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Assessing a novel microfluidic interface for shotgun proteome analyses
Author(s) -
Staes An,
Timmerman Evy,
Van Damme Jozef,
Helsens Kenny,
Vandekerckhove Joël,
Vollmer Martin,
Gevaert Kris
Publication year - 2007
Publication title -
journal of separation science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.72
H-Index - 102
eISSN - 1615-9314
pISSN - 1615-9306
DOI - 10.1002/jssc.200700012
Subject(s) - chromatography , chemistry , shotgun proteomics , mass spectrometry , proteome , high performance liquid chromatography , peptide , microfluidics , proteomics , shotgun , analytical chemistry (journal) , tandem mass spectrometry , nanotechnology , materials science , biochemistry , gene
Microfluidic interfaces coupled to ESI mass spectrometers hold great potential for proteomics as they have been shown to augment the overall sensitivity of measurements and require only a minimum of operator manipulations as compared to conventional nano‐LC interfaces. Here, we evaluated a new type of HPLC‐Chips holding larger enrichment columns (thus an increased sample loading capacity) for gel‐free proteome studies. A tryptic digest of a human T‐cell proteome was fractionated by strong cation exchange chromatography and selected fractions were analyzed by MS/MS on an IT mass spectrometer using both the new HPLC‐Chip as well as a conventional nano‐LC‐MS/MS interface. Our results indicate that the HPLC‐Chip is capable of handling very complex peptide mixtures and, in fact, leads to the identification of more peptides and proteins as compared to when a conventional interface was used. The HPLC‐Chip preferentially produced doubly charged tryptic peptides. We further show that MS/MS spectra of doubly charged tryptic peptide ions are more readily identified by MASCOT as compared to those from triply charged precursors and thus argue that besides the improved chromatographic conditions provided by the HPLC‐Chip, its peptide charging profile might be a secondary factor leading to an increased proteome coverage.