Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry: The ABRF glycoprotein research multi-institutional study 2012

Nancy Leymarie, Paula J. Griffin, Karen Jonscher, Daniel Kolarich, Ron Orlando, Mark McComb, Joseph Zaia, Jennifer T. Aguilan, William R. Alley, Friederich Altmann, Lauren E. Ball, Lipika Basumallick, Carthene R. Bazemore-Walker, Henning Behnken, Michael A. Blank, Kristy J. Brown, Svenja Catharina Bunz, Christopher W. Cairo, John F. Cipollo, Rambod DaneshfarHeather Desaire, Richard R. Drake, Eden P. Go, Radoslav Goldman, Clemens Gruber, Adnan Halim, Yetrib Hathout, Paul J. Hensbergen, David M. Horn, Deanna Hurum, Wolfgang Jabs, Göran Larson, Mellisa Ly, Benjamin F. Mann, Kristina Marx, Yehia Mechref, Bernd Meyer, Uwe Möginger, Christian Neusüß, Jonas Nilsson, Milos V. Novotny, Julius O. Nyalwidhe, Nicolle H. Packer, Petr Pompach, Bela Reiz, Anja Resemann, Jeffrey S. Rohrer, Alexandra Ruthenbeck, Miloslav Sanda, Jan Mirco Schulz, Ulrike Schweiger-Hufnagel, Carina Sihlbom, Ehwang Song, Gregory O. Staples, Detlev Suckau, Haixu Tang, Morten Thaysen-Andersen, Rosa I. Viner, Yanming An, Leena Valmu, Yoshinao Wada, Megan Watson, Markus Windwarder, Randy Whittal, Manfred Wuhrer, Yiying Zhu, Chunxia Zou

Research output: Contribution to journalArticle

78 Citations (Scopus)

Abstract

One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.

Original languageEnglish (US)
Pages (from-to)2935-2951
Number of pages17
JournalMolecular and Cellular Proteomics
Volume12
Issue number10
DOIs
StatePublished - Oct 2013

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Glycosylation
Mass spectrometry
Mass Spectrometry
Glycoproteins
Prostate-Specific Antigen
Glycomics
Research
Polysaccharides
Prostatic Neoplasms
Proteins
Peptides
Statistical Data Interpretation
Glycopeptides
Biomarkers
Tumor Biomarkers
Proteomics
Cluster Analysis
Labels
Neoplasms
Blood

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Analytical Chemistry

Cite this

Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry : The ABRF glycoprotein research multi-institutional study 2012. / Leymarie, Nancy; Griffin, Paula J.; Jonscher, Karen; Kolarich, Daniel; Orlando, Ron; McComb, Mark; Zaia, Joseph; Aguilan, Jennifer T.; Alley, William R.; Altmann, Friederich; Ball, Lauren E.; Basumallick, Lipika; Bazemore-Walker, Carthene R.; Behnken, Henning; Blank, Michael A.; Brown, Kristy J.; Bunz, Svenja Catharina; Cairo, Christopher W.; Cipollo, John F.; Daneshfar, Rambod; Desaire, Heather; Drake, Richard R.; Go, Eden P.; Goldman, Radoslav; Gruber, Clemens; Halim, Adnan; Hathout, Yetrib; Hensbergen, Paul J.; Horn, David M.; Hurum, Deanna; Jabs, Wolfgang; Larson, Göran; Ly, Mellisa; Mann, Benjamin F.; Marx, Kristina; Mechref, Yehia; Meyer, Bernd; Möginger, Uwe; Neusüß, Christian; Nilsson, Jonas; Novotny, Milos V.; Nyalwidhe, Julius O.; Packer, Nicolle H.; Pompach, Petr; Reiz, Bela; Resemann, Anja; Rohrer, Jeffrey S.; Ruthenbeck, Alexandra; Sanda, Miloslav; Schulz, Jan Mirco; Schweiger-Hufnagel, Ulrike; Sihlbom, Carina; Song, Ehwang; Staples, Gregory O.; Suckau, Detlev; Tang, Haixu; Thaysen-Andersen, Morten; Viner, Rosa I.; An, Yanming; Valmu, Leena; Wada, Yoshinao; Watson, Megan; Windwarder, Markus; Whittal, Randy; Wuhrer, Manfred; Zhu, Yiying; Zou, Chunxia.

In: Molecular and Cellular Proteomics, Vol. 12, No. 10, 10.2013, p. 2935-2951.

