognition of a pathogen, they mature and migrate to draining lymph nodes to prime and polarize T cell responses. Although it is known that helminths and helminth-derived molecules condition DCs to polarize T helper (Th) cells towards Th2, the underlying mechanisms remain incompletely understood. OBJECTIVES The aim of this study was to conduct a proteome analysis of helminth antigen-stimulated DCs in order to gain more insight into the cellular processes associated with their ability to polarize immune responses. METHODS We analyzed the maturation and polarization of monocyte-derived DCs from 9 donors at 2 different time points after stimulation with different Th1- and Th2-polarizing pathogen-derived molecules. The samples were measured using liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry for relative quantitation. RESULTS Lipopolysaccharide-induced maturation promoted the expression of proteins related to metabolic, cellular, and immune system processes. Th1-polarizing DCs, conditioned by IFN-γ during maturation, displayed accelerated maturation by differentially expressing cytoskeletal proteins and proteins involved in immune regulation. The stimulation of DCs with soluble egg antigens and omega-1 derived from Schistosoma mansoni, which are both Th2-inducing stimuli, increased 60S acidic ribosomal protein P2, and vesicle amine transferase 1 while decreasing the expression of proteins related to antigen processing and presentation. CONCLUSION Our data indicate that not only proteins involved in the interaction between T cells and DCs at the level of the immunological synapse, but also those related to cellular metabolism and stress, may promote Th2 polarization.
Collapse
Affiliation(s)
- Leonie Hussaarts
- Department of Parasitology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
2
|
van der Plas-Duivesteijn SJ, Wulff T, Klychnikov O, Ohana D, Dalebout H, van Veelen PA, de Keijzer J, Nessen MA, van der Burgt YEM, Deelder AM, Palmblad M. Differentiating samples and experimental protocols by direct comparison of tandem mass spectra. Rapid Commun Mass Spectrom 2016; 30:731-738. [PMID: 26864526 DOI: 10.1002/rcm.7494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Peptide tandem mass spectra can be analyzed by a number of means. They can be compared against predicted spectra of peptides derived from genome sequences, compared against previously acquired and identified spectra, or - sometimes - sequenced de novo. We recently introduced another method which compares spectra between liquid chromatography/tandem mass spectrometry (LC/MS/MS) datasets to determine the shared spectral content, and demonstrated how this can be applied in a molecular phylogenetic study using sera from human and non-human primates. We will here explore if such a method have other, serendipitous uses. METHODS We used the existing compareMS2 algorithm without modification on a diverse set of experiments. RESULTS First we conducted a small phylogenetic study, using (mammalian) bone samples to study old material, and human pathogens aiming to distinguish clinically important strains. Although not as straightforward as primate sera analysis, the method shows significant promise for all these applications. We also used the algorithm to compare 24 different protocols for extraction of proteins from muscle tissue. The results provided useful information in comparing protocols. Finally, we applied compareMS2 aiming for quality control of two traceable protein reference standards (troponin) used in clinical chemistry assays, by analysing the effect of storage conditions. CONCLUSIONS The results illustrate a broad applicability of the metric based on shared tandem mass spectra between LC/MS/MS datasets for analysing protein digests in different types of experiments. There is no reason to assume that our instance of this method is optimal in any of these situations, as it makes limited or no use of accurate mass and chromatographic retention time. We propose that with further improvement and refinement, this type of analysis can be applied as a simple but informative first step in many pipelines for bottom-up tandem mass spectrometry data analysis in proteomics and other fields, comparing or analysing large numbers of samples or datasets.
Collapse
Affiliation(s)
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Oleg Klychnikov
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dana Ohana
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen de Keijzer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry, Leiden University Medical Center, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
3
|
Heemskerk AAM, Deelder AM, Mayboroda OA. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. Mass Spectrom Rev 2016; 35:259-271. [PMID: 24852088 DOI: 10.1002/mas.21432] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.
Collapse
Affiliation(s)
- Anthonius A M Heemskerk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| |
Collapse
|
4
|
Nicolardi S, Bogdanov B, Deelder AM, Palmblad M, van der Burgt YEM. Developments in FTICR-MS and Its Potential for Body Fluid Signatures. Int J Mol Sci 2015; 16:27133-44. [PMID: 26580595 PMCID: PMC4661870 DOI: 10.3390/ijms161126012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 01/01/2023] Open
Abstract
Fourier transform mass spectrometry (FTMS) is the method of choice for measurements that require ultra-high resolution. The establishment of Fourier transform ion cyclotron resonance (FTICR) MS, the availability of biomolecular ionization techniques and the introduction of the Orbitrap™ mass spectrometer have widened the number of FTMS-applications enormously. One recent example involves clinical proteomics using FTICR-MS to discover and validate protein biomarker signatures in body fluids such as serum or plasma. These biological samples are highly complex in terms of the type and number of components, their concentration range, and the structural identity of each species, and thus require extensive sample cleanup and chromatographic separation procedures. Clearly, such an elaborate and multi-step sample preparation process hampers high-throughput analysis of large clinical cohorts. A final MS read-out at ultra-high resolution enables the analysis of a more complex sample and can thus simplify upfront fractionations. To this end, FTICR-MS offers superior ultra-high resolving power with accurate and precise mass-to-charge ratio (m/z) measurement of a high number of peptides and small proteins (up to 20 kDa) at isotopic resolution over a wide mass range, and furthermore includes a wide variety of fragmentation strategies to characterize protein sequence and structure, including post-translational modifications (PTMs). In our laboratory, we have successfully applied FTICR “next-generation” peptide profiles with the purpose of cancer disease classifications. Here we will review a number of developments and innovations in FTICR-MS that have resulted in robust and routine procedures aiming for ultra-high resolution signatures of clinical samples, exemplified with state-of-the-art examples for serum and saliva.
Collapse
Affiliation(s)
- Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Bogdan Bogdanov
- Perkin Elmer, San Jose Technology Center, San Jose, CA 95134, USA.
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden, The Netherlands.
| |
Collapse
|
5
|
Holst S, Deuss AJM, van Pelt GW, van Vliet SJ, Garcia-Vallejo JJ, Koeleman CAM, Deelder AM, Mesker WE, Tollenaar RA, Rombouts Y, Wuhrer M. N-glycosylation Profiling of Colorectal Cancer Cell Lines Reveals Association of Fucosylation with Differentiation and Caudal Type Homebox 1 (CDX1)/Villin mRNA Expression. Mol Cell Proteomics 2015; 15:124-40. [PMID: 26537799 PMCID: PMC4762531 DOI: 10.1074/mcp.m115.051235] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 01/05/2023] Open
Abstract
Various cancers such as colorectal cancer (CRC) are associated with alterations in protein glycosylation. CRC cell lines are frequently used to study these (glyco)biological changes and their mechanisms. However, differences between CRC cell lines with regard to their glycosylation have hitherto been largely neglected. Here, we comprehensively characterized the N-glycan profiles of 25 different CRC cell lines, derived from primary tumors and metastatic sites, in order to investigate their potential as glycobiological tumor model systems and to reveal glycans associated with cell line phenotypes. We applied an optimized, high-throughput membrane-based enzymatic glycan release for small sample amounts. Released glycans were derivatized to stabilize and differentiate between α2,3- and α2,6-linked N-acetylneuraminic acids, followed by N-glycosylation analysis by MALDI-TOF(/TOF)-MS. Our results showed pronounced differences between the N-glycosylation patterns of CRC cell lines. CRC cell line profiles differed from tissue-derived N-glycan profiles with regard to their high-mannose N-glycan content but showed a large overlap for complex type N-glycans, supporting their use as a glycobiological cancer model system. Importantly, we could show that the high-mannose N-glycans did not only occur as intracellular precursors but were also present at the cell surface. The obtained CRC cell line N-glycan features were not clearly correlated with mRNA expression levels of glycosyltransferases, demonstrating the usefulness of performing the structural analysis of glycans. Finally, correlation of CRC cell line glycosylation features with cancer cell markers and phenotypes revealed an association between highly fucosylated glycans and CDX1 and/or villin mRNA expression that both correlate with cell differentiation. Together, our findings provide new insights into CRC-associated glycan changes and setting the basis for more in-depth experiments on glycan function and regulation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yoann Rombouts
- From the ‡Center for Proteomics and Metabolomics, ¶Department of RheumatologyLeiden University Medical Center, Leiden, The Netherlands; ‡‡Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - Manfred Wuhrer
- From the ‡Center for Proteomics and Metabolomics, ‖Department of Molecular Cell Biology and Immunology and **Division of BioAnalytical Chemistry, VU University Medical Center, Amsterdam, The Netherlands;
| |
Collapse
|
6
|
Smit CH, van Diepen A, Nguyen DL, Wuhrer M, Hoffmann KF, Deelder AM, Hokke CH. Glycomic Analysis of Life Stages of the Human Parasite Schistosoma mansoni Reveals Developmental Expression Profiles of Functional and Antigenic Glycan Motifs. Mol Cell Proteomics 2015; 14:1750-69. [PMID: 25883177 PMCID: PMC4587318 DOI: 10.1074/mcp.m115.048280] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 11/30/2022] Open
Abstract
Glycans present on glycoproteins and glycolipids of the major human parasite Schistosoma mansoni induce innate as well as adaptive immune responses in the host. To be able to study the molecular characteristics of schistosome infections it is therefore required to determine the expression profiles of glycans and antigenic glycan-motifs during a range of critical stages of the complex schistosome lifecycle. We performed a longitudinal profiling study covering schistosome glycosylation throughout worm- and egg-development using a mass spectrometry-based glycomics approach. Our study revealed that during worm development N-glycans with Galβ1–4(Fucα1–3)GlcNAc (LeX) and core-xylose motifs were rapidly lost after cercariae to schistosomula transformation, whereas GalNAcβ1–4GlcNAc (LDN)-motifs gradually became abundant and predominated in adult worms. LeX-motifs were present on glycolipids up to 2 weeks of schistosomula development, whereas glycolipids with mono- and multifucosylated LDN-motifs remained present up to the adult worm stage. In contrast, expression of complex O-glycans diminished to undetectable levels within days after transformation. During egg development, a rich diversity of N-glycans with fucosylated motifs was expressed, but with α3-core fucose and a high degree of multifucosylated antennae only in mature eggs and miracidia. N-glycan antennae were exclusively LDN-based in miracidia. O-glycans in the mature eggs were also diverse and contained LeX- and multifucosylated LDN, but none of these were associated with miracidia in which we detected only the Galβ1–3(Galβ1–6)GalNAc core glycan. Immature eggs also exhibited short O-glycan core structures only, suggesting that complex fucosylated O-glycans of schistosome eggs are derived primarily from glycoproteins produced by the subshell envelope in the developed egg. Lipid glycans with multifucosylated GlcNAc repeats were present throughout egg development, but with the longer highly fucosylated stretches enriched in mature eggs and miracidia. This global analysis of the developing schistosome's glycome provides new insights into how stage-specifically expressed glycans may contribute to different aspects of schistosome-host interactions.
