Proteomic investigation of natural killer cell microsomes using gas-phase fractionation by mass spectrometry

We have explored the utility of gas-phase fractionation by mass spectrometry (MS) in the mass-to-charge ( m/ z) dimension (GPF m/ z ) for increasing the effective number of protein identifications in cases where sample quantity limits the use of multi-dimensional chromatographic fractionation. A pep...

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Bibliographic Details
Published in:Biochimica et biophysica acta 2004-04, Vol.1698 (1), p.87-95
Main Authors: Blonder, Josip, Rodriguez-Galan, Maria Cecilia, Lucas, David A., Young, Howard A., Issaq, Haleem J., Veenstra, Timothy D., Conrads, Thomas P.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Animals
Cation Transport Proteins - chemistry
Cation Transport Proteins - genetics
Cation Transport Proteins - metabolism
Gas-phase fractionation
Killer Cells, Natural - chemistry
Killer Cells, Natural - metabolism
Mass Spectrometry
Membrane Proteins - chemistry
Membrane Proteins - genetics
Membrane Proteins - metabolism
Membrane proteomic
Mice
Microsome
Microsomes - chemistry
Microsomes - metabolism
Molecular Sequence Data
Natural killer cell
Peptides - chemistry
Peptides - metabolism
Proteome - chemistry
Proteome - metabolism
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Summary:We have explored the utility of gas-phase fractionation by mass spectrometry (MS) in the mass-to-charge ( m/ z) dimension (GPF m/ z ) for increasing the effective number of protein identifications in cases where sample quantity limits the use of multi-dimensional chromatographic fractionation. A peptide digestate from proteins isolated from the membrane fraction of natural killer (NK) cells was analyzed by microcapillary reversed-phase liquid chromatography coupled online to an ion-trap (IT) mass spectrometer. Performing GPF m/ z using eight narrow precursor ion scan m/ z ranges enabled the identification of 340 NK cell proteins from 12 μg of digestate, representing more than a fivefold increase in the number of proteins identified as compared to the same experiment employing a standard precursor ion survey scan m/ z range (i.e., m/ z 400–2000). The results show that GPF m/ z represents an effective technique for increasing protein identifications in global proteomic investigations especially when sample quantity is limited.
ISSN:1570-9639
0006-3002
1878-1454
DOI:10.1016/j.bbapap.2003.10.009