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Sánchez-López E, Kammeijer GSM, Crego AL, Marina ML, Ramautar R, Peters DJM, Mayboroda OA. Sheathless CE-MS based metabolic profiling of kidney tissue section samples from a mouse model of Polycystic Kidney Disease. Sci Rep 2019; 9:806. [PMID: 30692602 PMCID: PMC6349881 DOI: 10.1038/s41598-018-37512-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 07/30/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022] Open
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) using a sheathless porous tip interface emerged as an attractive tool in metabolomics thanks to its numerous advantages. One of the main advantages compared to the classical co-axial sheath liquid interface is the increased sensitivity, while maintaining the inherent properties of CE, such as a high separation efficiency and low sample consumption. Specially, the ability to perform nanoliter-based injections from only a few microliters of material in the sample vial makes sheathless CE-MS a well-suited and unique approach for highly sensitive metabolic profiling of limited sample amounts. Therefore, in this work, we demonstrate the utility of sheathless CE-MS for metabolic profiling of biomass-restricted samples, namely for 20 µm-thick tissue sections of kidney from a mouse model of polycystic kidney disease (PKD). The extraction method was designed in such a way to keep a minimum sample-volume in the injection vial, thereby still allowing multiple nanoliter injections for repeatability studies. The developed strategy enabled to differentiate between different stages of PKD and as well changes in a variety of different metabolites could be annotated over experimental groups. These metabolites include carnitine, glutamine, creatine, betaine and creatinine. Overall, this study shows the utility of sheathless CE-MS for biomass-limited metabolomics studies.
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Affiliation(s)
- Elena Sánchez-López
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Madrid, Spain
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Antonio L Crego
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Madrid, Spain
| | - María Luisa Marina
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Madrid, Spain
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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2
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Clerc F, Novokmet M, Dotz V, Reiding KR, de Haan N, Kammeijer GSM, Dalebout H, Bladergroen MR, Vukovic F, Rapp E, Targan SR, Barron G, Manetti N, Latiano A, McGovern DPB, Annese V, Lauc G, Wuhrer M. Plasma N-Glycan Signatures Are Associated With Features of Inflammatory Bowel Diseases. Gastroenterology 2018; 155:829-843. [PMID: 29792883 DOI: 10.1053/j.gastro.2018.05.030] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [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: 08/18/2017] [Revised: 04/07/2018] [Accepted: 05/15/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Biomarkers are needed for early detection of Crohn's disease (CD) and ulcerative colitis (UC) or to predict patient outcomes. Glycosylation is a common and complex posttranslational modification of proteins that affects their structure and activity. We compared plasma N-glycosylation profiles between patients with CD or UC and healthy individuals (controls). METHODS We analyzed the total plasma N-glycomes of 2635 patients with inflammatory bowel diseases and 996 controls by mass spectrometry with a linkage-specific sialic acid derivatization technique. Plasma samples were acquired from 2 hospitals in Italy (discovery cohort, 1989 patients with inflammatory bowel disease [IBD] and 570 controls) and 1 medical center in the United States (validation cohort, 646 cases of IBD and 426 controls). Sixty-three glycoforms met our criteria for relative quantification and were extracted from the raw data with the software MassyTools. Common features shared by the glycan compositions were combined in 78 derived traits, including the number of antennae of complex-type glycans and levels of fucosylation, bisection, galactosylation, and sialylation. Associations of plasma N-glycomes with age, sex, CD, UC, and IBD-related parameters such as disease location, surgery and medication, level of C-reactive protein, and sedimentation rate were tested by linear and logistic regression. RESULTS Plasma samples from patients with IBD had a higher abundance of large-size glycans compared with controls, a decreased relative abundance of hybrid and high-mannose structures, lower fucosylation, lower galactosylation, and higher sialylation (α2,3- and α2,6-linked). We could discriminate plasma from patients with CD from that of patients with UC based on higher bisection, lower galactosylation, and higher sialylation (α2,3-linked). Glycosylation patterns were associated with disease location and progression, the need for a more potent medication, and surgery. These results were replicated in a large independent cohort. CONCLUSIONS We performed high-throughput analysis to compare total plasma N-glycomes of individuals with vs without IBD and to identify patterns associated with disease features and the need for treatment. These profiles might be used in diagnosis and for predicting patients' responses to treatment.