Collapse
Affiliation(s)
- Cornelis H Smit
- From the ‡Department of Parasitology, Center of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Angela van Diepen
- From the ‡Department of Parasitology, Center of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - D Linh Nguyen
- From the ‡Department of Parasitology, Center of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- §Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Karl F Hoffmann
- ¶Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais Campus, Aberystwyth SY23 3FG, United Kingdom
| | - André M Deelder
- §Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Cornelis H Hokke
- From the ‡Department of Parasitology, Center of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
| |
Collapse
|
7
|
Wuhrer M, Stavenhagen K, Koeleman CAM, Selman MHJ, Harper L, Jacobs BC, Savage COS, Jefferis R, Deelder AM, Morgan M. Skewed Fc Glycosylation Profiles of Anti-proteinase 3 Immunoglobulin G1 Autoantibodies from Granulomatosis with Polyangiitis Patients Show Low Levels of Bisection, Galactosylation, and Sialylation. J Proteome Res 2015; 14:1657-65. [DOI: 10.1021/pr500780a] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Division
of BioAnalytical Chemistry, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department
of Molecular Cell Biology and Immunology, VU University Medical Center, 1081 BT Amsterdam, The Netherlands
| | - Kathrin Stavenhagen
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Division
of BioAnalytical Chemistry, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Carolien A. M. Koeleman
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Maurice H. J. Selman
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Lorraine Harper
- School
of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, U.K
| | - Bart C. Jacobs
- Department
of Immunology and Department of Neurology, Erasmus MC, University Medical Center Rotterdam, 3015 CE Rotterdam, The Netherlands
| | - Caroline O. S. Savage
- School
of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, U.K
| | - Roy Jefferis
- School
of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, U.K
| | - André M. Deelder
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Matthew Morgan
- School
of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, U.K
| |
Collapse
|
8
|
van den Broek I, Nouta J, Razavi M, Yip R, Bladergroen MR, Romijn FPHTM, Smit NPM, Drews O, Paape R, Suckau D, Deelder AM, van der Burgt YEM, Pearson TW, Anderson NL, Cobbaert CM. Quantification of serum apolipoproteins A-I and B-100 in clinical samples using an automated SISCAPA-MALDI-TOF-MS workflow. Methods 2015; 81:74-85. [PMID: 25766926 DOI: 10.1016/j.ymeth.2015.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 01/09/2023] Open
Abstract
A fully automated workflow was developed and validated for simultaneous quantification of the cardiovascular disease risk markers apolipoproteins A-I (apoA-I) and B-100 (apoB-100) in clinical sera. By coupling of stable-isotope standards and capture by anti-peptide antibodies (SISCAPA) for enrichment of proteotypic peptides from serum digests to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS detection, the standardized platform enabled rapid, liquid chromatography-free quantification at a relatively high throughput of 96 samples in 12h. The average imprecision in normo- and triglyceridemic serum pools was 3.8% for apoA-I and 4.2% for apoB-100 (4 replicates over 5 days). If stored properly, the MALDI target containing enriched apoA-1 and apoB-100 peptides could be re-analyzed without any effect on bias or imprecision for at least 7 days after initial analysis. Validation of the workflow revealed excellent linearity for daily calibration with external, serum-based calibrators (R(2) of 0.984 for apoA-I and 0.976 for apoB-100 as average over five days), and absence of matrix effects or interference from triglycerides, protein content, hemolysates, or bilirubins. Quantification of apoA-I in 93 normo- and hypertriglyceridemic clinical sera showed good agreement with immunoturbidimetric analysis (slope = 1.01, R(2) = 0.95, mean bias = 4.0%). Measurement of apoB-100 in the same clinical sera using both methods, however, revealed several outliers in SISCAPA-MALDI-TOF-MS measurements, possibly as a result of the lower MALDI-TOF-MS signal intensity (slope = 1.09, R(2) = 0.91, mean bias = 2.0%). The combination of analytical performance, rapid cycle time and automation potential validate the SISCAPA-MALDI-TOF-MS platform as a valuable approach for standardized and high-throughput quantification of apoA-I and apoB-100 in large sample cohorts.
Collapse
Affiliation(s)
- Irene van den Broek
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands.
| | - Jan Nouta
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Morteza Razavi
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - Richard Yip
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - Marco R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Oliver Drews
- Bruker Daltonics GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Rainer Paape
- Bruker Daltonics GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Detlev Suckau
- Bruker Daltonics GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Terry W Pearson
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - N Leigh Anderson
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| |
Collapse
|
9
|
Nicolardi S, Switzar L, Deelder AM, Palmblad M, van der Burgt YE. Top-Down MALDI-In-Source Decay-FTICR Mass Spectrometry of Isotopically Resolved Proteins. Anal Chem 2015; 87:3429-37. [DOI: 10.1021/ac504708y] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Simone Nicolardi
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Linda Switzar
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - André M. Deelder
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Yuri E.M. van der Burgt
- Center for Proteomics and
Metabolomics, Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
| |
Collapse
|
10
|
Rombouts Y, Willemze A, van Beers JJBC, Shi J, Kerkman PF, van Toorn L, Janssen GMC, Zaldumbide A, Hoeben RC, Pruijn GJM, Deelder AM, Wolbink G, Rispens T, van Veelen PA, Huizinga TWJ, Wuhrer M, Trouw LA, Scherer HU, Toes REM. Extensive glycosylation of ACPA-IgG variable domains modulates binding to citrullinated antigens in rheumatoid arthritis. Ann Rheum Dis 2015; 75:578-85. [PMID: 25587188 DOI: 10.1136/annrheumdis-2014-206598] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/16/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To understand the molecular features distinguishing anti-citrullinated protein antibodies (ACPA) from 'conventional' antibodies in rheumatoid arthritis (RA). METHODS Serum of ACPA-positive RA patients was fractionated by size exclusion chromatography and analysed for the presence of ACPA-IgG by ELISA. ACPA-IgG and non-citrulline-specific IgG were affinity purified from serum, plasma and/or synovial fluid and analysed by gel electrophoresis. Electrophoresis bands were excised, enzymatically digested and analysed by mass spectrometry. Binding affinity to citrullinated antigens was measured by ELISA and imaging surface plasmon resonance using recombinant monoclonal ACPA with molecular modifications. RESULTS In all donor samples studied (n=24), ACPA-IgG exhibited a 10-20 kDa higher molecular weight compared with non-autoreactive IgG. This feature also distinguished ACPA-IgG from antibodies against recall antigens or other disease-specific autoantibodies. Structural analysis revealed that a high frequency of N-glycans in the (hyper)variable domains of ACPA is responsible for this observation. In line with their localisation, these N-glycans were found to modulate binding avidity of ACPA to citrullinated antigens. CONCLUSIONS The vast majority of ACPA-IgG harbour N-glycans in their variable domains. As N-linked glycosylation requires glycosylation consensus sites in the protein sequence and as these are lacking in the 'germline-counterparts' of identified variable domains, our data indicate that the N-glycosylation sites in ACPA variable domains have been introduced by somatic hypermutation. This finding also suggests that ACPA-hyperglycosylation confers a selective advantage to ACPA-producing B cells. This unique and completely novel feature of the citrulline-specific immune response in RA elucidates our understanding of the underlying B cell response.
Collapse
Affiliation(s)
- Yoann Rombouts
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Annemiek Willemze
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joyce J B C van Beers
- Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jing Shi
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Priscilla F Kerkman
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Linda van Toorn
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Arnaud Zaldumbide
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Rob C Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ger J M Pruijn
- Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Gertjan Wolbink
- Sanquin Research and Landsteiner Laboratory, Academic Medical Center, Amsterdam, the Netherlands Jan van Breemen Research Institute Reade, Amsterdam, the Netherlands
| | - Theo Rispens
- Sanquin Research and Landsteiner Laboratory, Academic Medical Center, Amsterdam, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Leendert A Trouw
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans U Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
11
|
Demirkan A, Henneman P, Verhoeven A, Dharuri H, Amin N, van Klinken JB, Karssen LC, de Vries B, Meissner A, Göraler S, van den Maagdenberg AMJM, Deelder AM, C ’t Hoen PA, van Duijn CM, van Dijk KW. Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. PLoS Genet 2015; 11:e1004835. [PMID: 25569235 PMCID: PMC4287344 DOI: 10.1371/journal.pgen.1004835] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/16/2014] [Indexed: 12/20/2022] Open
Abstract
Metabolite quantitative traits carry great promise for epidemiological studies, and their genetic background has been addressed using Genome-Wide Association Studies (GWAS). Thus far, the role of less common variants has not been exhaustively studied. Here, we set out a GWAS for metabolite quantitative traits in serum, followed by exome sequence analysis to zoom in on putative causal variants in the associated genes. 1H Nuclear Magnetic Resonance (1H-NMR) spectroscopy experiments yielded successful quantification of 42 unique metabolites in 2,482 individuals from The Erasmus Rucphen Family (ERF) study. Heritability of metabolites were estimated by SOLAR. GWAS was performed by linear mixed models, using HapMap imputations. Based on physical vicinity and pathway analyses, candidate genes were screened for coding region variation using exome sequence data. Heritability estimates for metabolites ranged between 10% and 52%. GWAS replicated three known loci in the metabolome wide significance: CPS1 with glycine (P-value = 1.27×10−32), PRODH with proline (P-value = 1.11×10−19), SLC16A9 with carnitine level (P-value = 4.81×10−14) and uncovered a novel association between DMGDH and dimethyl-glycine (P-value = 1.65×10−19) level. In addition, we found three novel, suggestively significant loci: TNP1 with pyruvate (P-value = 1.26×10−8), KCNJ16 with 3-hydroxybutyrate (P-value = 1.65×10−8) and 2p12 locus with valine (P-value = 3.49×10−8). Exome sequence analysis identified potentially causal coding and regulatory variants located in the genes CPS1, KCNJ2 and PRODH, and revealed allelic heterogeneity for CPS1 and PRODH. Combined GWAS and exome analyses of metabolites detected by high-resolution 1H-NMR is a robust approach to uncover metabolite quantitative trait loci (mQTL), and the likely causative variants in these loci. It is anticipated that insight in the genetics of intermediate phenotypes will provide additional insight into the genetics of complex traits. Human metabolic individuality is under strict control of genetic and environmental factors. In our study, we aimed to find the genetic determinants of circulating molecules in sera of large set of individuals representing the general population. First, we performed a hypothesis-free genome wide screen in this population to identify genetic regions of interest. Our study confirmed four known gene metabolite connections, but also pointed to four novel ones. Genome-wide screens enriched for common intergenic variants may miss causal genetic variations directly changing the protein sequence. To investigate this further, we zoomed into regions of interest and tested whether the association signals obtained in the first stage were direct, or whether they represent causal variations, which were not captured in the initial panel. These subsequent tests showed that protein coding and regulatory variations are involved in metabolite levels. For two genomic regions we also found that genes harbour more than one causal variant influencing metabolite levels independent of each other. We also observed strong connection between markers of cardio-metabolic health and metabolites. Taken together, our novel loci are of interest for further research to investigate the causal relation to for instance type 2 diabetes and cardiovascular disease.
