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Mass Spectrometry Working Group Kong-Joo Lee (Chaired by Sang Won Lee)

Mass Spectrometry Working Group Kong-Joo Lee (Chaired by Sang Won Lee) Participants: MS group from FHCR, PNNL, China, Korea, Taiwan, France Future MS user from Mexico, Singapore. Mission of MS working group

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Mass Spectrometry Working Group Kong-Joo Lee (Chaired by Sang Won Lee)

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  1. Mass Spectrometry Working Group Kong-Joo Lee (Chaired by Sang Won Lee) Participants: MS group from FHCR, PNNL, China, Korea, Taiwan, France Future MS user from Mexico, Singapore • Mission of MS working group • Provide an assessment of instruments and procedures to help other teams make the best investments of resources. • Identify methods and assess performance for techniques to identify low abundance peptides / proteins using MS approaches (e.g. ICAT, SISCAPA,) The most suitable MS techniques for global proteomic profiling in biomarker discovery mode Performance (reproducibility, accuracy, throughput, sensitivity, dynamic range, etc) depending on purpose of proteomics vs Easy-of-use and robustness vs Budget

  2. Biomarker Discovery Platform to be considered high-throughput, sensitivity, reproducibility, speed, accuracy, quantitation, flexibility, information management Various samples Serum/plasma, cell/tissue Fractionation, labeling and Enrichment Reproducibility Comprehensiveness ICAT, glyco-capturing, disulfide-capturing, AQUA (Absolute Quantitation), SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies) MS Platform Triple Quad Ion Trap TOF TOF/TOF Q-TOF ICR (FTMS) Orbitrap Sensitivity (fmol ~ amol) Mass accuracy (>1 ppm) Resolution (3,000 ~100,000) Dynamic range (1,000 ~10,000) Maintenance and Price Data Analysis & storage Combine the discovery mode by MS with biological approach (Ab etc.) Biological & functional validation

  3. orbitrap FT/MS (LC/MS) Orbitrap (LC/MS) From “Strategic Directions International. Liquid Chromatography-Mass Spectrometry: A Plethora of Hyphenated techniques Addressing a Challenging Market Environment”, (Market Analysis and Perspective Report, Los Angeles, California, USA, October 2003)

  4. Mass Spectrometry Working Group • Suggestions • List the topics to discuss before meeting from various groups in advance – discuss the details for specific topics • Prepare the basic specific guideline for the MS experiments • Necessary to have a network to compare the data with others using new instruments • Publish the newsletter or web-based board for discussion for internal members “Throughput is important, but we also need to focus on generating highest quality data: inaccuracy will eventually plague already acquired information.”

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