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Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Viktoria Dotz
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Marco R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Frano Vukovic
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; glyXera GmbH, Magdeburg, Germany
| | | | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gildardo Barron
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Natalia Manetti
- Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy
| | - Anna Latiano
- Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Vito Annese
- Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy; Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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Abstract
The concentration of prostate-specific antigen (PSA) in serum is used as an early detection method of prostate cancer (PCa); however, it shows low sensitivity, specificity, and a poor predictive value. Initial studies suggested the glycosylation of PSA to be a promising marker for a more specific yet noninvasive PCa diagnosis. Recent studies on the molecular features of PSA glycosylation (such as antenna modification and core fucosylation) were not successful in demonstrating its potential for an improved PCa diagnosis, probably due to the lack of analytical sensitivity and specificity of the applied assays. In this study, we established for the first time a high-performance PSA Glycomics Assay (PGA), allowing differentiation of α2,6- and α2,3-sialylated isomers, the latter one being suggested to be a hallmark of aggressive types of cancer. After affinity purification from urine and tryptic digestion, PSA samples were analyzed by CE-ESI-MS (capillary electrophoresis-electrospray ionization coupled to mass spectrometry). Based on positive controls, an average interday relative standard deviation of 14% for 41 N-glycopeptides was found. The assay was further verified by analyzing PSA captured from patients' urine samples. A total of 67 N-glycopeptides were identified from the PSA pooled from the patients. In summary, the first PGA successfully established in this study allows an in-depth relative quantitation of PSA glycoforms from urine. The PGA is a promising tool for the determination of potential glycomic biomarkers for the differentiation between aggressive PCa, indolent PCa, and benign prostate hyperplasia in larger cohort studies.
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Affiliation(s)
- Guinevere S M Kammeijer
- Leiden University Medical Center , Center for Proteomics and Metabolomics , 2300 RC Leiden , The Netherlands
| | - Jan Nouta
- Leiden University Medical Center , Center for Proteomics and Metabolomics , 2300 RC Leiden , The Netherlands
| | | | - Theo M de Reijke
- Academic Medical Center , Department of Urology , 1105 AZ Amsterdam , The Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center , Center for Proteomics and Metabolomics , 2300 RC Leiden , The Netherlands
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Kammeijer GSM, Kohler I, Jansen BC, Hensbergen PJ, Mayboroda OA, Falck D, Wuhrer M. Dopant Enriched Nitrogen Gas Combined with Sheathless Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Improved Sensitivity and Repeatability in Glycopeptide Analysis. Anal Chem 2016; 88:5849-56. [PMID: 27119460 DOI: 10.1021/acs.analchem.6b00479] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the last years, numerous strategies have been proposed to enhance both ionization efficiency and spray stability in electrospray ionization (ESI), in particular for nanospray applications. In nano-liquid chromatography-mass spectrometry (nano-LC-ESI-MS), a better ESI performance has been observed when a coaxial gas flow is added around the ESI emitter. Moreover, enrichment of the gas with an organic dopant has led to an improved desolvation and ionization efficiency with an overall enhanced sensitivity. In this study, the use of a dopant enriched nitrogen (DEN)-gas combined with sheathless capillary electrophoresis (CE)-ESI-MS was evaluated for glycopeptide analysis. Using acetonitrile as a dopant, an increased sensitivity was observed compared to conventional sheathless CE-ESI-MS. Up to 25-fold higher sensitivities for model glycopeptides were obtained, allowing for limits of detection unachieved by state-of-the-art nano-LC-ESI-MS. The effect of DEN-gas on the repeatability and intermediate precision was also investigated. When compared to previously reported nano-LC-ESI-MS measurements, similar values were found for CE-ESI-MS with DEN-gas. The enhanced repeatability fosters the use of DEN-gas sheathless CE-ESI-MS in protein glycosylation analysis, where precision is essential. The use of DEN-gas opens new avenues for highly sensitive sheathless CE-ESI-MS approaches in glycoproteomics research, by significantly improving sensitivity and precision.
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Affiliation(s)
- Guinevere S M Kammeijer
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Isabelle Kohler
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Bas C Jansen
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Paul J Hensbergen
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Oleg A Mayboroda
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - David Falck
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center , Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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Jansen BC, Bondt A, Reiding KR, Lonardi E, de Jong CJ, Falck D, Kammeijer GSM, Dolhain RJEM, Rombouts Y, Wuhrer M. Pregnancy-associated serum N-glycome changes studied by high-throughput MALDI-TOF-MS. Sci Rep 2016; 6:23296. [PMID: 27075729 PMCID: PMC4831011 DOI: 10.1038/srep23296] [Citation(s) in RCA: 44] [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] [Received: 12/16/2015] [Accepted: 02/15/2016] [Indexed: 01/30/2023] Open
Abstract
Pregnancy requires partial suppression of the immune system to ensure maternal-foetal tolerance. Protein glycosylation, and especially terminal sialic acid linkages, are of prime importance in regulating the pro- and anti-inflammatory immune responses. However, little is known about pregnancy-associated changes of the serum N-glycome and sialic acid linkages. Using a combination of recently developed methods, i.e. derivatisation that allows the distinction between α2,3- and α2,6-linked sialic acids by high-throughput MALDI-TOF-MS and software-assisted data processing, we analysed the serum N-glycome of a cohort of 29 healthy women at 6 time points during and after pregnancy. A total of 77 N-glycans were followed over time, confirming in part previous findings while also revealing novel associations (e.g. an increase of FA2BG1S1(6), FA2G1S1(6) and A2BG2S2(6) with delivery). From the individual glycans we calculated 42 derived traits. With these, an increase during pregnancy and decrease after delivery was observed for both α2,3- and α2,6-linked sialylation. Additionally, a difference in the recovery speed after delivery was observed for α2,3- and α2,6-linked sialylation of triantennary glycans. In conclusion, our new high-throughput workflow allowed the identification of novel plasma glycosylation changes with pregnancy.