Collapse
Affiliation(s)
- Ayşe Demirkan
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter Henneman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Harish Dharuri
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jan Bert van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lennart C. Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Boukje de Vries
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Axel Meissner
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sibel Göraler
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Arn M. J. M. van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - André M. Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A. C ’t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
- * E-mail:
| |
Collapse
|
12
|
Kaprio T, Satomaa T, Heiskanen A, Hokke CH, Deelder AM, Mustonen H, Hagström J, Carpen O, Saarinen J, Haglund C. N-glycomic profiling as a tool to separate rectal adenomas from carcinomas. Mol Cell Proteomics 2014; 14:277-88. [PMID: 25452313 PMCID: PMC4350025 DOI: 10.1074/mcp.m114.041632] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All human cells are covered by glycans, the carbohydrate units of glycoproteins, glycolipids, and proteoglycans. Most glycans are localized to cell surfaces and participate in events essential for cell viability and function. Glycosylation evolves during carcinogenesis, and therefore carcinoma-related glycan structures are potential cancer biomarkers. Colorectal cancer is one of the world's three most common cancers, and its incidence is rising. Novel biomarkers are essential to identify patients for targeted and individualized therapy. We compared the N-glycan profiles of five rectal adenomas and 18 rectal carcinomas of different stages by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. Paraffin-embedded tumor samples were deparaffinized, and glycans were enzymatically released and purified. We found differences in glycosylation between adenomas and carcinomas: monoantennary, sialylated, pauci-mannose, and small high-mannose N-glycan structures were more common in carcinomas than in adenomas. We also found differences between stage I-II and stage III carcinomas. Based on these findings, we selected two glycan structures: pauci-mannose and sialyl Lewis a, for immunohistochemical analysis of their tissue expression in 220 colorectal cancer patients. In colorectal cancer, poor prognosis correlated with elevated expression of sialyl Lewis a, and in advanced colorectal cancer, poor prognosis correlated with elevated expression of pauci-mannose. In conclusion, by mass spectrometry we found several carcinoma related glycans, and we demonstrate a method of transforming these results into immunohistochemistry, a readily applicable method to study biomarker expression in patient samples.
Collapse
Affiliation(s)
- Tuomas Kaprio
- From the ‡Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; §Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland;
| | | | | | - Cornelis H Hokke
- ‖Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, The Netherlands
| | - André M Deelder
- ‖Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, The Netherlands
| | - Harri Mustonen
- From the ‡Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Jaana Hagström
- **Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, Helsinki
| | - Olli Carpen
- ‡‡Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Caj Haglund
- From the ‡Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; §Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
13
|
Balluff B, Frese CK, Maier SK, Schöne C, Kuster B, Schmitt M, Aubele M, Höfler H, Deelder AM, Heck A, Hogendoorn PCW, Morreau J, Maarten Altelaar AF, Walch A, McDonnell LA. De novo discovery of phenotypic intratumour heterogeneity using imaging mass spectrometry. J Pathol 2014; 235:3-13. [PMID: 25201776 DOI: 10.1002/path.4436] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 12/31/2022]
Abstract
An essential and so far unresolved factor influencing the evolution of cancer and the clinical management of patients is intratumour clonal and phenotypic heterogeneity. However, the de novo identification of tumour subpopulations is so far both a challenging and an unresolved task. Here we present the first systematic approach for the de novo discovery of clinically detrimental molecular tumour subpopulations. In this proof-of-principle study, spatially resolved, tumour-specific mass spectra were acquired, using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry, from tissues of 63 gastric carcinoma and 32 breast carcinoma patients. The mass spectra, representing the proteomic heterogeneity within tumour areas, were grouped by a corroborated statistical clustering algorithm in order to obtain segmentation maps of molecularly distinct regions. These regions were presumed to represent different phenotypic tumour subpopulations. This was confirmed by linking the presence of these tumour subpopulations to the patients' clinical data. This revealed several of the detected tumour subpopulations to be associated with a different overall survival of the gastric cancer patients (p = 0.025) and the presence of locoregional metastases in patients with breast cancer (p = 0.036). The procedure presented is generic and opens novel options in cancer research, as it reveals microscopically indistinct tumour subpopulations that have an adverse impact on clinical outcome. This enables their further molecular characterization for deeper insights into the biological processes of cancer, which may finally lead to new targeted therapies.
Collapse
Affiliation(s)
- Benjamin Balluff
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Huijbers A, Mesker WE, Mertens BJ, Bladergroen MR, Deelder AM, van der Burgt YEM, Tollenaar RAEM. Case-controlled identification of colorectal cancer based on proteomic profiles and the potential for screening. Colorectal Dis 2014; 16:907-13. [PMID: 25243779 DOI: 10.1111/codi.12782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 05/17/2014] [Indexed: 01/25/2023]
Abstract
AIM Colorectal cancer (CRC) screening programmes detect early cancers but unfortunately have limited sensitivity and specificity. Mass spectrometry-based determination of serum peptide and protein profiles provides a new approach for improved screening. METHOD Serum samples were obtained from 126 CRC patients before treatment and 277 control individuals. An additional group of samples from 50 CRC patients and 82 controls was used for validation. Peptide and protein enrichments were carried out using reverse-phase C18 and weak-cation exchange magnetic beads in an automated solid-phase extraction and spotting procedure. Profiles were acquired on a matrix-assisted laser desorption/ionization time-of-flight system. Discriminant rules using logistic regression were calibrated for the peptide and protein signatures separately, followed by combining the classifications to obtain double cross-validated predicted class probabilities. Results were validated on an identical patient set. RESULTS A discriminative power was found for patients with CRC representative for all histopathological stages compared with controls with an area under the curve of 0.95 in the test set (0.93 for the validation set) and with a high specificity (94-95%). CONCLUSION The study has shown that a serum peptide and protein biomarker signature can be used to distinguish CRC patients from healthy controls with high discriminative power. This relatively simple and cheap test is promising for CRC screening.
Collapse
Affiliation(s)
- A Huijbers
- Department of Surgery, Leiden Universal Medical Center, Leiden, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
15
|
Morello J, Nevedomskaya E, Pacchiarotta T, Schoemaker B, Derks R, Voet NBM, Meissner A, Deelder AM, van Engelen BGM, Mayboroda OA. Effect of Suboptimal Sampling and Handling Conditions on Urinary Metabolic Profiles. Chromatographia 2014. [DOI: 10.1007/s10337-014-2778-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
16
|
Velstra B, Vonk MA, Bonsing BA, Mertens BJ, Nicolardi S, Huijbers A, Vasen H, Deelder AM, Mesker WE, van der Burgt YEM, Tollenaar RAEM. Serum peptide signatures for pancreatic cancer based on mass spectrometry: a comparison to CA19-9 levels and routine imaging techniques. J Cancer Res Clin Oncol 2014; 141:531-41. [DOI: 10.1007/s00432-014-1812-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/21/2014] [Indexed: 12/26/2022]
|
17
|
Fleurbaaij F, Heemskerk AAM, Russcher A, Klychnikov OI, Deelder AM, Mayboroda OA, Kuijper EJ, van Leeuwen HC, Hensbergen PJ. Capillary-electrophoresis mass spectrometry for the detection of carbapenemases in (multi-)drug-resistant Gram-negative bacteria. Anal Chem 2014; 86:9154-61. [PMID: 25155175 DOI: 10.1021/ac502049p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In a time in which the spread of multidrug resistant microorganisms is ever increasing, there is a need for fast and unequivocal identification of suspect organisms to supplement existing techniques in the clinical laboratory, especially in single bacterial colonies. Mass-spectrometry coupled with efficient peptide separation techniques offer great potential for identification of resistant-related proteins in complex microbiological samples in an unbiased manner. Here, we developed a capillary electrophoresis-electrospray ionization-tandem mass spectrometry CE-ESI-MS/MS bottom-up proteomics workflow for sensitive and specific peptide analysis with the emphasis on the identification of β-lactamases (carbapenemases OXA-48 and KPC in particular) in bacterial species. For this purpose, tryptic peptides from whole cell lysates were analyzed by sheathless CE-ESI-MS/MS and proteins were identified after searching of the spectral data against bacterial protein databases. The CE-ESI-MS/MS workflow was first evaluated using a recombinant TEM-1 β-lactamase, resulting in 68% of the amino acid sequence being covered by 20 different unique peptides. Subsequently, a resistant and susceptible Escherichia coli lab strain were analyzed and based on the observed β-lactamase peptides, the two strains could easily be discriminated. Finally, the method was tested in an unbiased setup using a collection of in-house characterized OXA-48 (n = 17) and KPC (n = 10) clinical isolates. The developed CE-ESI-MS/MS method was able to identify the presence of OXA-48 and KPC in all of the carbapenemase positive samples, independent of species and degree of susceptibility. Four negative controls were tested and classified as negative by this method. Furthermore, a number of extended-spectrum beta-lactamases (ESBL) were identified in the same analyses, confirming the multiresistant character in 19 out of 27 clinical isolates. Importantly, the method performed equally well on protein lysates from single colonies. As such, it demonstrates CE-ESI-MS/MS as a potential next generation mass spectrometry platform within the clinical microbiology laboratory.
