Anal. Chem. 2008, 80, 8840–8844
Dual Desorption Electrospray Ionization-Laser Desorption Ionization Mass Spectrometry on a Common Nanoporous Alumina Platform for Enhanced Shotgun Proteomic Analysis Ranu Nayak, Jian Liu, Ashis K Sen, and Daniel R. Knapp* Department of Pharmacology, Medical University of South Carolina, Charleston, South Carolina 29425 A gold coated nanoporous alumina surface was used for dual ionization mode mass spectrometric analysis using desorption electrospray ionization (DESI) and laser desorption ionization (LDI). DESI and LDI mass spectrometry (MS) from the nanoporous alumina surface were compared with conventional electrospray ionization (ESI) mass spectrometry and matrix assisted laser desorption ionization (MALDI) for analysis of tryptic digests of proteins. Combined use of DESI and LDI offer greater peptide coverage than either method alone and comparable peptide coverage as with dual MALDI and ESI. This dual ionization technique using a common platform with same sample spot demonstrates a potential time and costeffective tool for improved shotgun proteomic analysis. Proteomic analysis entails study of very complex mixtures of proteins at widely varying levels. It is estimated that through various modes of splicing and post-translational modifications, the human genome gives rise to hundreds of thousands of different protein forms, and just the known proteins present in plasma range in concentrations over more than 10 orders of magnitude.1 Identifying and quantitating these very large numbers of proteins at widely varying concentration levels presents an enormous analytical challenge. Two-dimensional (2D) liquid chromatography (LC)-MS is being increasingly applied in proteomics in the form of “shotgun” analysis where the protein mixture is digested at the outset, and the resulting peptide mixture is separated by 2D-LC prior to MS analysis. In 2D-LC based analysis, more components can be observed by improved separation (i.e., increasing the “separation space” and sampling more fractions), albeit at the expense of increased methodological complexity, time, and effort. Another effective way to observe more components of a separated mixture is to increase the number of components observed in the fractions collected in a given separation, i.e., increasing the “depth” of analysis. The two most common MS ionization modes used in proteomic analysis are electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI). It is well-known that ESI and MALDI analysis of a peptide mixture usually result in observation * To whom correspondence should be addressed. Phone: 843-792-5830. Fax843-792-9946. E-mail:
[email protected]. (1) Anderson, N. L.; Anderson, N. G. Mol. Cell. Proteomics 2002, 1, 845–867.
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of overlapping complementary sets of peptides, and that application of both modes gives significantly increased coverage of the peptides present in a sample compared to either method alone. 2-6 However, conventional ESI and MALDI analysis need different sample formats (liquid solution for ESI and dried matrix-cocrystallized solid for MALDI) requiring more sample and effort to carry out both modes of analysis separately. In recent years, matrix-free laser desorption ionization (LDI) and desorption electrospray ionization (DESI) MS methods have emerged as promising alternatives to conventional MALDI and ESI. Although MALDI is a well-established technique with many advantages, the use of matrix to form a homogeneous cocrystallization with analyte molecules to transfer the energy received from the laser complicates the process. Moreover, matrix background interference also generates significant background ion signals that limit the detection of low mass molecules (
