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Titulaer MK, de Costa D, Stingl C, Dekker LJ, Sillevis Smitt PAE, Luider TM. Label-free peptide profiling of Orbitrap™ full mass spectra. BMC Res Notes 2011; 4:21. [PMID: 21272362 PMCID: PMC3042405 DOI: 10.1186/1756-0500-4-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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: 09/25/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We developed a new version of the open source software package Peptrix that can yet compare large numbers of Orbitrap™ LC-MS data. The peptide profiling results for Peptrix on MS1 spectra were compared with those obtained from a small selection of open source and commercial software packages: msInspect, Sieve™ and Progenesis™. The properties compared in these packages were speed, total number of detected masses, redundancy of masses, reproducibility in numbers and CV of intensity, overlap of masses, and differences in peptide peak intensities. Reproducibility measurements were taken for the different MS1 software applications by measuring in triplicate a complex peptide mixture of immunoglobulin on the Orbitrap™ mass spectrometer. Values of peptide masses detected from the high intensity peaks of the MS1 spectra by peptide profiling were verified with values of the MS2 fragmented and sequenced masses that resulted in protein identifications with a significant score. FINDINGS Peptrix finds about the same number of peptide features as the other packages, but peptide masses are in some cases approximately 5 to 10 times less redundant present in the peptide profile matrix. The Peptrix profile matrix displays the largest overlap when comparing the number of masses in a pair between two software applications. The overlap of peptide masses between software packages of low intensity peaks in the spectra is remarkably low with about 50% of the detected masses in the individual packages. Peptrix does not differ from the other packages in detecting 96% of the masses that relate to highly abundant sequenced proteins. MS1 peak intensities vary between the applications in a non linear way as they are not processed using the same method. CONCLUSIONS Peptrix is capable of peptide profiling using Orbitrap™ files and finding differential expressed peptides in body fluid and tissue samples. The number of peptide masses detected in Orbitrap™ files can be increased by using more MS1 peptide profiling applications, including Peptrix, since it appears from the comparison of Peptrix with the other applications that all software packages have likely a high false negative rate of low intensity peptide peaks (missing peptides).
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Affiliation(s)
- Mark K Titulaer
- Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Academic Medical Center, University of Amsterdam, Meibergdreef 9, P.O. Box 22660, 1100 DD Amsterdam, The Netherlands
| | - Dominique de Costa
- Department of Pulmonology, Erasmus University Medical Center, Dr. Molewaterplein 50, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Christoph Stingl
- Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Lennard J Dekker
- Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Peter AE Sillevis Smitt
- Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Theo M Luider
- Laboratory of Neuro-Oncology and Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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Alves RDAM, Eijken M, Swagemakers S, Chiba H, Titulaer MK, Burgers PC, Luider TM, van Leeuwen JPTM. Proteomic analysis of human osteoblastic cells: relevant proteins and functional categories for differentiation. J Proteome Res 2011; 9:4688-700. [PMID: 20690663 DOI: 10.1021/pr100400d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Osteoblasts are the bone forming cells, capable of secreting an extracellular matrix with mineralization potential. The exact mechanism by which osteoblasts differentiate and form a mineralized extracellular matrix is presently not fully understood. To increase our knowledge about this process, we conducted proteomics analysis in human immortalized preosteoblasts (SV-HFO) able to differentiate and mineralize. We identified 381 proteins expressed during the time course of osteoblast differentiation. Gene ontology analysis revealed an overrepresentation of protein categories established as important players for osteoblast differentiation, bone formation, and mineralization such as pyrophosphatases. Proteins involved in antigen presentation, energy metabolism and cytoskeleton rearrangement constitute other overrepresented processes, whose function, albeit interesting, is not fully understood in the context of osteoblast differentiation and bone formation. Correlation analysis, based on quantitative data, revealed a biphasic osteoblast differentiation, encompassing a premineralization and a mineralization period. Identified differentially expressed proteins between mineralized and nonmineralized cells include cytoskeleton (e.g., CCT2, PLEC1, and FLNA) and extracellular matrix constituents (FN1, ANXA2, and LGALS1) among others. FT-ICR-MS data obtained for FN1, ANXA2, and LMNA shows a specific regulation of these proteins during the different phases of osteoblast differentiation. Taken together, this study increases our understanding of the proteomics changes that accompany osteoblast differentiation and may permit the discovery of novel modulators of bone formation.