Collapse
Affiliation(s)
- Frank Fleurbaaij
- Department of Medical Microbiology, Section Experimental Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Kloos DP, Gay E, Lingeman H, Bracher F, Müller C, Mayboroda OA, Deelder AM, Niessen WMA, Giera M. Comprehensive gas chromatography-electron ionisation mass spectrometric analysis of fatty acids and sterols using sequential one-pot silylation: quantification and isotopologue analysis. Rapid Commun Mass Spectrom 2014; 28:1507-1514. [PMID: 24861601 DOI: 10.1002/rcm.6923] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Fatty acids and sterol lipids play crucial roles in several biological processes and several biological facts underline the interconnection between these lipid classes. Therefore, it is of interest to develop a comprehensive method analysing both classes in the form of their most favourable derivatives suitable for quantification and isotopologue analysis. METHODS Lipids were derivatised by a sequential one-pot procedure using N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MtBSTFA) and N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA). No clean-up or concentration steps were necessary. The prepared samples were directly available for gas chromatography-electron ionisation mass spectrometric (GC-EI-MS) analysis on a standard column. For quantification, the SIM mode was used and for isotopologue analysis scheduled scan mode was applied. RESULTS Development of a sequential one-pot derivatisation for GC-EI-MS allowing comprehensive analysis of fatty acids and sterols as their most favourable derivatives. Validation carried out using human plasma, comparison with certified NIST plasma. LLOQ of usually 3.3 ng/mL achieved. Isotopologue analysis of 2-[(13)C]-acetate incorporation in HL-60 cells proving feasibility of method. CONCLUSIONS The presented method successfully combines two consecutive silylation reactions in one pot, enabling the analysis of both fatty acids and sterols in a comprehensive analytical method. The method has great potential for the quantification of lipids as well as the comprehensive study of both biochemical pathways, using [(13)C]-flux analysis.
Collapse
Affiliation(s)
- Dick-Paul Kloos
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2300, RC, Leiden, The Netherlands; AIMMS Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Vaarhorst AAM, Verhoeven A, Weller CM, Böhringer S, Göraler S, Meissner A, Deelder AM, Henneman P, Gorgels APM, van den Brandt PA, Schouten LJ, van Greevenbroek MM, Merry AHH, Verschuren WMM, van den Maagdenberg AMJM, van Dijk KW, Isaacs A, Boomsma D, Oostra BA, van Duijn CM, Jukema JW, Boer JMA, Feskens E, Heijmans BT, Slagboom PE. A metabolomic profile is associated with the risk of incident coronary heart disease. Am Heart J 2014; 168:45-52.e7. [PMID: 24952859 DOI: 10.1016/j.ahj.2014.01.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 01/24/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND Metabolomics, defined as the comprehensive identification and quantification of low-molecular-weight metabolites to be found in a biological sample, has been put forward as a potential tool for classifying individuals according to their risk of coronary heart disease (CHD). Here, we investigated whether a single-point blood measurement of the metabolome is associated with and predictive for the risk of CHD. METHODS AND RESULTS We obtained proton nuclear magnetic resonance spectra in 79 cases who developed CHD during follow-up (median 8.1 years) and in 565 randomly selected individuals. In these spectra, 100 signals representing 36 metabolites were identified. Applying least absolute shrinkage and selection operator regression, we defined a weighted metabolite score consisting of 13 proton nuclear magnetic resonance signals that optimally predicted CHD. This metabolite score, including signals representing a lipid fraction, glucose, valine, ornithine, glutamate, creatinine, glycoproteins, citrate, and 1.5-anhydrosorbitol, was associated with the incidence of CHD independent of traditional risk factors (TRFs) (hazard ratio 1.50, 95% CI 1.12-2.01). Predictive performance of this metabolite score on its own was moderate (C-index 0.75, 95% CI 0.70-0.80), but after adding age and sex, the C-index was only modestly lower than that of TRFs (C-index 0.81, 95% CI 0.77-0.85 and C-index 0.82, 95% CI 0.78-0.87, respectively). The metabolite score was also associated with prevalent CHD independent of TRFs (odds ratio 1.59, 95% CI 1.19-2.13). CONCLUSION A metabolite score derived from a single-point metabolome measurement is associated with CHD, and metabolomics may be a promising tool for refining and improving the prediction of CHD.
Collapse
Affiliation(s)
- Anika A M Vaarhorst
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Aswin Verhoeven
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia M Weller
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefan Böhringer
- Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sibel Göraler
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Axel Meissner
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - André M Deelder
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anton P M Gorgels
- Department of Cardiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Piet A van den Brandt
- Department of Epidemiology (CAPHRI School for Public Health and Primary Care), Maastricht University, Maastricht, The Netherlands; Department of Epidemiology (GROW School of Oncology and Developmental Biology), Maastricht University, Maastricht, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology (GROW School of Oncology and Developmental Biology), Maastricht University, Maastricht, The Netherlands
| | - Marleen M van Greevenbroek
- Department of Internal Medicine (CARIM School for Cardiovascular diseases), Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Audrey H H Merry
- Department of Epidemiology (CAPHRI School for Public Health and Primary Care), Maastricht University, Maastricht, The Netherlands
| | | | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; Department of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aaron Isaacs
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dorret Boomsma
- Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Ben A Oostra
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands; The Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands; Interuniversity Cardiology Institute of the Netherlands (ICIN), Utrecht, The Netherlands
| | - Jolanda M A Boer
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Edith Feskens
- Division of Human Nutrition, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Bastiaan T Heijmans
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands; Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands.
| |
Collapse
|
20
|
Huffman JE, Pučić-Baković M, Klarić L, Hennig R, Selman MHJ, Vučković F, Novokmet M, Krištić J, Borowiak M, Muth T, Polašek O, Razdorov G, Gornik O, Plomp R, Theodoratou E, Wright AF, Rudan I, Hayward C, Campbell H, Deelder AM, Reichl U, Aulchenko YS, Rapp E, Wuhrer M, Lauc G. Comparative performance of four methods for high-throughput glycosylation analysis of immunoglobulin G in genetic and epidemiological research. Mol Cell Proteomics 2014; 13:1598-610. [PMID: 24719452 PMCID: PMC4047478 DOI: 10.1074/mcp.m113.037465] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/14/2014] [Indexed: 11/06/2022] Open
Abstract
The biological and clinical relevance of glycosylation is becoming increasingly recognized, leading to a growing interest in large-scale clinical and population-based studies. In the past few years, several methods for high-throughput analysis of glycans have been developed, but thorough validation and standardization of these methods is required before significant resources are invested in large-scale studies. In this study, we compared liquid chromatography, capillary gel electrophoresis, and two MS methods for quantitative profiling of N-glycosylation of IgG in the same data set of 1201 individuals. To evaluate the accuracy of the four methods we then performed analysis of association with genetic polymorphisms and age. Chromatographic methods with either fluorescent or MS-detection yielded slightly stronger associations than MS-only and multiplexed capillary gel electrophoresis, but at the expense of lower levels of throughput. Advantages and disadvantages of each method were identified, which should inform the selection of the most appropriate method in future studies.
Collapse
Affiliation(s)
- Jennifer E Huffman
- From the ‡MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - René Hennig
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖glyXera GmbH, Magdeburg, Germany
| | - Maurice H J Selman
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | - Thilo Muth
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖glyXera GmbH, Magdeburg, Germany
| | - Ozren Polašek
- ‡‡Faculty of Medicine, University of Split, Split, Croatia
| | - Genadij Razdorov
- §§University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Olga Gornik
- §§University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Rosina Plomp
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Evropi Theodoratou
- ¶¶Centre for Population Health Sciences, School of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Alan F Wright
- From the ‡MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Igor Rudan
- ¶¶Centre for Population Health Sciences, School of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- From the ‡MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- ¶¶Centre for Population Health Sciences, School of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - André M Deelder
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Udo Reichl
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖‖Otto-von-Guericke University, Chair of Bioprocess Engineering, Magdeburg, Germany
| | - Yurii S Aulchenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; "Yurii Aulchenko" consulting, Groningen, The Netherlands
| | - Erdmann Rapp
- ¶Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; ‖glyXera GmbH, Magdeburg, Germany
| | - Manfred Wuhrer
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gordan Lauc
- §Genos Glycoscience Laboratory, Zagreb, Croatia; §§University of Zagreb, Faculty of Pharmacy and Biochemistry, Zagreb, Croatia;
| |
Collapse
|
21
|
Mohammed Y, Domański D, Jackson AM, Smith DS, Deelder AM, Palmblad M, Borchers CH. PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J Proteomics 2014; 106:151-61. [DOI: 10.1016/j.jprot.2014.04.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 01/08/2023]
|
22
|
Reiding KR, Blank D, Kuijper DM, Deelder AM, Wuhrer M. High-throughput profiling of protein N-glycosylation by MALDI-TOF-MS employing linkage-specific sialic acid esterification. Anal Chem 2014; 86:5784-93. [PMID: 24831253 DOI: 10.1021/ac500335t] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein glycosylation is an important post-translational modification associated, among others, with diseases and the efficacy of biopharmaceuticals. Matrix-assisted laser desorption/ionization (MALDI) time-of-fight (TOF) mass spectrometry (MS) can be performed to study glycosylation in a high-throughput manner, but is hampered by the instability and ionization bias experienced by sialylated glycan species. Stabilization and neutralization of these sialic acids can be achieved by permethylation or by specific carboxyl group derivatization with the possibility of discrimination between α2,3- and α2,6-linked sialic acids. However, these methods typically require relatively pure glycan samples, show sensitivity to side reactions, and need harsh conditions or long reaction times. We established a rapid, robust and linkage-specific high-throughput method for sialic acid stabilization and MALDI-TOF-MS analysis, to allow direct modification of impure glycan-containing mixtures such as PNGase F-released human plasma N-glycome. Using a combination of carboxylic acid activators in ethanol achieved near-complete ethyl esterification of α2,6-linked sialic acids and lactonization of α2,3-linked variants, in short time using mild conditions. Glycans were recovered by hydrophilic interaction liquid chromatography solid phase extraction and analyzed by MALDI-TOF-MS in reflectron positive mode with 2,5-dihydroxybenzoic acid as the matrix substance. Analysis of the human plasma N-glycome allowed high-throughput detection and relative quantitation of more than 100 distinct N-glycan compositions with varying sialic acid linkages.
