Dear Colleagues, Do some of you have experience working with tandem-ms data for biomarker discovery (not for sequencing/identification as it's often used)? The data at hand are generated with a HTP microspray peptide LC then into Tandem MS. The biologist is looking at the 3D data of time by m/z by intensity (relative abundance) 'Time' resulted from the LC part separates proteins by their hydrophobic properties. So this kind of data has one extra dimension 'time' than the MALDI/SELDI spectra. Tips, tech reports and weblinks on analysing such data are greatly appreiciated. Xiaochun

> From: Xiaochun Li <xiaochun@jimmy.harvard.edu> > To: bioconductor@stat.math.ethz.ch > Sent: Wednesday, December 01, 2004 5:33 PM > Subject: [BioC] tandem MS question > > Do some of you have experience working with tandem-ms > data for biomarker discovery (not for sequencing/identification > as it's often used)? > > The data at hand are generated with a HTP microspray > peptide LC then into Tandem MS. The biologist is looking > at the 3D data of time by m/z by intensity (relative abundance) > 'Time' resulted from the LC part separates proteins by their > hydrophobic properties. So this kind of data has one extra > dimension 'time' than the MALDI/SELDI spectra. You might want to investigrate the "chemometric" multi-way (also called N-way) analysis techniques. Excellent sources for information and software are www.models.kvl.dk/users/rasmus/ and www.eigenvector.com Dave David Lee Duewer National Institute of Standards and Technology 100 Bureau Drive Stop 8390 Gaithersburg, MD 20899-8390 USA