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

Baiwir, Dominique; Mazzucchelli, Gabriel; Smargiasso, Nicolas; QUESADA CALVO, Florence; De Pauw, Edwin; MALAISE, Michel; Louis, Edouard; MEUWIS, Marie-Alice

doi:10.1016/j.euprot.2015.07.009

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

Baiwir, Dominique; Mazzucchelli, Gabriel; Smargiasso, Nicolas et al.

2015 • In EuPA Open Proteomics, 9, p. 14-22

Peer Reviewed verified by ORBi

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https://hdl.handle.net/2268/185851

DOI
10.1016/j.euprot.2015.07.009

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Keywords :

Serum prefractionnation; Repeatability; Label-free Proteomics; Data Independent; DEpletion; Equalization

Abstract :

[en] 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.

Disciplines :

Human health sciences: Multidisciplinary, general & others
Chemistry
Biochemistry, biophysics & molecular biology

Author, co-author :

Baiwir, Dominique ; Université de Liège > GIGA-Management : Plate-forme protéomique

Mazzucchelli, Gabriel ; Université de Liège > Center for Analytical Research and Technology (CART)

Smargiasso, Nicolas ; Université de Liège > Département de chimie (sciences) > Laboratoire de spectrométrie de masse (L.S.M.)

QUESADA CALVO, Florence ; Centre Hospitalier Universitaire de Liège - CHU > Gastro-Entérologie-Hépatologie

De Pauw, Edwin ; Université de Liège > Département de chimie (sciences) > Laboratoire de spectrométrie de masse (L.S.M.)

MALAISE, Michel ; Centre Hospitalier Universitaire de Liège - CHU > Rhumatologie

Louis, Edouard ; Université de Liège > Département des sciences cliniques > Hépato-gastroentérologie

MEUWIS, Marie-Alice ; Centre Hospitalier Universitaire de Liège - CHU > Gastro-Entérologie-Hépatologie

Language :

English

Title :

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

Publication date :

December 2015

Journal title :

EuPA Open Proteomics

eISSN :

2212-9685

Publisher :

Elsevier

Volume :

Pages :

14-22

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

http://dx.doi.org/10.1016/j.euprot.2015.07.009

Available on ORBi :