Collapse
Affiliation(s)
- Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center , 2300 RC Leiden, The Netherlands
| | | | | | | | | |
Collapse
|
23
|
Nicolardi S, Deelder AM, Palmblad M, van der Burgt YEM. Structural analysis of an intact monoclonal antibody by online electrochemical reduction of disulfide bonds and Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 2014; 86:5376-82. [PMID: 24780057 DOI: 10.1021/ac500383c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Structural confirmation and quality control of recombinant monoclonal antibodies (mAbs) by top-down mass spectrometry is still challenging due to the size of the proteins, disulfide content, and post-translational modifications such as glycosylation. In this study we have applied electrochemistry (EC) to overcome disulfide bridge complexity in top-down analysis of mAbs. To this end, an electrochemical cell was coupled directly to an electrospray ionization (ESI) source and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer (MS) equipped with a 15 T magnet. By performing online EC-assisted reduction of interchain disulfide bonds in an intact mAb, the released light chains could be selected for tandem mass spectrometry (MS/MS) analysis without interference from heavy-chain fragments. Moreover, the acquisition of full MS scans under denaturing conditions allowed profiling of all abundant mAb glycoforms. Ultrahigh-resolution FTICR-MS measurements provided fully resolved isotopic distributions of intact mAb and enabled the identification of the most abundant adducts and other interfering species. Furthermore, it was found that reduction of interchain disulfide bonds occurs in the ESI source dependent on capillary voltage and solvent composition. This phenomenon was systematically evaluated and compared with the results obtained from reduction in the electrochemical cell.
Collapse
Affiliation(s)
- Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center , Albinusdreef 2, 2300 RC Leiden, The Netherlands
| | | | | | | |
Collapse
|
24
|
Hensbergen PJ, Klychnikov OI, Bakker D, van Winden VJC, Ras N, Kemp AC, Cordfunke RA, Dragan I, Deelder AM, Kuijper EJ, Corver J, Drijfhout JW, van Leeuwen HC. A novel secreted metalloprotease (CD2830) from Clostridium difficile cleaves specific proline sequences in LPXTG cell surface proteins. Mol Cell Proteomics 2014; 13:1231-44. [PMID: 24623589 DOI: 10.1074/mcp.m113.034728] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacterial secreted proteins constitute a biologically important subset of proteins involved in key processes related to infection such as adhesion, colonization, and dissemination. Bacterial extracellular proteases, in particular, have attracted considerable attention, as they have been shown to be indispensable for bacterial virulence. Here, we analyzed the extracellular subproteome of Clostridium difficile and identified a hypothetical protein, CD2830, as a novel secreted metalloprotease. Following the identification of a CD2830 cleavage site in human HSP90β, a series of synthetic peptide substrates was used to identify the favorable CD2830 cleavage motif. This motif was characterized by a high prevalence of proline residues. Intriguingly, CD2830 has a preference for cleaving Pro-Pro bonds, unique among all hitherto described proteases. Strikingly, within the C. difficile proteome two putative adhesion molecules, CD2831 and CD3246, were identified that contain multiple CD2830 cleavage sites (13 in total). We subsequently found that CD2830 efficiently cleaves CD2831 between two prolines at all predicted cleavage sites. Moreover, native CD2830, secreted by live cells, cleaves endogenous CD2831 and CD3246. These findings highlight CD2830 as a highly specific endoproteinase with a preference for proline residues surrounding the scissile bond. Moreover, the efficient cleavage of two putative surface adhesion proteins points to a possible role of CD2830 in the regulation of C. difficile adhesion.
Collapse
Affiliation(s)
- Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Cynthia Martin F, Hiller M, Spitali P, Oonk S, Dalebout H, Palmblad M, Chaouch A, Guglieri M, Straub V, Lochmüller H, Niks EH, Verschuuren JJGM, Aartsma‐Rus A, Deelder AM, Burgt YEM, 't Hoen PAC. Fibronectin is a serum biomarker for
D
uchenne muscular dystrophy. Proteomics Clin Appl 2014; 8:269-78. [DOI: 10.1002/prca.201300072] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/05/2013] [Accepted: 11/17/2013] [Indexed: 01/23/2023]
Affiliation(s)
- F. Cynthia Martin
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Monika Hiller
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Pietro Spitali
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Stijn Oonk
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Amina Chaouch
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Michela Guglieri
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Volker Straub
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Hanns Lochmüller
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - Erik H. Niks
- Department of Neurology Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | | | - Annemieke Aartsma‐Rus
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
- Institute of Genetic Medicine Newcastle University, International Centre for Life Newcastle upon Tyne UK
| | - André M. Deelder
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Yuri E. M. Burgt
- Center for Proteomics and Metabolomics >Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| | - Peter A. C. 't Hoen
- Department of Human Genetics Leiden University Medical Center (LUMC) RC Leiden The Netherlands
| |
Collapse
|
26
|
Rombouts Y, Willemze A, van Beers JJBC, Shi J, Kerkman PF, Janssen GMC, van Veelen PA, Zaldumbide A, Hoeben RC, Pruijn GJ, Deelder AM, Wolbink G, Rispens T, García-Vallejo JJ, van Kooyk Y, Huizinga TWJ, Wuhrer M, Trouw LA, Scherer HU, Toes REM. A1.45 Hyperglycosylation of ACPA-IGG variable domains modulates reactivity to citrullinated antigens. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2013-205124.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
27
|
Nicolardi S, Velstra B, Mertens BJ, Bonsing B, Mesker WE, Tollenaar RA, Deelder AM, van der Burgt YE. Ultrahigh resolution profiles lead to more detailed serum peptidome signatures of pancreatic cancer. Translational Proteomics 2014. [DOI: 10.1016/j.trprot.2013.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
28
|
Affiliation(s)
- L. Renee Ruhaak
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
- Department
of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Hae-Won Uh
- Department
of Medical Statistics and Bioinformatics, Section of Medical Statistics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - André M. Deelder
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Radboud E. J. M. Dolhain
- Department
of Rheumatology, Erasmus MC University Medical Center, Rotterdam 3015 CE, The Netherlands
| | - M. Wuhrer
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
- Division
of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| |
Collapse
|
29
|
Fokkink WJR, Selman MHJ, Dortland JR, Durmuş B, Kuitwaard K, Huizinga R, van Rijs W, Tio-Gillen AP, van Doorn PA, Deelder AM, Wuhrer M, Jacobs BC. IgG Fc N-glycosylation in Guillain-Barré syndrome treated with immunoglobulins. J Proteome Res 2014; 13:1722-30. [PMID: 24533874 DOI: 10.1021/pr401213z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intravenous immunoglobulin (IVIg) is the treatment of choice for Guillain-Barré syndrome (GBS), an immune-mediated peripheral neuropathy causing rapidly progressive limb weakness and respiratory failure. The working mechanism of IVIg in autoimmune diseases has not been elucidated, but previous studies indicate that some anti-inflammatory effects may be mediated by the N-glycosylation of the Fc-portion of IgG. GBS is a model disease to investigate these effects because GBS is an acute and monophasic disorder usually affecting healthy persons, which is treated with a standard course of IVIg, although the clinical response is highly variable. In the current study, the N-glycosylation of the Fc-portion of serum IgG was investigated in patients with GBS before and after treatment with IVIg in relation to clinical course and outcome. Glycoforms of serum IgG1 and IgG2 were determined separately by liquid chromatography mass spectrometry. These IgG subclasses were purified from the serum of 174 GBS patients before and in 150 patients 2 weeks after standard IVIg treatment regimen. Treatment-naive GBS patients compared with age- and sex-matched controls had lower levels of galactosylation of IgG1 and IgG2. IVIg preparations contained relatively high levels of galactosylated and sialylated IgG Fc glycoforms compared with serum IgG in patients. Treatment with IVIg resulted in an increase in serum of the Fc-galactosylation and -sialylation of both IgG1 and IgG2. The extent of normalization in serum IgG Fc glycosylation varied between patients. Multiple logistic regression analysis showed that patients with persistent low IgG galactosylation and sialylation despite IVIg treatment had the most severe forms of GBS and needed ventilator support more often. Kaplan-Meier analysis showed that these patients also needed more time to be able to walk again compared with patients with a normalized IgG Fc glycosylation profile. In conclusion, our results suggest that serum IgG Fc glycosylation in GBS is related to disease severity and clinical recovery after IVIg and may help to develop new measures to monitor the efficacy of treatment.
Collapse
Affiliation(s)
- Willem-Jan R Fokkink
- Department of Immunology, ‡Department of Neurology, and §Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam , Dr. Molewaterplein 50, 3000 CA Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
van der Plas-Duivesteijn SJ, Mohammed Y, Dalebout H, Meijer A, Botermans A, Hoogendijk JL, Henneman AA, Deelder AM, Spaink HP, Palmblad M. Identifying proteins in zebrafish embryos using spectral libraries generated from dissected adult organs and tissues. J Proteome Res 2014; 13:1537-44. [PMID: 24460240 DOI: 10.1021/pr4010585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectral libraries provide a sensitive and accurate method for identifying peptides from tandem mass spectra, complementary to searching genome-derived databases or sequencing de novo. Their application requires comprehensive libraries including peptides from low-abundant proteins. Here we describe a method for constructing such libraries using biological differentiation to "fractionate" the proteome by harvesting adult organs and tissues and build comprehensive libraries for identifying proteins in zebrafish (Danio rerio) embryos and larvae (an important and widely used model system). Hierarchical clustering using direct comparison of spectra was used to prioritize organ selection. The resulting and publicly available library covers 14,164 proteins, significantly improved the number of peptide-spectrum matches in zebrafish developmental stages, and can be used on data from different instruments and laboratories. The library contains information on tissue and organ expression of these proteins and is also applicable for adult experiments. The approach itself is not limited to zebrafish but would work for any model system.