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Affiliation(s)
- Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Albert Bondt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.,Department of Rheumatology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Emanuela Lonardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Coen J de Jong
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- 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
| | - Yoann Rombouts
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.,Univ. Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F 59 000 Lille, France
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Clerc F, Reiding KR, Jansen BC, Kammeijer GSM, Bondt A, Wuhrer M. Human plasma protein N-glycosylation. Glycoconj J 2015; 33:309-43. [PMID: 26555091 PMCID: PMC4891372 DOI: 10.1007/s10719-015-9626-2] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/30/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
Abstract
Glycosylation is the most abundant and complex protein modification, and can have a profound structural and functional effect on the conjugate. The oligosaccharide fraction is recognized to be involved in multiple biological processes, and to affect proteins physical properties, and has consequentially been labeled a critical quality attribute of biopharmaceuticals. Additionally, due to recent advances in analytical methods and analysis software, glycosylation is targeted in the search for disease biomarkers for early diagnosis and patient stratification. Biofluids such as saliva, serum or plasma are of great use in this regard, as they are easily accessible and can provide relevant glycosylation information. Thus, as the assessment of protein glycosylation is becoming a major element in clinical and biopharmaceutical research, this review aims to convey the current state of knowledge on the N-glycosylation of the major plasma glycoproteins alpha-1-acid glycoprotein, alpha-1-antitrypsin, alpha-1B-glycoprotein, alpha-2-HS-glycoprotein, alpha-2-macroglobulin, antithrombin-III, apolipoprotein B-100, apolipoprotein D, apolipoprotein F, beta-2-glycoprotein 1, ceruloplasmin, fibrinogen, immunoglobulin (Ig) A, IgG, IgM, haptoglobin, hemopexin, histidine-rich glycoprotein, kininogen-1, serotransferrin, vitronectin, and zinc-alpha-2-glycoprotein. In addition, the less abundant immunoglobulins D and E are included because of their major relevance in immunology and biopharmaceutical research. Where available, the glycosylation is described in a site-specific manner. In the discussion, we put the glycosylation of individual proteins into perspective and speculate how the individual proteins may contribute to a total plasma N-glycosylation profile determined at the released glycan level.
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Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Albert Bondt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands. .,Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands.
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7
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Plomp R, Dekkers G, Rombouts Y, Visser R, Koeleman CAM, Kammeijer GSM, Jansen BC, Rispens T, Hensbergen PJ, Vidarsson G, Wuhrer M. Hinge-Region O-Glycosylation of Human Immunoglobulin G3 (IgG3). Mol Cell Proteomics 2015; 14:1373-84. [PMID: 25759508 PMCID: PMC4424406 DOI: 10.1074/mcp.m114.047381] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [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: 12/09/2014] [Indexed: 01/18/2023] Open
Abstract
Immunoglobulin G (IgG) is one of the most abundant proteins present in human serum and a fundamental component of the immune system. IgG3 represents ∼8% of the total amount of IgG in human serum and stands out from the other IgG subclasses because of its elongated hinge region and enhanced effector functions. This study reports partial O-glycosylation of the IgG3 hinge region, observed with nanoLC-ESI-IT-MS(/MS) analysis after proteolytic digestion. The repeat regions within the IgG3 hinge were found to be in part O-glycosylated at the threonine in the triple repeat motif. Non-, mono- and disialylated core 1-type O-glycans were detected in various IgG3 samples, both poly- and monoclonal. NanoLC-ESI-IT-MS/MS with electron transfer dissociation fragmentation and CE-MS/MS with CID fragmentation were used to determine the site of IgG3 O-glycosylation. The O-glycosylation site was further confirmed by the recombinant production of mutant IgG3 in which potential O-glycosylation sites had been knocked out. For IgG3 samples from six donors we found similar O-glycan structures and site occupancies, whereas for the same samples the conserved N-glycosylation of the Fc CH2 domain showed considerable interindividual variation. The occupancy of each of the three O-glycosylation sites was found to be ∼10% in six serum-derived IgG3 samples and ∼13% in two monoclonal IgG3 allotypes.
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Affiliation(s)
- Rosina Plomp
- From the ‡Center for Proteomics and Metabolomics
| | | | - Yoann Rombouts
- From the ‡Center for Proteomics and Metabolomics, §Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Bas C Jansen
- From the ‡Center for Proteomics and Metabolomics
| | - Theo Rispens
- ¶¶Department of Immunopathology, Sanquin Research, and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - Manfred Wuhrer
- From the ‡Center for Proteomics and Metabolomics, **Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
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