Top down proteomics of human membrane proteins from enriched mitochondrial fractions

Adam D. Catherman; Mingxi Li; John C. Tran; Kenneth R. Durbin; Philip D. Compton; Bryan P. Early; Paul M. Thomas; Neil L. Kelleher

doi:10.1021/ac3031527

Top down proteomics of human membrane proteins from enriched mitochondrial fractions

Adam D. Catherman, Mingxi Li, John C. Tran, Kenneth R. Durbin, Philip D. Compton, Bryan P. Early, Paul M. Thomas, Neil L. Kelleher^*

^*Corresponding author for this work

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

66 Scopus citations

Abstract

The interrogation of intact integral membrane proteins has long been a challenge for biological mass spectrometry. Here, we demonstrate the application of top down mass spectrometry to whole membrane proteins below 60 kDa with up to 8 transmembrane helices. Analysis of enriched mitochondrial membrane preparations from human cells yielded identification of 83 integral membrane proteins, along with 163 membrane-associated or soluble proteins, with a median q value of 3 × 10^-10. An analysis of matching fragment ions demonstrated that significantly more fragment ions were found within transmembrane domains than would be expected based upon the observed protein sequence. In total, 46 proteins from the complexes of oxidative phosphorylation were identified which exemplifies the increasing ability of top down proteomics to provide extensive coverage in a biological network.

Original language	English (US)
Pages (from-to)	1880-1888
Number of pages	9
Journal	Analytical Chemistry
Volume	85
Issue number	3
DOIs	https://doi.org/10.1021/ac3031527
State	Published - Feb 5 2013

ASJC Scopus subject areas

Analytical Chemistry

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title = "Top down proteomics of human membrane proteins from enriched mitochondrial fractions",

abstract = "The interrogation of intact integral membrane proteins has long been a challenge for biological mass spectrometry. Here, we demonstrate the application of top down mass spectrometry to whole membrane proteins below 60 kDa with up to 8 transmembrane helices. Analysis of enriched mitochondrial membrane preparations from human cells yielded identification of 83 integral membrane proteins, along with 163 membrane-associated or soluble proteins, with a median q value of 3 × 10-10. An analysis of matching fragment ions demonstrated that significantly more fragment ions were found within transmembrane domains than would be expected based upon the observed protein sequence. In total, 46 proteins from the complexes of oxidative phosphorylation were identified which exemplifies the increasing ability of top down proteomics to provide extensive coverage in a biological network.",

author = "Catherman, {Adam D.} and Mingxi Li and Tran, {John C.} and Durbin, {Kenneth R.} and Compton, {Philip D.} and Early, {Bryan P.} and Thomas, {Paul M.} and Kelleher, {Neil L.}",

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AU - Catherman, Adam D.

AU - Li, Mingxi

AU - Tran, John C.

AU - Durbin, Kenneth R.

AU - Compton, Philip D.

AU - Early, Bryan P.

AU - Thomas, Paul M.

AU - Kelleher, Neil L.

PY - 2013/2/5

Y1 - 2013/2/5

N2 - The interrogation of intact integral membrane proteins has long been a challenge for biological mass spectrometry. Here, we demonstrate the application of top down mass spectrometry to whole membrane proteins below 60 kDa with up to 8 transmembrane helices. Analysis of enriched mitochondrial membrane preparations from human cells yielded identification of 83 integral membrane proteins, along with 163 membrane-associated or soluble proteins, with a median q value of 3 × 10-10. An analysis of matching fragment ions demonstrated that significantly more fragment ions were found within transmembrane domains than would be expected based upon the observed protein sequence. In total, 46 proteins from the complexes of oxidative phosphorylation were identified which exemplifies the increasing ability of top down proteomics to provide extensive coverage in a biological network.

AB - The interrogation of intact integral membrane proteins has long been a challenge for biological mass spectrometry. Here, we demonstrate the application of top down mass spectrometry to whole membrane proteins below 60 kDa with up to 8 transmembrane helices. Analysis of enriched mitochondrial membrane preparations from human cells yielded identification of 83 integral membrane proteins, along with 163 membrane-associated or soluble proteins, with a median q value of 3 × 10-10. An analysis of matching fragment ions demonstrated that significantly more fragment ions were found within transmembrane domains than would be expected based upon the observed protein sequence. In total, 46 proteins from the complexes of oxidative phosphorylation were identified which exemplifies the increasing ability of top down proteomics to provide extensive coverage in a biological network.

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Top down proteomics of human membrane proteins from enriched mitochondrial fractions

Abstract

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