Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry

Josip Blonder; Maria C. Rodriguez-Galan; King C. Chan; David A. Lucas; Li Rong Yu; Thomas P. Conrads; Haleem J. Issaq; Howard A. Young; Timothy D. Veenstra

doi:10.1021/pr049927e

Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry

Josip Blonder, Maria C. Rodriguez-Galan, King C. Chan, David A. Lucas, Li Rong Yu, Thomas P. Conrads, Haleem J. Issaq, Howard A. Young, Timothy D. Veenstra^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

Abstract

This study describes the application of a single tube sample preparation technique coupled with multidimensional fractionation for the analysis of a complex membrane protein sample from murine natural killer (NK) cells. A solution-based method that facilitates the solubilization and tryptic digestion of integral membrane proteins is conjoined with strong cation exchange (SCX) liquid chromatography (LC) fractionation followed by microcapillary reversed-phase (μRP) LC tandem mass spectrometric analysis of each SCXLC fraction in second dimension. Sonication in buffered methanol solution was employed to solubilize, and tryptically digest murine NK cell microsomal proteins, allowing for the large-scale identification of integral membrane proteins, including the mapping of the membrane-spanning peptides. Bioinformatic analysis of the acquired tandem mass spectra versus the murine genome database resulted in 11 967 matching tryptic peptide sequences, corresponding to 5782 unique peptide identifications. These peptides resulted in identification of 2563 proteins of which 876 (34%) are classified as membrane proteins.

Original language	English
Pages (from-to)	862-870
Number of pages	9
Journal	Journal of Proteome Research
Volume	3
Issue number	4
DOIs	https://doi.org/10.1021/pr049927e
State	Published - Jul 2004
Externally published	Yes

Keywords

Large-scale membrane proteomics
Membrane proteins
Solution-based multidimensional proteomic analysis

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10.1021/pr049927e

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Blonder, J., Rodriguez-Galan, M. C., Chan, K. C., Lucas, D. A., Yu, L. R., Conrads, T. P., Issaq, H. J., Young, H. A., & Veenstra, T. D. (2004). Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry. Journal of Proteome Research, 3(4), 862-870. https://doi.org/10.1021/pr049927e

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title = "Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry",

abstract = "This study describes the application of a single tube sample preparation technique coupled with multidimensional fractionation for the analysis of a complex membrane protein sample from murine natural killer (NK) cells. A solution-based method that facilitates the solubilization and tryptic digestion of integral membrane proteins is conjoined with strong cation exchange (SCX) liquid chromatography (LC) fractionation followed by microcapillary reversed-phase (μRP) LC tandem mass spectrometric analysis of each SCXLC fraction in second dimension. Sonication in buffered methanol solution was employed to solubilize, and tryptically digest murine NK cell microsomal proteins, allowing for the large-scale identification of integral membrane proteins, including the mapping of the membrane-spanning peptides. Bioinformatic analysis of the acquired tandem mass spectra versus the murine genome database resulted in 11 967 matching tryptic peptide sequences, corresponding to 5782 unique peptide identifications. These peptides resulted in identification of 2563 proteins of which 876 (34%) are classified as membrane proteins.",

keywords = "Large-scale membrane proteomics, Membrane proteins, Solution-based multidimensional proteomic analysis",

author = "Josip Blonder and Rodriguez-Galan, {Maria C.} and Chan, {King C.} and Lucas, {David A.} and Yu, {Li Rong} and Conrads, {Thomas P.} and Issaq, {Haleem J.} and Young, {Howard A.} and Veenstra, {Timothy D.}",

year = "2004",

month = jul,

doi = "10.1021/pr049927e",

language = "English",

volume = "3",

pages = "862--870",

journal = "Journal of Proteome Research",

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Blonder, J, Rodriguez-Galan, MC, Chan, KC, Lucas, DA, Yu, LR, Conrads, TP, Issaq, HJ, Young, HA & Veenstra, TD 2004, 'Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry', Journal of Proteome Research, vol. 3, no. 4, pp. 862-870. https://doi.org/10.1021/pr049927e

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T1 - Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry

AU - Blonder, Josip

AU - Rodriguez-Galan, Maria C.

AU - Chan, King C.

AU - Lucas, David A.

AU - Yu, Li Rong

AU - Conrads, Thomas P.

AU - Issaq, Haleem J.

AU - Young, Howard A.

AU - Veenstra, Timothy D.

PY - 2004/7

Y1 - 2004/7

N2 - This study describes the application of a single tube sample preparation technique coupled with multidimensional fractionation for the analysis of a complex membrane protein sample from murine natural killer (NK) cells. A solution-based method that facilitates the solubilization and tryptic digestion of integral membrane proteins is conjoined with strong cation exchange (SCX) liquid chromatography (LC) fractionation followed by microcapillary reversed-phase (μRP) LC tandem mass spectrometric analysis of each SCXLC fraction in second dimension. Sonication in buffered methanol solution was employed to solubilize, and tryptically digest murine NK cell microsomal proteins, allowing for the large-scale identification of integral membrane proteins, including the mapping of the membrane-spanning peptides. Bioinformatic analysis of the acquired tandem mass spectra versus the murine genome database resulted in 11 967 matching tryptic peptide sequences, corresponding to 5782 unique peptide identifications. These peptides resulted in identification of 2563 proteins of which 876 (34%) are classified as membrane proteins.

AB - This study describes the application of a single tube sample preparation technique coupled with multidimensional fractionation for the analysis of a complex membrane protein sample from murine natural killer (NK) cells. A solution-based method that facilitates the solubilization and tryptic digestion of integral membrane proteins is conjoined with strong cation exchange (SCX) liquid chromatography (LC) fractionation followed by microcapillary reversed-phase (μRP) LC tandem mass spectrometric analysis of each SCXLC fraction in second dimension. Sonication in buffered methanol solution was employed to solubilize, and tryptically digest murine NK cell microsomal proteins, allowing for the large-scale identification of integral membrane proteins, including the mapping of the membrane-spanning peptides. Bioinformatic analysis of the acquired tandem mass spectra versus the murine genome database resulted in 11 967 matching tryptic peptide sequences, corresponding to 5782 unique peptide identifications. These peptides resulted in identification of 2563 proteins of which 876 (34%) are classified as membrane proteins.

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Analysis of murine natural killer cell microsomal proteins using two-dimensional liquid chromatography coupled to tandem electrospray ionization mass spectrometry

Abstract

Keywords

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