since 12 September 2015

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Bibliography

Polanski M., Anderson N.L. A list of candidate cancer biomarkers for targeted proteomics. Biomark. Insights 2007, 1:1-48.
Pernemalm M., Lewensohn R., Lehtio J. Affinity prefractionation for MS-based plasma proteomics. Proteomics 2009, 9:1420-1427.
Anderson N.L., Anderson N.G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1:845-867.
Keidel E.M., Ribitsch D., Lottspeich F. Equalizer technology-equal rights for disparate beads. Proteomics 2010, 10:2089-2098.
Domon B., Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 2010, 28:710-721.
Whiteaker J.R., Zhang H., Eng J.K., Fang R., Piening B.D., Feng L.C., et al. Head-to-head comparison of serum fractionation techniques. J. Proteome Res. 2007, 6:828-836.
Geromanos S.J., Vissers J.P., Silva J.C., Dorschel C.A., Li G.Z., Gorenstein M.V., et al. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009, 9:1683-1695.
Li G.Z., Vissers J.P., Silva J.C., Golick D., Gorenstein M.V., Geromanos S.J. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 2009, 9:1696-1719.
Choi Y.S. Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome. Arch. Pharm. Res. 2012, 35:1861-1870.
Zhang Q., Faca V., Hanash S. Mining the plasma proteome for disease applications across seven logs of protein abundance. J. Proteome Res. 2011, 10:46-50.
Huang L., Fang X. Immunoaffinity fractionation of plasma proteins by chicken IgY antibodies. Methods Mol. Biol. 2008, 425:41-51.
Smith M.P., Wood S.L., Zougman A., Ho J.T., Peng J., Jackson D., et al. A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics 2011, 11:2222-2235.
Tu C., Rudnick P.A., Martinez M.Y., Cheek K.L., Stein S.E., Slebos R.J., et al. Depletion of abundant plasma proteins and limitations of plasma proteomics. J. Proteome Res. 2010, 9:4982-4991.
Qian W.J., Kaleta D.T., Petritis B.O., Jiang H., Liu T., Zhang X., et al. Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy. Mol. Cell. Proteomics 2008, 7:1963-1973.
Shi T., Zhou J.Y., Gritsenko M.A., Hossain M., Camp 2nd D.G., Smith R.D., et al. IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomics biomarker discovery. Methods 2012, 56:246-253.
Righetti P.G., Boschetti E., Lomas L., Citterio A. Protein equalizer technology: the quest for a democratic proteome. Proteomics 2006, 6:3980-3992.
Righetti P.G., Boschetti E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass Spectrom. Rev. 2008, 27:596-608.
Sihlbom C., Kanmert I., Bahr H., Davidsson P. Evaluation of the combination of bead technology with SELDI-TOF-MS and 2-D DIGE for detection of plasma proteins. J. Proteome Res. 2008, 7:4191-4198.
Guerrier L., Claverol S., Fortis F., Rinalducci S., Timperio A.M., Antonioli P., et al. Exploring the platelet proteome via combinatorial, hexapeptide ligand libraries. J. Proteome Res. 2007, 6:4290-4303.
Dwivedi R.C., Krokhin O.V., Cortens J.P., Wilkins J.A. Assessment of the reproducibility of random hexapeptide peptide library-based protein normalization. J. Proteome Res. 2010, 1144-1149.
Rivers J., Hughes C., McKenna T., Woolerton Y., Vissers J.P., Langridge J.I., et al. Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library. PLoS One 2011, 6:e28902.
Bandow J.E. Comparison of protein enrichment strategies for proteome analysis of plasma. Proteomics 2010, 10:1416-1425.
De Bock M., de Seny D., Meuwis M.A., Servais A.C., Minh T.Q., Closset J., et al. Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis. Talanta 2010, 82:245-254.
Echan L.A., Tang H.Y., Ali-Khan N., Lee K., Speicher D.W. Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics 2005, 5:3292-3303.
Cao Z., Tang H.Y., Wang H., Liu Q., Speicher D.W. Systematic comparison of fractionation methods for in-depth analysis of plasma proteomes. J. Proteome Res. 2012.
Liebler D.C., Ham A.J. Spin filter-based sample preparation for shotgun proteomics. Nat. Methods 2009, 6:785.
Hakimi A., Auluck J., Jones G.D., Ng L.L., Jones D.J. Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label-free quantitative data-independent LC-MS. Proteomics 2013.
Fleron M., Greffe Y., Musmeci D., Massart A.C., Hennequiere V., Mazzucchelli G., et al. Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis. J. Proteomics 2010, 73:1986-2005.
Silva J.C., Denny R., Dorschel C., Gorenstein M.V., Li G.Z., Richardson K., et al. Simultaneous qualitative and quantitative analysis of the E. coli proteome: a sweet tale. Mol. Cell. Proteomics 2006, 5:589-607.
Silva J.C., Gorenstein M.V., Li G.Z., Vissers J.P., Geromanos S.J. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5:144-156.
Vissers J.P., Langridge J.I., Aerts J.M. Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol. Cell. Proteomics 2007, 6:755-766.
Urbas L., Brne P., Gabor B., Barut M., Strlic M., Petric T.C., et al. Depletion of high-abundance proteins from human plasma using a combination of an affinity and pseudo-affinity column. J. Chromatogr. A 2009, 1216:2689-2694.
Tang K., et al. Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 2004, 15(10):1416-1423.
Guerrier L., Righetti P.G., Boschetti E. Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library. Nat. Protoc. 2008, 3:883-890.
Blanton D., Han Z., Bierschenk L., Linga-Reddy M.V., Wang H., Clare-Salzler M., et al. Reduced serum vitamin D-binding protein levels are associated with type 1 diabetes. Diabetes 2011, 60:2566-2570.
Hortin G.L., Sviridov D., Anderson N.L. High-abundance polypeptides of the human plasma proteome comprising the top 4 logs of polypeptide abundance. Clin. Chem. 2008, 54:1608-1616.
Haab B.B., Geierstanger B.H., Michailidis G., Vitzthum F., Forrester S., Okon R., et al. Immunoassay and antibody microarray analysis of the HUPO plasma proteome project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics 2005, 5:3278-3291.
Farrah T., Deutsch E.W., Omenn G.S., Campbell D.S., Sun Z., Bletz J.A., et al. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell. Proteomics 2011, 10:M110.6353.