Journal Articles and Posters

BD™ FFE System

• Cell Organelles
• Proteins, Membrane Proteins and Peptides
• Human Plasma
• Drug Discovery
• Cell Separation
• General Publications
  

• Comparative Human Plasma Peptidome Analysis: P100 vs EDTA
• Comparative Human Plasma Peptidome Analysis: P100 vs Serum
• AQUA Peptide Plasma and Serum Studies
• Mechanical Separator Studies
• Thrombin Studies: Nonspecific Proteolysis Induction in Serum Samples

• AQUA Peptide Plasma and Serum Studies

BD™ FFE System

Cell Organelles

Journal Articles

Zischka H, Larochette N, Hoffmann F, Hamöller D, Jägemann N, Lichtmannegger J, Jennen L, Müller-Höcker J, Roggel F, Göttlicher M, Vollmar AM, Guido Kroemer
“Electrophoretic analysis of the mitochondrial outer membrane rupture induced by permeability transition”
Anal.Chem (2008)

Zischka H, Lichtmannegger J, Jägemann N, Jennen L, Hamöller D, Huber E, Walch A, Summer KH, Göttlicher M
“Isolation of highly pure rat liver mitochondria with the aid of zone-electrophoresis in a free flow device (ZE-FFE)”
Methods Mol Biol., 424: 333-48 (2008)

Mark P Simons, Kevin G Leidal, William M Nauseef and Thomas S Griffith
“TNF-related apoptosis-inducing ligand (TRAIL) is expressed troughout myeloid development, resulting in a broad distribution among neutrophil granules”
Journal of Leukocyte Biology, 83 (March 2008)

Zischka H, Kinkl N, Braun RJ, Ueffing M
“Purification of Saccharomyces cerevisiae Mitochondria by Zone Electrophoresis in a Free Flow Device”
Methods Mol Biol., 432: 51-64 (2008)

Eubel, H., Lee, C. P., Kuo, J., Meyer, E. H., Taylor, N. L., Millar, A. H
“Free-flow electrophoresis of purification of plant mitochondria by surface charge”
The Plant Journal (2007)

Bronwyn J. Barkla, Rosario Vera-Estrella, and Omar Pantoja
"Enhanced Separation of Membranes during Free Flow Zonal Electrophoresis in Plants"
Analytical Chemistry, June (2007)

Zischka H, Braun R J, et al
"Differential analysis of Saccharomyces cerevisiae mitochondria by free-flow electrophoresis"
Mol Cell Proteomics, 5:2185-2200 (2006) click here for a copy

Painter, R. G., Valentine, V. G., Lanson, N. A., Jr., Leidal, K., Zhang, Q., Lombard, G., Thompson, C., Viswanathan, A., Nauseef, W. M., Wang, G., Wang, G.
“CFTR Expression in human neutrophils and the phagolysosomal chlorination defect in cystic fibrosis”
Biochemistry, Aug. 45 (34), 10260-9 (2006)

Cutillas PR, Biber J, Marks J, Jacob R, Stieger B, Cramer R, Waterfield M, Burlingame A,
Unwinn R
“Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex”
Proteomics, 5, 101-112 (2005)

Prokisch H, Scharfe C, Camp DG,  Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM.
"Integrative analysis of the mitochondrial proteome in yeast"
PLoS Biol, 2(6): e160 (2004)

Zischka H, Weber G, Weber PJ, Posch A, Braun RJ, Buhringer D, Schneider U, Nissum M, Meitinger T, Ueffing M, Eckerskorn C
"Improved proteome analysis of Saccharomyces cerevisiae mitochondria by free-flow electrophoresis"
Proteomics, Jun: 3(6): 906-16 (2003)

Mohr H, Voelkl A
"Isolation of peroxisomal subpopulations from mouse liver by immune free-flow electrophoresis"
Electrophoresis, Jul: 23(13):2130-7 (2002)

Voelkl A, Mohr H and Fahimi HD
"Peroxisome subpopulations of the rat liver. Isolation by immune free flow electrophoresis”
J Histochem Cytochem, 47(9), 1111-1118, (1999)

Fuchs R, Male P, Mellman I
"Acidification and Ion Permeabilities of highly purified Rat Liver Endosomes"
Journal of Biol Chem, 264 (No4), 2212-2220, (1989)

Marsh M
"Endosome and lysosome purification by free-flow electrophoresis"
Methods in Cell Biology, 31(), 319-334, (1989) 