Collapse
|
31
|
Koukounari A, Donnelly CA, Moustaki I, Tukahebwa EM, Kabatereine NB, Wilson S, Webster JP, Deelder AM, Vennervald BJ, van Dam GJ. A latent Markov modelling approach to the evaluation of circulating cathodic antigen strips for schistosomiasis diagnosis pre- and post-praziquantel treatment in Uganda. PLoS Comput Biol 2013; 9:e1003402. [PMID: 24367250 PMCID: PMC3868541 DOI: 10.1371/journal.pcbi.1003402] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/28/2013] [Indexed: 01/19/2023] Open
Abstract
Regular treatment with praziquantel (PZQ) is the strategy for human schistosomiasis control aiming to prevent morbidity in later life. With the recent resolution on schistosomiasis elimination by the 65th World Health Assembly, appropriate diagnostic tools to inform interventions are keys to their success. We present a discrete Markov chains modelling framework that deals with the longitudinal study design and the measurement error in the diagnostic methods under study. A longitudinal detailed dataset from Uganda, in which one or two doses of PZQ treatment were provided, was analyzed through Latent Markov Models (LMMs). The aim was to evaluate the diagnostic accuracy of Circulating Cathodic Antigen (CCA) and of double Kato-Katz (KK) faecal slides over three consecutive days for Schistosoma mansoni infection simultaneously by age group at baseline and at two follow-up times post treatment. Diagnostic test sensitivities and specificities and the true underlying infection prevalence over time as well as the probabilities of transitions between infected and uninfected states are provided. The estimated transition probability matrices provide parsimonious yet important insights into the re-infection and cure rates in the two age groups. We show that the CCA diagnostic performance remained constant after PZQ treatment and that this test was overall more sensitive but less specific than single-day double KK for the diagnosis of S. mansoni infection. The probability of clearing infection from baseline to 9 weeks was higher among those who received two PZQ doses compared to one PZQ dose for both age groups, with much higher re-infection rates among children compared to adolescents and adults. We recommend LMMs as a useful methodology for monitoring and evaluation and treatment decision research as well as CCA for mapping surveys of S. mansoni infection, although additional diagnostic tools should be incorporated in schistosomiasis elimination programs. Schistosomiasis remains one of the most prevalent parasitic diseases in developing countries, with Schistosoma mansoni being the most widespread of the human-infecting schistosomes. For the routine surveillance of human S. mansoni infection more “field-applicable,” sensitive, and cost-effective diagnostics that replicate faecal samples over several consecutive days [the Kato-Katz (KK) method], are needed. We propose a statistical modelling framework in order to evaluate the diagnostic performance of the urine strip test for Circulating Cathodic Antigen (CCA) and single-day double KK measurements over three consecutive days for the diagnosis of S. mansoni infection in two different age groups from Uganda pre- and post- praziquantel (PZQ) treatment. We demonstrate that CCA is an appropriate tool for mapping surveys of S. mansoni infection. Our findings should allow for evaluation of the risk of potential misinterpretation with regards to diagnosis of S. mansoni infection through CCA or KK in this endemic setting pre- and post- PZQ treatment as the numbers and infection intensities are brought down, bridging existing important gaps in schistosomiasis diagnostics research. More generally, the proposed statistical analysis can reveal important biological insights from other diseases without gold standard diagnostic tools whenever longitudinal data are available.
Collapse
Affiliation(s)
- Artemis Koukounari
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Department of Statistics, London School of Economics and Political Science, London, United Kingdom
- * E-mail:
| | - Christl A. Donnelly
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Irini Moustaki
- Department of Statistics, London School of Economics and Political Science, London, United Kingdom
| | - Edridah M. Tukahebwa
- Schistosomiasis Control Initiative at Vector Control Division – Ministry of Health, Kampala, Uganda
| | - Narcis B. Kabatereine
- Schistosomiasis Control Initiative at Vector Control Division – Ministry of Health, Kampala, Uganda
| | - Shona Wilson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Joanne P. Webster
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - André M. Deelder
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Birgitte J. Vennervald
- Section for Parasitology and Aquatic Diseases, University of Copenhagen, Copenhagen, Denmark
| | - Govert J. van Dam
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
32
|
Plomp R, Hensbergen PJ, Rombouts Y, Zauner G, Dragan I, Koeleman CAM, Deelder AM, Wuhrer M. Site-Specific N-Glycosylation Analysis of Human Immunoglobulin E. J Proteome Res 2013; 13:536-46. [DOI: 10.1021/pr400714w] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
33
|
Nicolardi S, Giera M, Kooijman P, Kraj A, Chervet JP, Deelder AM, van der Burgt YEM. On-line electrochemical reduction of disulfide bonds: improved FTICR-CID and -ETD coverage of oxytocin and hepcidin. J Am Soc Mass Spectrom 2013; 24:1980-7. [PMID: 24018861 PMCID: PMC3837188 DOI: 10.1007/s13361-013-0725-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/25/2013] [Accepted: 07/25/2013] [Indexed: 05/21/2023]
Abstract
Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80% (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.
Collapse
Affiliation(s)
- Simone Nicolardi
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Martin Giera
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Pieter Kooijman
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | | | | | - André M. Deelder
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| |
Collapse
|
34
|
van den Broek I, Smit NPM, Romijn FPHTM, van der Laarse A, Deelder AM, van der Burgt YEM, Cobbaert CM. Evaluation of interspecimen trypsin digestion efficiency prior to multiple reaction monitoring-based absolute protein quantification with native protein calibrators. J Proteome Res 2013; 12:5760-74. [PMID: 24168082 DOI: 10.1021/pr400763d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Implementation of quantitative clinical chemistry proteomics (qCCP) requires targeted proteomics approaches, usually involving bottom-up multiple reaction monitoring-mass spectrometry (MRM-MS) with stable-isotope labeled standard (SIS) peptides, to move toward more accurate measurements. Two aspects of qCCP that deserve special attention are (1) proper calibration and (2) the assurance of consistent digestion. Here, we describe the evaluation of tryptic digestion efficiency by monitoring various signature peptides, missed cleavages, and modifications during proteolysis of apolipoprotein A-I and B in normo- and hypertriglyceridemic specimens. Absolute quantification of apolipoprotein A-I and B was performed by LC-MRM-MS with SIS peptide internal standards at two time points (4 and 20 h), using three native protein calibrators. Comparison with an immunoturbidimetric assay revealed recoveries of 99.4 ± 6.5% for apolipoprotein A-I and 102.6 ± 7.2% for apolipoprotein B after 4 h of trypsin digestion. Protein recoveries after 20 h trypsin incubation equaled 95.9 ± 6.9% and 106.0 ± 10.0% for apolipoproteins A-I and B, respectively. In conclusion, the use of metrologically traceable, native protein calibrators looks promising for accurate quantification of apolipoprotein A-I and B. Selection of rapidly formed peptides, that is, with no or minor missed cleavages, and the use of short trypsin incubation times for these efficiently cleaved peptides are likely to further reduce the variability introduced by trypsin digestion and to improve the traceability of test results to reach the desirable analytical performance for clinical chemistry application.
Collapse
Affiliation(s)
- Irene van den Broek
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC) , Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | | | | | | | | | | | | |
Collapse
|
35
|
Holst S, Stavenhagen K, Balog CIA, Koeleman CAM, McDonnell LM, Mayboroda OA, Verhoeven A, Mesker WE, Tollenaar RAEM, Deelder AM, Wuhrer M. Investigations on aberrant glycosylation of glycosphingolipids in colorectal cancer tissues using liquid chromatography and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Mol Cell Proteomics 2013; 12:3081-93. [PMID: 23878401 PMCID: PMC3820925 DOI: 10.1074/mcp.m113.030387] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/24/2013] [Indexed: 11/06/2022] Open
Abstract
Cancer is a leading cause of death and alterations of glycosylation are characteristic features of malignant cells. Colorectal cancer is one of the most common cancers and its exact causes and biology are not yet well understood. Here, we compared glycosylation profiles of colorectal tumor tissues and corresponding control tissues of 13 colorectal cancer patients to contribute to the understanding of this cancer. Using MALDI-TOF(/TOF)-MS and 2-dimensional LC-MS/MS we characterized enzymatically released and 2-aminobenzoic acid labeled glycans from glycosphingolipids. Multivariate data analysis revealed significant differences between tumor and corresponding control tissues. Main discriminators were obtained, which represent the overall alteration in glycosylation of glycosphingolipids during colorectal cancer progression, and these were found to be characterized by (1) increased fucosylation, (2) decreased acetylation, (3) decreased sulfation, (4) reduced expression of globo-type glycans, as well as (5) disialyl gangliosides. The findings of our current research confirm former reports, and in addition expand the knowledge of glycosphingolipid glycosylation in colorectal cancer by revealing new glycans with discriminative power and characteristic, cancer-associated glycosylation alterations. The obtained discriminating glycans can contribute to progress the discovery of biomarkers to improve diagnostics and patient treatment.
Collapse
Affiliation(s)
- Stephanie Holst
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kathrin Stavenhagen
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Crina I. A. Balog
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Carolien A. M. Koeleman
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Liam M. McDonnell
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Oleg A. Mayboroda
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aswin Verhoeven
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wilma E. Mesker
- §Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | | | - André M. Deelder
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- From the ‡Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
36
|
Palmblad M, Henkel CV, Dirks RP, Meijer AH, Deelder AM, Spaink HP. Parallel deep transcriptome and proteome analysis of zebrafish larvae. BMC Res Notes 2013; 6:428. [PMID: 24156766 PMCID: PMC4016144 DOI: 10.1186/1756-0500-6-428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 10/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Sensitivity and throughput of transcriptomic and proteomic technologies have advanced tremendously in recent years. With the use of deep sequencing of RNA samples (RNA-seq) and mass spectrometry technology for protein identification and quantitation, it is now feasible to compare gene and protein expression on a massive scale and for any organism for which genomic data is available. Although these technologies are currently applied to many research questions in various model systems ranging from cell cultures to the entire organism level, there are few comparative studies of these technologies in the same system, let alone on the same samples. Here we present a comparison between gene and protein expression in embryos of zebrafish, which is an upcoming model in disease studies. Results We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis, showing as expected a high degree of correlation of expression of a common set of 18,230 genes. Gene expression was also found to correlate with the abundance of 963 distinct proteins, with several categories of genes as exceptions. These exceptions include ribosomal proteins, histones and vitellogenins, for which biological and technical explanations are discussed. Conclusions By comparing state of the art transcriptomic and proteomic technologies on samples derived from the same group of organisms we have for the first time benchmarked the differences in these technologies with regard to sensitivity and bias towards detection of particular gene categories in zebrafish. Our datasets submitted to public repositories are a good starting point for researchers interested in disease progression in zebrafish at a stage of development highly suited for high throughput screening technologies.
