Comparison of serum fractionation methods by data independent label-free proteomics

Comparison of serum fractionation methods by data independent label-free proteomics

Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the prot...

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Main Authors: D. Baiwir, G. Mazzucchelli, N. Smargiasso, F. Quesada-Calvo, E. De Pauw, M. Malaise, E. Louis, M.-A. Meuwis
Format: Article
Language:English
Published: Elsevier 2015-12-01
Series:EuPA Open Proteomics
Online Access:http://www.sciencedirect.com/science/article/pii/S2212968515300118
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spelling doaj-11d6eeee2c4c452db89a11ea336a5a852020-11-24T21:16:07ZengElsevierEuPA Open Proteomics2212-96852015-12-0191422Comparison of serum fractionation methods by data independent label-free proteomicsD. Baiwir0G. Mazzucchelli1N. Smargiasso2F. Quesada-Calvo3E. De Pauw4M. Malaise5E. Louis6M.-A. Meuwis7Proteomic Facility, GIGA, University of Liège, BelgiumLaboratory of Mass Spectrometry, GIGA-R, Chemistry Department, CART, ULg, BelgiumLaboratory of Mass Spectrometry, GIGA-R, Chemistry Department, CART, ULg, BelgiumGastroenterology Department, GIGA-R, Liège University Hospital, CHU-ULg, BelgiumLaboratory of Mass Spectrometry, GIGA-R, Chemistry Department, CART, ULg, BelgiumRheumathology Department, GIGA-R Liège, University Hospital, CHU-ULg, BelgiumGastroenterology Department, GIGA-R, Liège University Hospital, CHU-ULg, BelgiumGastroenterology Department, GIGA-R, Liège University Hospital, CHU-ULg, Belgium; Corresponding author.Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein identifications and 12.2% of reliable quantification were obtained. A 61 times lower limit of protein quantitation was reached compared to protein concentrations observed in raw serum. The concentrations of detected proteins were confronted to estimated reference values. Keywords: Serum prefractionation, Repeatability, Label-free proteomics, Data independent, Depletion, Equalizationhttp://www.sciencedirect.com/science/article/pii/S2212968515300118
collection DOAJ
language English
format Article
sources DOAJ
author D. Baiwir
G. Mazzucchelli
N. Smargiasso
F. Quesada-Calvo
E. De Pauw
M. Malaise
E. Louis
M.-A. Meuwis
spellingShingle D. Baiwir
G. Mazzucchelli
N. Smargiasso
F. Quesada-Calvo
E. De Pauw
M. Malaise
E. Louis
M.-A. Meuwis
Comparison of serum fractionation methods by data independent label-free proteomics
EuPA Open Proteomics
author_facet D. Baiwir
G. Mazzucchelli
N. Smargiasso
F. Quesada-Calvo
E. De Pauw
M. Malaise
E. Louis
M.-A. Meuwis
author_sort D. Baiwir
title Comparison of serum fractionation methods by data independent label-free proteomics
title_short Comparison of serum fractionation methods by data independent label-free proteomics
title_full Comparison of serum fractionation methods by data independent label-free proteomics
title_fullStr Comparison of serum fractionation methods by data independent label-free proteomics
title_full_unstemmed Comparison of serum fractionation methods by data independent label-free proteomics
title_sort comparison of serum fractionation methods by data independent label-free proteomics
publisher Elsevier
series EuPA Open Proteomics
issn 2212-9685
publishDate 2015-12-01
description Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein identifications and 12.2% of reliable quantification were obtained. A 61 times lower limit of protein quantitation was reached compared to protein concentrations observed in raw serum. The concentrations of detected proteins were confronted to estimated reference values. Keywords: Serum prefractionation, Repeatability, Label-free proteomics, Data independent, Depletion, Equalization
url http://www.sciencedirect.com/science/article/pii/S2212968515300118
work_keys_str_mv AT dbaiwir comparisonofserumfractionationmethodsbydataindependentlabelfreeproteomics
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