Research output: Contribution to journalArticle

Leymarie, N, Griffin, PJ, Jonscher, K, Kolarich, D, Orlando, R, McComb, M, Zaia, J, Aguilan, JT, Alley, WR, Altmann, F, Ball, LE, Basumallick, L, Bazemore-Walker, CR, Behnken, H, Blank, MA, Brown, KJ, Bunz, SC, Cairo, CW, Cipollo, JF, Daneshfar, R, Desaire, H, Drake, RR, Go, EP, Goldman, R, Gruber, C, Halim, A, Hathout, Y, Hensbergen, PJ, Horn, DM, Hurum, D, Jabs, W, Larson, G, Ly, M, Mann, BF, Marx, K, Mechref, Y, Meyer, B, Möginger, U, Neusüß, C, Nilsson, J, Novotny, MV, Nyalwidhe, JO, Packer, NH, Pompach, P, Reiz, B, Resemann, A, Rohrer, JS, Ruthenbeck, A, Sanda, M, Schulz, JM, Schweiger-Hufnagel, U, Sihlbom, C, Song, E, Staples, GO, Suckau, D, Tang, H, Thaysen-Andersen, M, Viner, RI, An, Y, Valmu, L, Wada, Y, Watson, M, Windwarder, M, Whittal, R, Wuhrer, M, Zhu, Y & Zou, C 2013, 'Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry: The ABRF glycoprotein research multi-institutional study 2012', Molecular and Cellular Proteomics, vol. 12, no. 10, pp. 2935-2951. https://doi.org/10.1074/mcp.M113.030643
Leymarie, Nancy ; Griffin, Paula J. ; Jonscher, Karen ; Kolarich, Daniel ; Orlando, Ron ; McComb, Mark ; Zaia, Joseph ; Aguilan, Jennifer T. ; Alley, William R. ; Altmann, Friederich ; Ball, Lauren E. ; Basumallick, Lipika ; Bazemore-Walker, Carthene R. ; Behnken, Henning ; Blank, Michael A. ; Brown, Kristy J. ; Bunz, Svenja Catharina ; Cairo, Christopher W. ; Cipollo, John F. ; Daneshfar, Rambod ; Desaire, Heather ; Drake, Richard R. ; Go, Eden P. ; Goldman, Radoslav ; Gruber, Clemens ; Halim, Adnan ; Hathout, Yetrib ; Hensbergen, Paul J. ; Horn, David M. ; Hurum, Deanna ; Jabs, Wolfgang ; Larson, Göran ; Ly, Mellisa ; Mann, Benjamin F. ; Marx, Kristina ; Mechref, Yehia ; Meyer, Bernd ; Möginger, Uwe ; Neusüß, Christian ; Nilsson, Jonas ; Novotny, Milos V. ; Nyalwidhe, Julius O. ; Packer, Nicolle H. ; Pompach, Petr ; Reiz, Bela ; Resemann, Anja ; Rohrer, Jeffrey S. ; Ruthenbeck, Alexandra ; Sanda, Miloslav ; Schulz, Jan Mirco ; Schweiger-Hufnagel, Ulrike ; Sihlbom, Carina ; Song, Ehwang ; Staples, Gregory O. ; Suckau, Detlev ; Tang, Haixu ; Thaysen-Andersen, Morten ; Viner, Rosa I. ; An, Yanming ; Valmu, Leena ; Wada, Yoshinao ; Watson, Megan ; Windwarder, Markus ; Whittal, Randy ; Wuhrer, Manfred ; Zhu, Yiying ; Zou, Chunxia. / Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry : The ABRF glycoprotein research multi-institutional study 2012. In: Molecular and Cellular Proteomics. 2013 ; Vol. 12, No. 10. pp. 2935-2951.
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abstract = "One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.",
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T1 - Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry

T2 - The ABRF glycoprotein research multi-institutional study 2012

AU - Leymarie, Nancy

AU - Griffin, Paula J.

AU - Jonscher, Karen

AU - Kolarich, Daniel

AU - Orlando, Ron

AU - McComb, Mark

AU - Zaia, Joseph

AU - Aguilan, Jennifer T.

AU - Alley, William R.

AU - Altmann, Friederich

AU - Ball, Lauren E.

AU - Basumallick, Lipika

AU - Bazemore-Walker, Carthene R.

AU - Behnken, Henning

AU - Blank, Michael A.

AU - Brown, Kristy J.

AU - Bunz, Svenja Catharina

AU - Cairo, Christopher W.

AU - Cipollo, John F.

AU - Daneshfar, Rambod

AU - Desaire, Heather

AU - Drake, Richard R.

AU - Go, Eden P.

AU - Goldman, Radoslav

AU - Gruber, Clemens

AU - Halim, Adnan

AU - Hathout, Yetrib

AU - Hensbergen, Paul J.

AU - Horn, David M.

AU - Hurum, Deanna

AU - Jabs, Wolfgang

AU - Larson, Göran

AU - Ly, Mellisa

AU - Mann, Benjamin F.

AU - Marx, Kristina

AU - Mechref, Yehia

AU - Meyer, Bernd

AU - Möginger, Uwe

AU - Neusüß, Christian

AU - Nilsson, Jonas

AU - Novotny, Milos V.

AU - Nyalwidhe, Julius O.

AU - Packer, Nicolle H.

AU - Pompach, Petr

AU - Reiz, Bela

AU - Resemann, Anja

AU - Rohrer, Jeffrey S.

AU - Ruthenbeck, Alexandra

AU - Sanda, Miloslav

AU - Schulz, Jan Mirco

AU - Schweiger-Hufnagel, Ulrike

AU - Sihlbom, Carina

AU - Song, Ehwang

AU - Staples, Gregory O.

AU - Suckau, Detlev

AU - Tang, Haixu

AU - Thaysen-Andersen, Morten

AU - Viner, Rosa I.

AU - An, Yanming

AU - Valmu, Leena

AU - Wada, Yoshinao

AU - Watson, Megan

AU - Windwarder, Markus

AU - Whittal, Randy

AU - Wuhrer, Manfred

AU - Zhu, Yiying

AU - Zou, Chunxia

PY - 2013/10

Y1 - 2013/10

N2 - One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.

AB - One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.

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