AnchorChip Based MALDI Sample Preparation.pdf

RESEARCHARTICLE An improved method of sample preparation on AnchorChip? targets for MALDI-MS and MS/MS and its application in the liver proteome project Xumin Zhang1, 2, Liang Shi1, Shaokung Shu1, Yuan Wang1, Kang Zhao1, Ningzhi Xu1, Siqi Liu1, 3 and Peter Roepstorff2* 1 Beijing Genomics institute, Chinese Academy of Science, Beijing, China 2 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark 3 Departement of Medicine, University of Louisville, Louisville, KY, USA An improved method for sample preparation for MALDI-MS and MS/MS using AnchorChip? targets is presented. The method, termed the SMW method (sample, matrix wash), results in better sensitivity for peptide mass fingerprinting as well as for sequencing by MS/MS than pre- viously published methods. The method allows up-concentration and desalting directly on the mass spectrometric target and should be amenable for automation. A draw back caused by extensive oxidation of methionine and tryptophan in the SMWmethod can be alleviated by the addition of n-octyl glucopyranoside and DTT to the sample solution. The method was validated for protein identification from a 2-DE based liver proteome study. The SMWmethod resulted in identification of many more proteins and in most cases with a better score than the previously published methods. Received: March 13, 2006 Revised: February 9, 2007 Accepted: April 9, 2007 Keywords: 2-DE / AnchorChip target / Liver proteome / MALDI-TOF-MS / Sample preparation 2340 Proteomics 2007, 7, 2340–2349 1. Introduction MALDI has gained widespread use in protein studies since its introduction in the late 1980’s by Karas and Hillenkamp [1, 2]. Due to high sensitivity, fast and easy sample prepara- tion, high tolerance to impurities and easy data analysis, it is now one of the key analytical techniques in proteomics. The recent introduction of MALDI-TOF/TOF tandem mass spec- trometers [3, 4] has greatly increased the utility of MALDI- MS in prot