Reliability of Human Serum Protein Profiles Generated with C8 Magnetic Beads Assisted Maldi-TOF Mass Spectrometry
Protein profiling with mass spectrometry is a promising approach for classification and identification of biomarkers; however, there is debate about measurement quality and reliability. Here, we present a pipeline for preprocessing, statistical data analysis and presentation. Serum samples of 16 hea...
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| Veröffentlicht in: | Analytical chemistry (Washington) 2005-11, Vol.77 (22), p.7232-7241 |
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| container_title | Analytical chemistry (Washington) |
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| creator | de Noo, Mirre E Tollenaar, Rob A. E. M Özalp, Aliye Kuppen, Peter J. K Bladergroen, Marco R Eilers, Paul H. C Deelder, André M |
| description | Protein profiling with mass spectrometry is a promising approach for classification and identification of biomarkers; however, there is debate about measurement quality and reliability. Here, we present a pipeline for preprocessing, statistical data analysis and presentation. Serum samples of 16 healthy individuals are used to generate protein profiles with high-resolution MALDI-TOF after isolation of peptides with C8 magnetic beads. Analysis of variance was performed after binning, baseline correction and normalization of the mean spectra. Relative variations in the spectra are expressed as coefficient of variation, which depending on the respective preanalytical variation parameter investigated, was found to range between 0.15 and 0.67 in this study. With this novel method, the reproducibility of our protein profiling procedure could be quantified. We showed that circadian rhythm and the number of freeze−thaw cycles had relatively limited influence on serum protein profiles, whereas the period between collection and serum centrifugation had a more pronounced effect. |
| doi_str_mv | 10.1021/ac050571f |
| format | Article |
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E. M ; Özalp, Aliye ; Kuppen, Peter J. K ; Bladergroen, Marco R ; Eilers, Paul H. C ; Deelder, André M</creator><creatorcontrib>de Noo, Mirre E ; Tollenaar, Rob A. E. M ; Özalp, Aliye ; Kuppen, Peter J. K ; Bladergroen, Marco R ; Eilers, Paul H. C ; Deelder, André M</creatorcontrib><description>Protein profiling with mass spectrometry is a promising approach for classification and identification of biomarkers; however, there is debate about measurement quality and reliability. Here, we present a pipeline for preprocessing, statistical data analysis and presentation. Serum samples of 16 healthy individuals are used to generate protein profiles with high-resolution MALDI-TOF after isolation of peptides with C8 magnetic beads. Analysis of variance was performed after binning, baseline correction and normalization of the mean spectra. Relative variations in the spectra are expressed as coefficient of variation, which depending on the respective preanalytical variation parameter investigated, was found to range between 0.15 and 0.67 in this study. With this novel method, the reproducibility of our protein profiling procedure could be quantified. 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Analysis of variance was performed after binning, baseline correction and normalization of the mean spectra. Relative variations in the spectra are expressed as coefficient of variation, which depending on the respective preanalytical variation parameter investigated, was found to range between 0.15 and 0.67 in this study. With this novel method, the reproducibility of our protein profiling procedure could be quantified. We showed that circadian rhythm and the number of freeze−thaw cycles had relatively limited influence on serum protein profiles, whereas the period between collection and serum centrifugation had a more pronounced effect.</description><subject>Analytical chemistry</subject><subject>Carbon - chemistry</subject><subject>Chemistry</subject><subject>Circadian Rhythm</subject><subject>Exact sciences and technology</subject><subject>Humans</subject><subject>Magnetics</subject><subject>Mass spectrometry</subject><subject>Protein Array Analysis - methods</subject><subject>Proteins</subject><subject>Reproducibility of Results</subject><subject>Spectrometric and optical methods</subject><subject>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</subject><issn>0003-2700</issn><issn>1520-6882</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc2LFDEQxYMo7rh68B-QICh4aE2lP5I-roMzq-yyizOeQ3W6oln7YzbpRue_t5sZdkAPnqqgfjxevcfYSxDvQUj4gFbkIlfgHrEF5FIkhdbyMVsIIdJEKiHO2LMY74QAEFA8ZWdQSJ0XSizY_VdqPFa-8cOe945fji12fENhbPlt6Afy3TydbyjyNXUUcKCa__LDD77U_Bq_dzR4yz8S1pFfxOjjfL_GpvbJ9mY1bTHyzY7sEPqWhrB_zp44bCK9OM5z9m31abu8TK5u1p-XF1cJZmk5JKlSWeEAS5sJZ620wpIEq0BpiVnlSOdVDQ6yElyqckwVgq5SVFSpXAuZnrO3B91d6O9HioNpfbTUNNhRP0ZTaFXqDNL_glCmWmX5rPj6L_CuH0M3PWHkZEsXUmYT9O4A2dDHGMiZXfAthr0BYea2zENbE_vqKDhWLdUn8ljPBLw5AhgtNi5gZ308cUpO3vTsLDlwc_q_H-4YfppCTemY7e3GKFiuV2K9MV9Oumjj6Yl_Df4BHDK1xg</recordid><startdate>20051115</startdate><enddate>20051115</enddate><creator>de Noo, Mirre E</creator><creator>Tollenaar, Rob A. 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| subjects | Analytical chemistry Carbon - chemistry Chemistry Circadian Rhythm Exact sciences and technology Humans Magnetics Mass spectrometry Protein Array Analysis - methods Proteins Reproducibility of Results Spectrometric and optical methods Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods |
| title | Reliability of Human Serum Protein Profiles Generated with C8 Magnetic Beads Assisted Maldi-TOF Mass Spectrometry |
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