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Affiliation(s)
- Rodrigo D A M Alves
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
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Dekker LJM, Burgers PC, Charif H, van Rijswijk ALCT, Titulaer MK, Jenster G, Bischoff R, Bangma CH, Luider TM. Differential expression of protease activity in serum samples of prostate carcinoma patients with metastases. Proteomics Clin Appl 2010. [DOI: 10.1002/prca.201090067] [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: 11/11/2022]
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Stoop MP, Singh V, Dekker LJ, Titulaer MK, Stingl C, Burgers PC, Sillevis Smitt PAE, Hintzen RQ, Luider TM. Proteomics comparison of cerebrospinal fluid of relapsing remitting and primary progressive multiple sclerosis. PLoS One 2010; 5:e12442. [PMID: 20805994 PMCID: PMC2929207 DOI: 10.1371/journal.pone.0012442] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [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: 04/13/2010] [Accepted: 08/03/2010] [Indexed: 01/16/2023] Open
Abstract
Background Based on clinical representation of disease symptoms multiple sclerosis (MScl) patients can be divided into two major subtypes; relapsing remitting (RR) MScl (85–90%) and primary progressive (PP) MScl (10–15%). Proteomics analysis of cerebrospinal fluid (CSF) has detected a number of proteins that were elevated in MScl patients. Here we specifically aimed to differentiate between the PP and RR subtypes of MScl by comparing CSF proteins. Methodology/Principal Findings CSF samples (n = 31) were handled according to the same protocol for quantitative mass spectrometry measurements we reported previously. In the comparison of PP MScl versus RR MScl we observed a number of differentially abundant proteins, such as protein jagged-1 and vitamin D-binding protein. Protein jagged-1 was over three times less abundant in PP MScl compared to RR MScl. Vitamin D-binding protein was only detected in the RR MScl samples. These two proteins were validated by independent techniques (western blot and ELISA) as differentially abundant in the comparison between both MScl types. Conclusions/Significance The main finding of this comparative study is the observation that the proteome profiles of CSF in PP and RR MScl patients overlap to a large extent. Still, a number of differences could be observed. Protein jagged-1 is a ligand for multiple Notch receptors and involved in the mediation of Notch signaling. It is suggested in literature that the Notch pathway is involved in the remyelination of MScl lesions. Aberration of normal homeostasis of Vitamin D, of which approximately 90% is bound to vitamin D-binding protein, has been widely implicated in MScl for some years now. Vitamin D directly and indirectly regulates the differentiation, activation of CD4+ T-lymphocytes and can prevent the development of autoimmune processes, and so it may be involved in neuroprotective elements in MScl.
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Affiliation(s)
- Marcel P. Stoop
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Vaibhav Singh
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Lennard J. Dekker
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Mark K. Titulaer
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Christoph Stingl
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Peter C. Burgers
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Peter A. E. Sillevis Smitt
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Rogier Q. Hintzen
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Theo M. Luider
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- * E-mail:
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Dekker LJM, Burgers PC, Charif H, van Rijswijk ALCT, Titulaer MK, Jenster G, Bischoff R, Bangma CH, Luider TM. Differential expression of protease activity in serum samples of prostate carcinoma patients with metastases. Proteomics 2010; 10:2348-58. [DOI: 10.1002/pmic.200900682] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Stoop MP, Dekker LJ, Titulaer MK, Lamers RJAN, Burgers PC, Sillevis Smitt PAE, van Gool AJ, Luider TM, Hintzen RQ. Quantitative matrix-assisted laser desorption ionization-fourier transform ion cyclotron resonance (MALDI-FT-ICR) peptide profiling and identification of multiple-sclerosis-related proteins. J Proteome Res 2009; 8:1404-14. [PMID: 19159215 DOI: 10.1021/pr8010155] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance (MALDI-FT-ICR) method for quantitative peptide profiling, using peak height as a measure for abundance. Relative standard deviations in peak height of peptides spiked over 3 orders of magnitude in concentration were below 10% and allowed for accurate comparisons between multiple sclerosis and controls. Application on a set of 163 cerebrospinal fluid (CSF) samples showed significantly differential abundant peptides, which were subsequently identified into proteins (e.g., chromogranin A, clusterin, and complement C3).