Schmid S and Mellman I
"Isolation of functionally distinct endosome subpopulations by free-flow electrophoresis" 
In: Cell Free Analysis of Membrane Transport (Editors: D.J.Morre, K.E.Howell and G.M.W.Cook) A.R.Liss, New York, pp. 35-49 (1988)

Marsh M, Kern H, Harms E, Schmid S, Mellman I and Helenius A
"Co-fractionation of BHK-21 cell endosomes and lysosomes by free-flow electrophoresis"
Prog Clin Biol Res, 270, 21-33 (1988) 

White Papers - Cell Organelles

Denter J and Nissum M
"Cell Organelle Separation Using BD Free Flow Electrophoresis System"
Summer 2007 Hotlines, BD Bioscience (July 2007)

Posters - Cell Organelles

HUPO, Seattle, Washington 2007

• Isolation of Highly Purified Peroxisomes Using Free-Flow Electrophoresis
  

ASCB, San Diego, California 2006

• Reproducible Organelle Purification Facilitates Analysis and Discovery of Organelle Proteins

Scientific Notes - Cell Organelles

• Isolation of peroxisome subpopulations from rat liver by immune free flow electorphoresis
  

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Proteins, Membrane Proteins and Peptides

Journal Articles

Islinger M, Weber G
“Free flow isoelectric focusing: A method for the separation of both hydrophilic and hydrophobic proteins of rat liver peroxisomes”
Methods Mol Biol.,  432: 199-215 (2008)

Xie Hongwei, Onsongo G, Popko J, de Jong E P, Cao J, Carlis J V,  Griffin R J, Rhodus N L, Griffin T J
“Proteomic analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry”
MCP,  in press M700146-MCP200

Bodenmiller B., Malmstrom J., Gerrits B., Campbell D., Lam H., Schmidt A., Rinner O., Mueller L.N., Shannon P.T., Pedrioli P.G., Panse C., Lee H.K., Schlapbach R., Aebersold R.
“PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells”
Molecular Systems Biology 3:139 (2007)

Drews O., Wildgruber R., Zong C., Sukop U., Nissum M., Gomes A. V., Weber G., Ping P.
“Mammalian proteasome subpopulations with distinct molecular  compositions and proteolytic activities“
Molecular & Cellular Proteomics (2007)

Brunner E. Ahrens C. H., Mohanty S., Baetschmann H., Loevenich S., Potthast F., Deutsch E. W., Panse C., de Lichtenberg U., Rinner O., Lee H., Pedrioli P. G., Malmstrom J., Koehler K.,Schrimpf S., Krijgsveld J., Kregenow F., Heck A. J., Hafen E., Schlapbach R., Aebersold R.
“A high-quality catalog of the Drosohpila melanogaster proteome”
Nature Biotechnolgy, Volume 25, (5), 576-583, May 2007

Xie, H., Bandhakavi, S., Roe, M. R., Griffin, T. J.
“Preparative Peptide Isoelectric Focusing as a Tool for Improving the Identification of Lysine-Acetylated Peptides from Complex Mixtures”
J Proteome Res, (2007)

Senis YA, Tomlinson MG, Garcia A, Dumon S, Heath VL, Herbert J, Cobbold SP, Spalton JC, Ayman S, Antrobus R, Zitzmann N, Bicknell R, Frampton J, Authi KS, Martin A, Wakelam MJ, Watson SP.
“A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein”
Molecular & Cellular Proteomics, 6, 548-564, (2007)

Malmström J, Lee H, Nesvizhskii A, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G,  Eckerskorn C and Aebersold R
"Optimized Peptide Separation and Identification for Mass Spectrometry Based Proteomics via Free-Flow Electrophoresis"
J Proteome Res, 5(9) 2241 – 2249 (2006)

Immler D, Greven S, Reinemer P
"Targeted proteomics in biomarker validation: Detection and quantification of proteins using a multi-dimensional peptide separation strategy"
Proteomics, 6, 2947-2958 (2006)

Moritz RL, Skandarajah A, Ji H, Simpson RJ
"Proteomic analysis of colorectal cancer: prefractionation strategies using two-dimensional free-flow electrophoresis"
Comparative and Functional Genomics, 6, 236-243 (2005)

Xie H, Rhodus NL, Griffin RJ, Carlis JV, Griffin TJ
"A Cataloque of Human Saliva Proteins Identified by Free Flow Electrophoresis-based Peptide Separation and Tandem Mass Spectrometry"
Mol Cell Proteomics, 4(11): 1026-30 (2005)

