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Nat Methods. 2014 Jan;11(1):59-62. doi: 10.1038/nmeth.2732. Epub 2013 Nov 17.

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Author information

1
1] Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. [2].
2
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
3
Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
4
Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
5
1] School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden. [2] Swedish e-Science Resource Center, KTH Royal Institute of Technology, Stockholm, Sweden.

Abstract

We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.

PMID:
24240322
DOI:
10.1038/nmeth.2732
[Indexed for MEDLINE]

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