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Affiliation(s)
- Marcel P Stoop
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam 3000 DR, The Netherlands
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Carvalho-Oliveira IM, Charro N, Aarbiou J, Buijs-Offerman RM, Wilke M, Schettgen T, Kraus T, Titulaer MK, Burgers P, Luider TM, Penque D, Scholte BJ. Proteomic Analysis of Naphthalene-Induced Airway Epithelial Injury and Repair in a Cystic Fibrosis Mouse Model. J Proteome Res 2009; 8:3606-16. [DOI: 10.1021/pr900021m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Isabel M. Carvalho-Oliveira
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nuno Charro
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jamil Aarbiou
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Ruvalic M. Buijs-Offerman
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martina Wilke
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Thomas Schettgen
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Thomas Kraus
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Mark K. Titulaer
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Peter Burgers
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Theo M. Luider
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Deborah Penque
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Bob J. Scholte
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands, Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, The Netherlands, Institut für Arbeitsmedizin und Sozialmedizin Universitätsklinikum Aachen, and Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
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Stoop MP, Dekker LJ, Titulaer MK, Burgers PC, Sillevis Smitt PAE, Luider TM, Hintzen RQ. Multiple sclerosis-related proteins identified in cerebrospinal fluid by advanced mass spectrometry. Proteomics 2008; 8:1576-85. [PMID: 18351689 DOI: 10.1002/pmic.200700446] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A total of 164 cerebrospinal fluid (CSF) samples taken from neurological patients were classed into four groups according to the clinical diagnosis: multiple sclerosis (MScl, n = 44), clinically isolated syndrome of demyelination (CIS, n = 40), other inflammatory neurological disease (OIND, n = 26) and other neurological disease (OND, n = 54). After tryptic digestion, the samples were measured by MALDI-TOF MS. Spectra were analyzed using the R-project software package, in which a peak detection algorithm was developed. Subsequently, the peak lists were compared based on ranked data (non-parametric). Significant differences were observed in the comparisons of MScl vs. OND and CIS vs. OND. The comparisons of MScl vs. OIND, and CIS vs. OIND showed fewer significant differences. No significant differences were found in comparisons MScl vs. CIS and OIND vs. OND. MScl and CIS had strikingly similar profiles, probably a reflection of common pathological mechanisms. Three differentially expressed proteins in the comparison of MScl vs. OND were identified: chromogranin A, a potential marker for neurodegeneration; and two important factors in complement-mediated inflammatory reaction, clusterin and complement C3. CSF chromogranin A levels were confirmed to be significantly elevated in the MScl group using an ELISA.
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Affiliation(s)
- Marcel P Stoop
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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Titulaer MK, Mustafa DAN, Siccama I, Konijnenburg M, Burgers PC, Andeweg AC, Smitt PAES, Kros JM, Luider TM. A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation. BMC Bioinformatics 2008; 9:133. [PMID: 18312684 PMCID: PMC2323386 DOI: 10.1186/1471-2105-9-133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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: 10/31/2007] [Accepted: 03/01/2008] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A Java application is presented, which compares large numbers (n > 100) of raw FTICR mass spectra from patients and controls. Two peptide profile matrices can be produced simultaneously, one with occurrences of peptide masses in samples and another with the intensity of common peak masses in all the measured samples, using the peak- and background intensities of the raw data. In latter way, more significantly differentially expressed peptides are found between groups than just using the presence or absence in samples of common peak masses. The software application is tested by searching angiogenesis related proteins in glioma by comparing laser capture micro dissected- and enzymatic by trypsin digested tissue sections. RESULTS By hierarchical clustering of the presence-absence matrix, it appears that proteins, such as hemoglobin alpha and delta subunit, fibrinogen beta and gamma chain precursor, tubulin specific chaperone A, epidermal fatty acid binding protein, neutrophil gelatinase-associated lipocalin precursor, peptidyl tRNA hydrolase 2 mitochondrial precursor, placenta specific growth hormone, and zinc finger CCHC domain containing protein 13 are significantly different expressed in glioma vessels. The up-regulated proteins in the glioma vessels with respect to the normal vessels determined by the Wilcoxon-Mann-Whitney test on the intensity matrix are vimentin, glial fibrillary acidic protein, serum albumin precursor, annexin A5, alpha cardiac and beta actin, type I cytoskeletal 10 keratin, calcium binding protein p22, and desmin. Peptide masses of calcium binding protein p22, Cdc42 effector protein 3, fibronectin precursor, and myosin-9 are exclusively present in glioma vessels. Some peptide fragments of non-muscular myosin-9 at the C-terminus are strongly up-regulated in the glioma vessels with respect to the normal vessels. CONCLUSION The less rigorous than in general used commercial propriety software de-isotope algorithm results in more mono-isotopic peptide masses and consequently more proteins. Centroiding of peptide masses takes place by taking the average over more spectra in the profile matrix. Cytoskeleton proteins and proteins involved in the calcium signaling pathway seem to be most up-regulated in glioma vessels. The finding that peptides at the C-terminus of myosin-9 are up-regulated could be ascribed to splicing or fragmentation by proteases.