Obermaier C et al.
"Free-flow isoelectric focusing of proteins remaining in cell fragments following sonication of thyroid carcinoma cells."
Electrophoresis, 26(11): 2109-16 (2005)

Xie H, Bandhakavi S, Griffin TJ
"Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae"
Anal Chem, 15, 77(10): 3198-107 (2005)

Hoffmann P, Olayioye MA
"Breast cancer protein StarD10 identified by three-dimensional separation using free-flow electrophoresis, reversed-phase high-performance liquid chromatography, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis."
Electrophoresis, 26(6): 1029-37 (2005)

Weber G, Islinger M, Weber P, Eckerskorn C, Voelkl A
"Efficient separation and analysis of peroxisomal membrane proteins using free-flow isoelectric focusing"
Electrophoresis, Jun; 5(12):1735-47 (2004)

Moritz RL, Ji H, Schutz F, Connolly LM, Kapp EA, Speed TP, Simpson RJ
"A Proteome Strategy for Fractionating Proteins and Peptides Using Continuous Free-Flow Electrophoresis Coupled Off-Line to Reverse-Phase High Performance Liquid Chromatography"
Analytical Chemistry, 76: 4811-4824 (2004)

Hoffmann P, Ji H, Moritz RL, Connolly LM, Frecklington DF, Layton MJ, Eddes JS and Simpson RJ
"Continuous free-flow electrophoresis separation of cytosolic proteins from the human colon carcinoma cell line LIM 1215: A non two-dimensional gel electrophoresis-based proteome analysis strategy"
Proteomics, 1, 807-818 (2001)

Bardy N, Carrasco A, Galaud J PH, Pont Lezica R and Canut H
"Free-flow Electrophoresis for fractionation of Arabidopsis thaliana membranes" 
Electrophoresis, 19, 1145-1153 (1998) 

Bauer J and Weber G
"Interval carrier free electrophoresis for high resolution protein purification"
J Disp Sci Tech, 19 937-950 (1998) 

Lasch J, Moschner S, Sann H, Zellmer S and Koelsch R
"Aminopeptidase P - a cell surface antigen of Endothelial and Lymphoid Cells: Catalytical and Immuno-Histotopical Evidences"
Biol Chem, Vol 379, 705-709 (1998) 

Murer H, Gmaj P, Stieger B and Hagenbuch B
"Transport studies with renal proximal tubular and small intestinal Brush border and Basolateral Membrane vesicles: Vesicles heterogeneity, Coexistence of Transport systems"
Meth Enzymol, 172, 346-364, (1989) 

Morre DJ, Nowack D, Paulik M, Brightman AO, Thornbrough K, Yim, J and Auderset G
"Transitional endoplasmic reticulum membranes and vesicles isolated from animals and plants. Homologous and Heterologous transfer to Golgi apparatus"
Protoplasma, 153, 1-13, (1989) 

Holzenburg A, Engel A, Kessier R, Manz HJ, Lustig A and Aebi U
"Rapid isolation of OmpF Porin-LPS complexes" 
Biochemistry, 28,4187 (1989)

Posters - Proteins, Membrane Proteins and Peptides

Association of Biomolecular Resource Facilities (ABRF) , Salt lake City, Utah Feb. 2008

• Phosphopeptide Enrichment Enabled by Free Flow Electrophoresis

HUPO, Seattle, Washington 2007

• Separation and Characterization of Dipeptidyl Peptidase IV Isoforms
• Increased Solubility of Membrane Proteins Using Interval Zone Free-Flow Electrophoresis

HUPO, Long Beach, California 2006

• Identification of Plasma Proteins Using In-Solution Isoelectric Focusing on the Peptide Level

The Protein Society, San Diego, California 2006

• Increasing Resolution in Shotgun Proteomics: In-Solution Isoelectric Focusing of Peptides Using Free Flow Electrophoresis

HUPO, Munich, Germany 2005

• Drilling the Human Plasma Proteome: Novel Advancements in Fractionation and Separation
• Free-Flow Isoelectric Focusing for Separation of Both Cytosolic and Membrane-Associated Human Proteins
• Separation of Functionally Active Wild-Type Enzyme and Point Mutants Using Free Flow Electrophoresis (FFE)
• FFE as a Multifunctional Separation for Isolating Isoforms of Protein Species
• Quantitative Fractionation and Separation of Human Plasma by FFE as a First Step Reduces the Complexity and Leads Reproducible to Low Abundant Proteins 
  

