Mass Spectrometry Working Group

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 (gt1
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.