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Week  2

Page history last edited by PBworks 14 years, 9 months ago

Some ideas for discussion:


  • (MJ)A unified instrument framework for life detection. Three-layer multiple instrument integrated measurement system is proposed. The first layer (physical layer) deals with fundamental physical and chemical parameter measurements. Some key components may include GC/MS, LC/MS, X-ray instruments, etc. The second layer (data processing layer) deals with raw data processing and integration. The third (decision making layer) conducts high level data integration and intelligent decision making, where advanced quantitative decision making and artificial intelligence methods are expected. The challenge is how we should define the fingerprints of life? Can the system be made portable?


  • (MJ)An entropy measurement system for fingerprints of life. Life is really about order. As firmly believed by Professor Thomas Cover, there is life in the universe. My thought the fundamental principle of life is about ratios of different chemical compounds and physical parameter combination in the universe. We may not easily claim where the life comes from. However, if there is life, the ratios of the fundamental chemical compounds and physical parameters hint the fingerprints. These ratios are changing as time goes. Life is gone because we are loosing this order. In other words, if we can define or measure this order, we may get some handles on past life. This all need to be happened in strict scientific manner, i.e., based on chemical and physical measurements of existing environment and defined in mathematical manner. This is also the reason I think entropy defined in information theory (or similar new concept needs to be introduced). We are really dealing with obtaining and interpreting information. It could be that the information about past life can be or has been measured using existing instruments; but we don't know how to interpret them. Existing techniques from information theory or new terminologies may need to be invented. I know it sounds odd to measure entropy. I guess what I mean here is a soft-sensing technique, i.e., measure a hard-to-be-directly-measured parameters through secondary measurements and calculation based on a mathematical model. Please note this is only an idea for discussion.


Some other Questions:


  • (MJ) Fingerprints of life. What can be considered as fingerprints? It seems many times we are talking about facts, but not fingerprints. By definition, fingerprint is a distinctive or identifying mark or characteristic, such as DNA fingerprint or chemical fingerprints. So what are fingerprints of life? Can we define some of them, a set of them, or some sets of them? Can the logics between these parameter be established; so that reasoning can be conducted on them regarding existence of life? How much can we learn from literature and what are conclusive, either qualatively or quantitatively?


  • (MJ) AFM/ATM. For your information, I spoke with Dr. Kovacs today. He suggested not to spend much time on AFM/ATM.


LC/MS Fundamentals:


  • (MJ) Similar to GC-MS, liquid chromatography mass spectrometry (LC/MS) separates compounds chromatographically before they are introduced to the ion source and mass spectrometer. It differs from GC/MS in that the mobile phase is liquid, usually a combination of water and organic solvents, instead of gas. Most commonly, an electrospray ionization source is used in LC/MS.


  • (MJ) LC-MS is a powerful technique used for many applications which has very high sensitivity and specificity. Generally its application is oriented towards the specific detection and potential identification of chemicals in the presence of other chemicals (in a complex mixture).


  • (MJ) A major difference between traditional HPLC and the chromatography used in LC-MS is that the scale is usually much smaller. 1mm columns were standard for LC-MS (as opposed to 4.6mm for HPLC). More recently 300μm and even "capillary" 75μm columns have become more prevalent. At the low end of these column diameters the flow rates approach 100nL/min and are generally used with nanospray sources.


  • (MJ) Most mass spectrometers can be used in LC-MS however quadrupole and quadrupole ion traps are most common.


LC/MS Applications:


  • (MJ) Pharmacokinetics: very commonly used in pharmacokinetic studies of pharmaceuticals (how quickly the drug clears the body) in animals and humans.


  • (MJ) Proteomics: also often used in the study of proteomics where again components of a complex mixture must be detected and identified in some manner. The bottom-up LC-MS approach to proteomics generally involves protease digestion (usually Trypsin) followed by LC-MS with peptide mass fingerprinting or LC-MS/MS (tandem MS) to derive sequence of indiviual peptides.

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