Protein profiling by the combination of two independent mass spectrometry techniques

Wei Qiang Chen, Sung Ung Kang, Gert Lubec

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


Protein profiling in the high-throughput mode is a most useful technique that allows formation of reference databases for cells and tissues and performance of comparative proteomics. In the proposed protocol protein extraction from tissues is followed by 2D gel electrophoresis (2DE) with subsequent in-gel digestion and identification of soluble proteins by two individual mass spectrometric techniques, tandem matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and nano-liquid chromatography (nano-LC)-MS/MS. The proposed combined use of these two MS approaches leads to a very high identification rate of well-separated protein spots from a gel. In the first step 2DE separates high-abundance proteins (those visualized by nonsensitive Coomassie blue staining) that are subsequently picked, digested and aliquoted for MS applications. Protein samples not identified by MALDI-MS or MS/MS (77% of all spots) are finally unambiguously identified by nano-LC-MS/MS (total identification rate 94%). This protocol can be completed in 6 weeks.

Original languageEnglish (US)
Pages (from-to)1446-1452
Number of pages7
JournalNature protocols
Issue number3
StatePublished - Aug 1 2006
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


Dive into the research topics of 'Protein profiling by the combination of two independent mass spectrometry techniques'. Together they form a unique fingerprint.

Cite this