Collapse
Affiliation(s)
- Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Zone L04-Q, P,O, Box 9600, 2300 RC, Leiden, The Netherlands.
| | | | | | | | | | | |
Collapse
|
37
|
Wulff T, Nielsen ME, Deelder AM, Jessen F, Palmblad M. Authentication of Fish Products by Large-Scale Comparison of Tandem Mass Spectra. J Proteome Res 2013; 12:5253-9. [DOI: 10.1021/pr4006525] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tune Wulff
- National
Food Institute, Technical University of Denmark, Mørkhøj
Bygade 19, Soborg 2860, Denmark
- Leiden
University Medical Center (LUMC), Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - André M. Deelder
- Leiden
University Medical Center (LUMC), Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Flemming Jessen
- National
Food Institute, Technical University of Denmark, Mørkhøj
Bygade 19, Soborg 2860, Denmark
| | - Magnus Palmblad
- Leiden
University Medical Center (LUMC), Center for Proteomics and Metabolomics, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| |
Collapse
|
38
|
Meissner A, van der Plas AA, van Dasselaar NT, Deelder AM, van Hilten JJ, Mayboroda OA. 1H-NMR metabolic profiling of cerebrospinal fluid in patients with complex regional pain syndrome-related dystonia. Pain 2013; 155:190-196. [PMID: 24120462 DOI: 10.1016/j.pain.2013.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 11/26/2022]
Abstract
In complex regional pain syndrome (CRPS)-related dystonia, compelling evidence points to the involvement of the central nervous system, but the underpinning pathobiology is still unclear. Thus, to enable a hypothesis-free, unbiased view of the problem and to obtain new insight into the pathobiology of dystonia in CRPS, we applied an exploratory metabolomics analysis of cerebrospinal fluid (CSF) of patients with CRPS-related dystonia. (1)H-NMR spectroscopy in combination with multivariate modeling were used to investigate metabolic profiles of a total of 105 CSF samples collected from patients with CRPS-related dystonia and controls. We found a significantly different metabolic profile of CSF in CRPS patients compared to controls. The differences were already reflected in the first two principal components of the principal component analysis model, which is an indication that the variance associated with CRPS is stronger than variance caused by such classical confounders as gender, age, or individual differences. A supervised analysis generated a strong model pinpointing the most important metabolites contributed to the metabolic signature of patients with CRPS-related dystonia. From the set of identified discriminators, the most relevant metabolites were 2-keto-isovalerate, glucose, glutamine, and lactate, which all showed increased concentrations, and urea, which showed decreased concentration in CRPS subjects. Our findings point at a catabolic state in chronic CRPS patients with dystonia that is likely associated with inflammation.
Collapse
Affiliation(s)
- Axel Meissner
- Center for Proteomics and Metabolomics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands Department of Neurology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands Department of Anesthesiology, Reinier de Graaf Gasthuis, PO Box 5011, 2600 GA Delft, The Netherlands
| | | | | | | | | | | |
Collapse
|
39
|
Rombouts Y, Ewing E, van de Stadt LA, Selman MHJ, Trouw LA, Deelder AM, Huizinga TWJ, Wuhrer M, van Schaardenburg D, Toes REM, Scherer HU. Anti-citrullinated protein antibodies acquire a pro-inflammatory Fc glycosylation phenotype prior to the onset of rheumatoid arthritis. Ann Rheum Dis 2013; 74:234-41. [PMID: 24106048 DOI: 10.1136/annrheumdis-2013-203565] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To determine whether anticitrullinated protein antibodies (ACPA) exhibit specific changes in Fc glycosylation prior to the onset of arthritis. METHODS Serum samples of patients with ACPA-positive arthralgia (n=183) were collected at baseline and at various time points of follow-up. 105 patients developed arthritis after a median of 12 months (IQR 6-24) and were classified as having either rheumatoid arthritis (RA, n=48) or undifferentiated arthritis (UA, n=57) based on the 1987 American College of Rheumatology (ACR) criteria. ACPA and total serum IgG were isolated by affinity purification and cleaved by trypsin. ACPA-IgG1 Fc-glycopeptides were subsequently analysed by nano-liquid chromatography mass spectrometry and compared to those of total IgG1. RESULTS At baseline, ACPA-IgG1 and total IgG1 from arthralgia patients displayed similar Fc glycosylation patterns. By contrast, at the onset of arthritis, ACPA exhibited a decrease in galactose residues in RA patients, but not in UA patients. This decrease occurred around 3 months prior to diagnosis and was paralleled by an increase in systemic inflammation (erythrocyte sedimentation rate). Galactosylation of total IgG1 was also decreased in RA, but this did not precede the onset of arthritis. Interestingly, we additionally noted a higher degree of ACPA-IgG1 Fc core fucosylation at baseline as compared with total IgG1, which further increased prior to diagnosis. CONCLUSIONS ACPA display significant changes in Fc galactosylation and fucosylation prior to the onset of RA. These changes towards a more pro-inflammatory phenotype could be involved in driving the disease process.
Collapse
Affiliation(s)
- Yoann Rombouts
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ewoud Ewing
- Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Maurice H J Selman
- Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Leendert A Trouw
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Dirkjan van Schaardenburg
- Jan van Breemen Research Institute
- Reade, Amsterdam, The Netherlands Department of Rheumatology, VU University Medical Centre, Amsterdam, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hans U Scherer
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| |
Collapse
|
40
|
van Dam GJ, de Dood CJ, Lewis M, Deelder AM, van Lieshout L, Tanke HJ, van Rooyen LH, Corstjens PL. A robust dry reagent lateral flow assay for diagnosis of active schistosomiasis by detection of Schistosoma circulating anodic antigen. Exp Parasitol 2013; 135:274-82. [PMID: 23850995 PMCID: PMC3797160 DOI: 10.1016/j.exppara.2013.06.017] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 06/18/2013] [Accepted: 06/30/2013] [Indexed: 01/05/2023]
Abstract
UNLABELLED An earlier reported laboratory assay, performed in The Netherlands, to diagnose Schistosoma infections by detection of the parasite antigen CAA in serum was converted to a more user-friendly format with dry reagents. The improved assay requires less equipment and allows storage and worldwide shipping at ambient temperature. Evaluation of the new assay format was carried out by local staff at Ampath Laboratories, South Africa. The lateral flow (LF) based assay utilized fluorescent ultrasensitive up-converting phosphor (UCP) reporter particles, to be read by a portable reader (UPlink) that was also provided to the laboratory. Over a period of 18 months, about 2000 clinical samples were analyzed prospectively in parallel with a routinely carried out CAA-ELISA. LF test results and ELISA data correlated very well at CAA concentrations above 300 pg/mL serum. At lower concentrations the UCP-LF test indicates a better performance than the ELISA. The UCP-LF strips can be stored as a permanent record as the UCP label does not fade. At the end of the 18 months testing period, LF strips were shipped back to The Netherlands where scan results obtained in South Africa were validated with different UCP scanning equipment including a novel, custom developed, small lightweight UCP strip reader (UCP-Quant), well suited for testing in low resource settings. CONCLUSION The dry format UCP-LF assay was shown to provide a robust and easy to use format for rapid testing of CAA antigen in serum. It performed at least as good as the ELISA with respect to sensitivity and specificity, and was found to be superior with respect to speed and simplicity of use. Worldwide shipping at ambient temperature of the assay reagents, and the availability of small scanners to analyze the CAA UCP-LF strip, are two major steps towards point-of-care (POC) applications in remote and resource poor environments to accurately identify low (30 pg CAA/mL serum; equivalent to about 10 worm pairs) to heavy Schistosoma infections.
Collapse
Affiliation(s)
- Govert J. van Dam
- Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Claudia J. de Dood
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Melanie Lewis
- Ampath Laboratories, Department of Serology and Immunology, Private Bag X9, Highveld Techno Park, Centurion, Republic of South Africa
| | - André M. Deelder
- Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Lisette van Lieshout
- Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Hans J. Tanke
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Louis H. van Rooyen
- Ampath Laboratories, Department of Serology and Immunology, Private Bag X9, Highveld Techno Park, Centurion, Republic of South Africa
| | - Paul L.A.M. Corstjens
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| |
Collapse
|
41
|
Bondt A, Selman MHJ, Deelder AM, Hazes JM, Willemsen SP, Wuhrer M, Dolhain RJEM. Association between Galactosylation of Immunoglobulin G and Improvement of Rheumatoid Arthritis during Pregnancy Is Independent of Sialylation. J Proteome Res 2013; 12:4522-31. [DOI: 10.1021/pr400589m] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Albert Bondt
- Department
of Rheumatology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Maurice H. J. Selman
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - André M. Deelder
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Johanna M.W. Hazes
- Department
of Rheumatology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Sten P. Willemsen
- Department
of Biostatistics, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Radboud J. E. M. Dolhain
- Department
of Rheumatology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| |
Collapse
|
42
|
Velstra B, Bonsing BA, Mertens BJ, Burgt YEM, Huijbers A, Vasen H, Mesker WE, Deelder AM, Tollenaar RAEM. Detection of pancreatic cancer using serum protein profiling. HPB (Oxford) 2013; 15:602-10. [PMID: 23458426 PMCID: PMC3731581 DOI: 10.1111/hpb.12017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/18/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Currently, no suitable biomarkers for the early detection of pancreatic cancer (PC) are available. Proteins present in the serum could reflect a state of the disease. In this study, these profiles as a diagnostic marker for PC were evaluated. METHODS Serum samples were obtained from PC patients (n = 50 calibration set, n = 39 validation set) and healthy volunteers (n = 110 and n = 75 respectively) according to a uniform standardized collection and processing protocol. For peptide and protein isolation, automated solid-phase extraction (SPE) with Weak Cation Exchange (WCX) magnetic beads (MB) was performed using a 96-channel liquid handling platform. Protein profiles were obtained by mass spectrometry (MS) and evaluated by linear discriminant analysis with double cross-validation. RESULTS A discriminating profile for PC has been identified, with a sensitivity of 78% and a specificity of 89% in the calibration set with an area under the curve (AUC) of 90%. These results were validated with a sensitivity of 74% and a specificity of 91% (AUC 90%). CONCLUSION Serum profiles of healthy controls and PC can be discrimated between. Further research is warranted to evaluate specificity and whether this biosignature can be used for early detection in a high risk population.