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Affiliation(s)
- Mark K Titulaer
- Department of Neurology, Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Erasmus Medical Center, Dr, Molewaterplein 50, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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Mustafa DAN, Burgers PC, Dekker LJ, Charif H, Titulaer MK, Smitt PAES, Luider TM, Kros JM. Identification of Glioma Neovascularization-related Proteins by Using MALDI-FTMS and Nano-LC Fractionation to Microdissected Tumor Vessels. Mol Cell Proteomics 2007; 6:1147-57. [PMID: 17360931 DOI: 10.1074/mcp.m600295-mcp200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The identification of angiogenesis-related proteins is important for the development of new antiangiogenic therapies, and such proteins are potential new biomarkers for gliomas. The aim of this study was to identify proteins that are exclusively present in glioma neovasculature and not in the vasculature of normal brain. We combined advanced proteomics techniques to compare the expression profiles of microdissected blood vessels from glioma with blood vessels of normal control brain samples. We measured the enzymatic generated peptide profiles from these microdissected samples by MALDI-FTMS. Subsequently, the samples were fractionated by nano-LC prior to MALDI-TOF/TOF. This combined approach enabled us to identify four proteins that appeared to be exclusively expressed in the glioma blood vessels. Two of these proteins, fibronectin and colligin 2, were validated on tissue sections using specific antibodies. We found that both proteins are present in active angiogenesis in glioma, other neoplasms, and reactive conditions in which neoangiogenesis takes place. This work proves that gel-free mass spectrometric techniques can be used on relatively small numbers of cells generated by microdissection procedures to successfully identify differentially expressed proteins.
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Affiliation(s)
- Dana A N Mustafa
- Department of Pathology, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GD Rotterdam, The Netherlands
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Titulaer MK, Siccama I, Dekker LJ, van Rijswijk ALCT, Heeren RMA, Sillevis Smitt PA, Luider TM. A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls. BMC Bioinformatics 2006; 7:403. [PMID: 16953879 PMCID: PMC1594579 DOI: 10.1186/1471-2105-7-403] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [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: 04/13/2006] [Accepted: 09/05/2006] [Indexed: 11/10/2022] Open
Abstract
Background Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. Results A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. Conclusion The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the higher resolution and mass accuracy of the FT-ICR mass spectrometry prevents the clustering of peaks of different peptides and allows the identification of differentially expressed proteins from the peptide profiles.
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Affiliation(s)
- Mark K Titulaer
- Department of Neurology, Erasmus MC, Dr. Molewaterplein 40, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Ivar Siccama
- Department of Neurology, Erasmus MC, Dr. Molewaterplein 40, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Lennard J Dekker
- Department of Neurology, Erasmus MC, Dr. Molewaterplein 40, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Angelique LCT van Rijswijk
- Department of Urology, Erasmus MC, Dr. Molewaterplein 40, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Ron MA Heeren
- FOM-institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
| | - Peter A Sillevis Smitt
- Department of Neurology, Erasmus MC, Dr. Molewaterplein 40, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus MC, Dr. Molewaterplein 40, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
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