Scientific Notes - Proteins, Membrane Proteins and Peptides

• Separation of Peptides Using Free-Flow Electorphorese and a High Throughput Approach to Sample Clean-Up Prior to Mass Spectrometry
  

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Human Plasma

Journal Articles

Nissum M, Foucher AL
“Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis”
Expert Rev. Proteomics 5(4), (2008)

Wildgruber R, Yi J, Nissum M, Eckerskorn C, Weber G
“Free-flow electrophoresis system for plasma proteomic applications”
Methods Mol Biol., 424: 287-300 (2008)

Nissum M., Kuhfuss S., Hauptmann M., Obermaier C., Sukop U., Wildgruber R., Weber G., Eckerskorn C., Malmström J.
“Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis”
Proteomics (2007), 7, 4218-4227

Moritz RL et al.
"Application of 2-D free flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-adundance proteins"
Proteomics, 5(13): 3402-13 (2005)

Cho SY, Lee EY,  Lee JS, Paik YK et al.
"Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map"
Proteomics, 5, 3386-3396 (2005)

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Drug Discovery

Journal Articles

Schneiderman E, Gratz SR, Stalcup AM
"Optimization of preparative electrophoretic chiral separation of ritalin enantiomers"
J Pharm Biomed Anal, 27, p: 639-50 (2002)

Wind M, Hoffmann P, Wagner H, Thormann W
"Chiral capillary electrophoresis as a predictor for separation of drug enantiomers in continuous flow zone electrophoresis"
Journal of Chromatography A, 895, 51-65 (2000)

Hoffmann P, Wagner H, Weber G, Lanz M, Caslavska J and Thormann W
"Separation and Purification of Methadone Enantiomers by Continuous- and Interval-Flow Electrophoresis"
Analytical Chemistry, 71(9); 1840-1850 (1999)

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Cell Separation

Journal Articles

Heidrich HG, Hannig K
"Separation of cell populations by free-flow electrophoresis"
Methods in Enzymology, 171, 513-531, (1989)

Hansen E, Wustrow Pu and  Hannig K
"Antigen-Specific Electrophoretic Cell Separation for Immunological Investigations"
Electrophoresis, 10 (8-9), 645-652, (1989)

Baier TG, Weber G, Hartmann K, Heinrich U, Schönberg D
"Preparative separation of human-b and lymphocytes-t by free-flow electrophoresis"
Analytical Biochemistry, 171(N1), 91-95, (1988)

Bauer J, Kachel V and Hannig K
"The negative surface charge density is a maturation marker of human B-lymphocytes"
Cellular Immunology, 111: 354-364 (1988)

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General Publications

Journal Articles

Weber G, Wildgruber R
"Free-flow electrophoresis system for proteomics applications"
 Methods Mol Biol., 384: 703-16 (2008)

Moritz RL and Simpson RJ
"Liquid-based free-flow electrophoresis-reversed-phase HPLC: a proteomic tool"
 NAT Methods, 2(11): 863-73 (2005)

Wang Y, Hancock WS, Weber G, Eckerskorn C, Palmer-Toy D
"Free flow electrophoresis coupled with liquid chromatography-mass spectrometry for a proteomic study of the human cell line (K562/CR3)"
Journal of Chromatography A, 1053: 269-278 (2004)

Krivankova L and Bocek P
"Continuous free flow electrophoresis"
Electrophoresis, 19, 1064-1074 (1998)

Song JF, Liu X, Shen A, Gao-de W and Qi-chang X
"Application of Free Flow Electrophoresis to the purification of trichosanthin from a crude product of acetone fractional precipitation" 
Electrophoresis, 19 1097-1103 (1998)

Weber G and Bauer J
"Counterbalancing hydrodynamic sample distortion effects increases resolution of free flow zone electrophoresis"
Electrophoresis, 19, 1104-1109 (1998)

Weber G and Bocek P
"Recent developments in preparative free flow isoelectric focusing"
Electrophoresis, 19, 1649 - 1653 (1998) 

Heidrich HG
"Free-flow particle electrophoresis in cell biology and biochemistry - an updated review"
In: Electrophoresis '88, Proceedings of the Sixth Meeting of The International Electrophoresis Society, July 1988, Copenhagen (Ed.: C.Schafer-Nielseri) VCH Verlags. GmbH, Weinheim, FRG. pp. 187-200. (1988)

Morre DJ
"Free-flow electrophoresis: Preparative applications to cell-free analysis of exocytic membrane traffic"
In: Cell Free Analysis of Membrane Transport (Editors: D.J. Morre, K.E.Howell and G.M.W.Cook) A.R.Liss, New York, pp. 7-19 (1988) 

