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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] [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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D’Aguanno S, D’Alessandro A, Pieroni L, Roveri A, Zaccarin M, Marzano V, Canio MD, Bernardini S, Federici G, Urbani A. New Insights into Neuroblastoma Cisplatin Resistance: A Comparative Proteomic and Meta-Mining Investigation. J Proteome Res 2010; 10:416-28. [DOI: 10.1021/pr100457n] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simona D’Aguanno
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Annamaria D’Alessandro
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Luisa Pieroni
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Antonella Roveri
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Mattia Zaccarin
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Valeria Marzano
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Michele De Canio
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Sergio Bernardini
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Giorgio Federici
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Andrea Urbani
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
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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] [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, Lamers RJAN, Burgers PC, Sillevis Smitt PAE, Hintzen RQ, Luider TM. The Rate of False Positive Sequence Matches of Peptides Profiled by MALDI MS and Identified by MS/MS. J Proteome Res 2008; 7:4841-7. [DOI: 10.1021/pr800489a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel P. Stoop
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Robert-Jan A. N. Lamers
- 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
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