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

Participants: MS group from FHCR, PNNL, China, Korea, Taiwan, FranceFuture MS user from Mexico, Singapore

Mission of MS working group 1. Provide an assessment of instruments and procedures to help

other teams make the best investments of resources. 2. 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 proteomicsvsEasy-of-use and robustness vs Budget

Various samplesSerum/plasma, cell/tissue

Fractionation, labeling and Enrichment

MS PlatformTriple Quad

Ion TrapTOF

TOF/TOFQ-TOF

ICR (FTMS)Orbitrap

Data Analysis & storage

high-throughput, sensitivity, reproducibility, speed, accuracy, quantitation, flexibility, information management

Biomarker Discovery Platform to be considered

Biological & functional validation

Sensitivity (fmol ~ amol)Mass accuracy (>1 ppm)

Resolution (3,000 ~100,000)Dynamic range (1,000 ~10,000)

Maintenance and Price

Combine the discovery mode by MS with biological approach (Ab etc.)

Reproducibility Comprehensiveness ICAT, glyco-capturing, disulfide-capturing, AQUA (Absolute Quantitation), SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies)

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)

orbitrap

Orbitrap(LC/MS)

FT/MS(LC/MS)

Mass Spectrometry Working Group

Suggestions

1. List the topics to discuss before meeting from various groups in advance – discuss the details for specific topics

2. Prepare the basic specific guideline for the MS experiments3. Necessary to have a network to compare the data with others using

new instruments4. 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.”