Posters - General

HUPO, Long Beach, California 2006

• Free Flow Electrophoresis: A Highly Versatile Fractionation and Separation Method in Proteomics

Reviews

D'Aguanno S., Del Boccio P., Bernardini S., Ballone E., Di Ilio C., Federici G., Urbani A.
"Electrophoretic separations of cerebrospinal fluid proteins in clinical investigations"
Clin chem. Lab Med, 45 (4), 437-449 (2007)

Smith J. C., Lambert J. P., Elisma F., Figeys D.
"Proteomics in 2005/2006: Developments, Applications and Challenges"
 Analytical Chemistry, April (2007)

Braun R. J., Kinkl N., Beer M., Üffing M.
"Two-dimensional elctrophoresis of membrane proteins“
Anal. Bioanal. Chem., Accepted: 13 July 2007

Scientific Notes - General

• Free Flow Electorphorsis: Novel high-Resolution Separation of Complex Protein and Peptide Mixtures
  

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Comparative Human Plasma Peptidome Analysis: P100 vs EDTA

Journal Articles

J. Yi, et al.
"Inhibition of Intrinsic Proteolytic Activities Moderates Preanlaytical Variability and Instability of Human Plasma"
Journal of Proteome Research, 6:1768-1781 (2007). click here for a copy

Scientific Posters

HUPO, Seattle, Washington, 2007

• Preanalytical Variability of Plasma Samples and Mitigating Strategies
• Monitoring Peptidome Variance within Different Blood Collection to Further Understand Human Plasma Proteome Stability

PepTalk, San Diego, California, 2007

• Stabilization of the Human Plasma Peptidome by Protease Inhibitors

HUPO, Long Beach, California, 2006

• Using LC-MALDI-MS to Study the Variability and Stability of Plasma Proteins

Protein Society, San Diego, California, 2006

• A Deeper Look Into Sample Collection and Handling-induced Variability of Plasma Proteins in Proteomics

HUPO, Boston, Massachusetts, 2006

• Characterization of Intrinsic Proteolytic Damage of Human Plasma Proteins During Sample Preparation  (print 11"x17" size)

ASMS, Seattle, Washington, 2006

• Preanalytical Variability and the Stability of Human Plasma Proteins: Mass Spectrometry Changes After Blood Collection (print 11"x17" size)

US HUPO, Washington, DC, 2005

• Prevention of Proteolytic Digestion of Human Plasma Proteins by Protease Inhibitors

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Comparative Human Plasma Peptidome Analysis: P100 vs Serum

Journal Articles

J. Yi, et al.
"Inhibition of Intrinsic Proteolytic Activities Moderates Preanlaytical Variability and Instability of Human Plasma"
Journal of Proteome Research, 6:1768-1781 (2007). click here for a copy

Scientific Posters

HUPO, Seattle, Washington, 2007

• Preanalytical Variability of Plasma Samples and Mitigating Strategies

AACR, Washington, DC, 2007

• Inhibition of Intrinsic Proteolysis Stabilizes Plasma Samples

HUPO, Long Beach, California, 2006

• Inhibition of Intrinsic Proteolytic Activity Moderates Preanalytical Variability and Stabilizes the Human Plasma Proteome

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AQUA Peptide Plasma and Serum Studies

Scientific Posters

HUPO, Seoul, South Korea, 2007

• Demonstrating Instability of Peptide Biomarkers in Human Blood Plasma Using Time-Course Mass Spectrometry

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Mechanical Separator Studies

Scientific Posters

HUPO, Seattle, Washington, 2007

• Preanalytical Variability of Plasma Samples and Mitigating Strategies

AACC, Chicago, Illinois, 2006

• Effect of Plasma Separators on Peptide MALDI-TOF MS Spectra

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Thrombin Studies: Nonspecific Proteolysis Induction in Serum Samples

Scientific Posters

AACC, Chicago, Illinois, 2006

• Thrombin Exhibits Nonspecific Proteolysis in Serum; Observations with Fibrinopeptide A

HUPO, Munich, Germany, 2005

• Intrinsic Preanalytical Variability of Serum Samples is Evidenced in Peptide MALDI MS Spectra

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AQUA Peptide Plasma and Serum Studies

Scientific Posters

HUPO, Seoul, South Korea, 2007

• Demonstrating Instability of Peptide Biomarkers in Human Blood Plasma Using Time-Course Mass Spectrometry

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