Collapse
Affiliation(s)
- Berit Velstra
- Department of Surgery, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - Bert A Bonsing
- Department of Surgery, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - Bart J Mertens
- Department of Medical Statistics and Bioinformatics, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - Yuri E M Burgt
- Department of Parasitology, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - Anouck Huijbers
- Department of Surgery, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - Hans Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center (LUMC)Leiden, the Netherlands
| | - Wilma E Mesker
- Department of Surgery, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - André M Deelder
- Department of Parasitology, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| | - Rob A E M Tollenaar
- Department of Surgery, Biolomolecular Mass Spectometry UnitLeiden, the Netherlands
| |
Collapse
|
43
|
Victor B, Dorny P, Kanobana K, Polman K, Lindh J, Deelder AM, Palmblad M, Gabriël S. Use of expressed sequence tags as an alternative approach for the identification of Taenia solium metacestode excretion/secretion proteins. BMC Res Notes 2013; 6:224. [PMID: 23742691 PMCID: PMC3686625 DOI: 10.1186/1756-0500-6-224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/03/2013] [Indexed: 01/10/2023] Open
Abstract
Background Taenia solium taeniasis/cysticercosis is a zoonotic helminth infection mainly found in rural regions of Africa, Asia and Latin America. In endemic areas, diagnosis of cysticercosis largely depends on serology, but these methods have their drawbacks and require improvement. This implies better knowledge of the proteins secreted and excreted by the parasite. In a previous study, we used a custom protein database containing protein sequences from related helminths to identify T. solium metacestode excretion/secretion proteins. An alternative or complementary approach would be to use expressed sequence tags combined with BLAST and protein mapping to supercontigs of Echinococcus granulosus, a closely related cestode. In this study, we evaluate this approach and compare the results to those obtained in the previous study. Findings We report 297 proteins organized in 106 protein groups based on homology. Additional classification was done using Gene Ontology information on biological process and molecular function. Of the 106 protein groups, 58 groups were newly identified, while 48 groups confirmed previous findings. Blast2GO analysis revealed that the majority of the proteins were involved in catalytic activities and binding. Conclusions In this study, we used translated expressed sequence tags combined with BLAST and mapping strategies to both confirm and complement previous research. Our findings are comparable to recent studies on other helminth genera like Echinococcus, Schistosoma and Clonorchis, indicating similarities between helminth excretion/secretion proteomes.
Collapse
Affiliation(s)
- Bjorn Victor
- Veterinary Helminthology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Jónasdóttir HS, Nicolardi S, Jonker W, Derks R, Palmblad M, Ioan-Facsinay A, Toes R, van der Burgt YEM, Deelder AM, Mayboroda OA, Giera M. Detection and Structural Elucidation of Esterified Oxylipids in Human Synovial Fluid by Electrospray Ionization-Fourier Transform Ion-Cyclotron Mass Spectrometry and Liquid Chromatography-Ion Trap-MS3: Detection of Esterified Hydroxylated Docosapentaenoic Acid Containing Phospholipids. Anal Chem 2013; 85:6003-10. [DOI: 10.1021/ac400826z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hulda S. Jónasdóttir
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Simone Nicolardi
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Willem Jonker
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Rico Derks
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Magnus Palmblad
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Andreea Ioan-Facsinay
- Leiden University Medical Center (LUMC), Department of Rheumatology, Albinusdreef
2, 2300RC Leiden, The Netherlands
| | - René Toes
- Leiden University Medical Center (LUMC), Department of Rheumatology, Albinusdreef
2, 2300RC Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - André M. Deelder
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Oleg A. Mayboroda
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| | - Martin Giera
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics,
Albinusdreef 2, 2300RC Leiden, The Netherlands
| |
Collapse
|
45
|
Kloos DP, Lingeman H, Niessen WM, Deelder AM, Giera M, Mayboroda OA. Evaluation of different column chemistries for fast urinary metabolic profiling. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 927:90-6. [DOI: 10.1016/j.jchromb.2013.02.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/18/2013] [Accepted: 02/20/2013] [Indexed: 11/15/2022]
|
46
|
Nicolardi S, van der Burgt YEM, Dragan I, Hensbergen PJ, Deelder AM. Identification of new apolipoprotein-CIII glycoforms with ultrahigh resolution MALDI-FTICR mass spectrometry of human sera. J Proteome Res 2013; 12:2260-8. [PMID: 23527852 DOI: 10.1021/pr400136p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Apolipoprotein-CIII (apoCIII) is an abundant blood glycoprotein associated with lipoprotein particles. Three different glycoforms have been described, all containing a mucin-type core-1 O-glycosylation with either zero, one or two sialic acids. Changes in the relative abundance of these glycoforms have been observed in a variety of different pathologies. In this study, ultrahigh resolution 15T MALDI Fourier transform ion cyclotron resonance (FTICR) MS was used to analyze apoCIII isoforms in serum protein profiles. For this purpose, serum proteins were purified using both a fully automated RPC18-based magnetic bead method and an RPC4 cartridge-based solid phase extraction method. Six new apoCIII isoforms were identified with low-ppm mass measurement errors and ultrahigh precision. These were characterized by more complex glycan moieties that are fucosylated instead of sialylated. To confirm the glycan moiety and localize the glycosylation site, top-down ESI-FTICR-MS/MS and bottom-up LC-ion trap MS/MS were used. A large variation in the presence and abundance of the fucosylated isoforms was found in a set of 96 serum samples. These findings of fucosylated apolipoprotein-CIII isoforms warrant further research to elucidate the implications these glycoforms may have for the plethora of studies where alterations in apoCIII have been linked to the development of many different pathologies.
Collapse
Affiliation(s)
- Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2300 RC, Leiden, The Netherlands.
| | | | | | | | | |
Collapse
|
47
|
Guasch-Vidal B, Estévez J, Dardanelli MS, Soria-Díaz ME, de Córdoba FF, Balog CIA, Manyani H, Gil-Serrano A, Thomas-Oates J, Hensbergen PJ, Deelder AM, Megías M, van Brussel AAN. High NaCl concentrations induce the nod genes of Rhizobium tropici CIAT899 in the absence of flavonoid inducers. Mol Plant Microbe Interact 2013; 26:451-460. [PMID: 23216086 DOI: 10.1094/mpmi-09-12-0213-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The nodulation (nod) genes of Rhizobium tropici CIAT899 can be induced by very low concentrations (micromolar to nanomolar range) of several flavonoid molecules secreted by the roots of leguminous plants under a number of different conditions. Some of these conditions have been investigated and appear to have a great influence on the concentration and the number of different Nod factors, which can induce root nodule primordia and pseudonodules in several leguminous plant roots. In one such condition, we added up to 300 mM NaCl to the induction medium of R. tropici CIAT899 containing the nod gene inducer apigenin. At the higher concentrations of NaCl, larger amounts and more different Nod factors were produced than in the absence of extra NaCl. To our surprise, under control conditions (300 mM NaCl without apigenin), some Nod-factor-like spots were also observed on the thin-layer plates used to detect incorporation of radiolabeled glucosamine into newly synthesized Nod factors. This phenomenon was further investigated with thin-layer plates, fusions of nod genes to the lacZ gene, high-performance liquid chromatography, mass spectrometry, and the formation of pseudonodules on bean roots. Here, we report that, in the absence of flavonoid inducers, high concentrations of NaCl induced nod genes and the production of Nod factors.
Collapse
Affiliation(s)
- B Guasch-Vidal
- Departamento de Microbiologia, Universidad de Sevilla, Sevilla, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Jones EA, Schmitz N, Waaijer CJF, Frese CK, van Remoortere A, van Zeijl RJM, Heck AJR, Hogendoorn PCW, Deelder AM, Altelaar AFM, Bovée JVMG, McDonnell LA. Imaging Mass Spectrometry-based Molecular Histology Differentiates Microscopically Identical and Heterogeneous Tumors. J Proteome Res 2013; 12:1847-55. [DOI: 10.1021/pr301190g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Emrys A. Jones
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nicole Schmitz
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Christian K. Frese
- Biomolecular Mass Spectrometry
and Proteomics Group, Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Alexandra van Remoortere
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - René J. M. van Zeijl
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry
and Proteomics Group, Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - André M. Deelder
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular Mass Spectrometry
and Proteomics Group, Bijvoet Center for Biomolecular Research and
Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Liam A. McDonnell
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
49
|
Kempers AC, Scherer HU, Rombouts Y, Ewing E, Stadt LAVD, Selman MHJ, Deelder AM, Huizinga TWJ, Wuhrer M, Schaardenburg DV, Toes REM. A1.1 Anti-Citrullinated Protein Antibody Specific Fc Glycosylation Patterns in Arthralgia Patients. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-203214.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
50
|
Nicolardi S, van der Burgt YEM, Wuhrer M, Deelder AM. Mapping O-glycosylation of apolipoprotein C-III in MALDI-FT-ICR protein profiles. Proteomics 2013; 13:992-1001. [PMID: 23335445 DOI: 10.1002/pmic.201200293] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/29/2012] [Accepted: 10/23/2012] [Indexed: 01/10/2023]
Abstract
Ultrahigh resolution MALDI-FT-ICR profiles were obtained from human serum samples that were processed using a fully automated RPC18-based magnetic bead method. Proteins were profiled from m/z value 6630 with a resolving power of 73 000 up to m/z value 12 600 with a resolving power of 37 000. In this study, a detailed evaluation was performed of the isoforms of apolipoprotein C-III, i.e. the different mucin-type core 1 O-glycans with the addition of one or two sialic acid residues. The MALDI-FT-ICR profiles are discussed with regard to reproducibility of the signal intensities as well as the accurate mass measurements. ESI-FT-ICR-MS/MS analyses of the same serum samples were performed to confirm the identity of apolipoprotein C-III glycoforms.
Collapse
Affiliation(s)
- Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | | | | |
Collapse
|