Proteome Digest - Issue 1, November 2007

Issue 1, November 2007
Welcome to the first electronic edition of Proteome Digest! The goal of this newsletter is to provide you timely, relevant information about new tools and workflows in proteomics research. For this reason, we actively solicit contributions from our readers and other investigators describing new developments in proteomics theory and practice. Proteome Digest will also feature upcoming proteomics seminars, workshops and symposia. We invite you to give us feedback, your comments and contributions are always welcome!

Sample Prep Spotlight
Stable isotope labeling with amino acids in cell culture (SILAC) is a method for quantitation of differential changes in the proteome by mass spectrometry. SILAC incorporates metabolic labels with 'heavy' ¹³C- or ¹⁵N-tagged amino acids into proteins of actively growing cells. When used in combination with biotin enrichment, differentially expressed proteins involved in cell signaling can be monitored. Read the poster

ETD Product Support Bulletin
Confident assignment of the charge state of a precursor from which a particular MS/MS spectrum is derived is crucial for successful and efficient spectrum analysis. High quality spectra obtained by electron transfer dissociation (ETD) are usually observed from peptide precursors with charge states 3+ and higher. In the absence of precursor ion charge state information, several charge states were assumed for each precursor ion when a database search was performed – until now. A new ETD data pre-processing function was developed to automatically assign charge states to precursor ions according to the characteristics of ETD spectra, and is now included in BioWorks software version 3.3.1. Read the bulletin

Just Published
Just published in Science, JMJD6 is a Histone Arginine Demethylase. Bingsheng Chang, et al. describe their study of the cellular function of the Jumonji domain-containing 6 protein (JMJD6). To validate one of their findings, they employ electron transfer dissociation mass spectrometry to characterize in vivo and in vitro product formation, identifying the precise location of two oxidized lysine residues. Read the article

LTQ Orbitrap Webinar
Tips for Successful Mass Calibration of the LTQ Orbitrap by Michaela Scigelova and Wolfgang Metelmann-Strupat. This 17-minute presentation provides the step-by-step procedure for mass calibration on the LTQ Orbitrap instrument. Both normal and high mass range calibrations are discussed. The presentation also features a special section describing the use of a lock-masses (for internal calibration). Watch the webinar

HUPO 2007 in Review
Delegates from around the world attended HUPO's 6th Annual World Congress held October 6 - 10 in Seoul, Korea. The theme of the symposium this year was Proteomics: From Technology Development to Biomarker Applications. Thermo Scientific had an exciting program of presentations including protein quantitation, electron transfer dissociation (ETD) techniques, bioinformatics and tissue imaging. View technical posters

LSMS Abstracts Database Rev 1.6 now available!
With over twenty-nine hundred mass spec abstracts, the CD now includes the following application and technology areas:
● Over 1450 proteomics application abstracts
● 200 MALDI application abstracts
● 160 biomarker discovery abstracts
● 115 PTM analysis abstracts
● Top-down, bottom-up, and high-throughput protein ID
● LCQ, LTQ, LTQ hybrid, TSQ Quantum, and MSQ applications
Request your copy of the CD

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