The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
Friday, January 9, 2015
SysBio15 Asgn_3A_Class_03_Article_03_2015_01_13
Read Article 03 J. A. Mclean, W. B. Ridenour, and R. M. Caprioli.
Profiling and imaging of tissues by imaging ion mobility-mass
spectrometry. J.Mass Spectrom. 42 (8):1099-1105, 2007.. Read carefully -
it is the future of biology. Post a PCRC on the Blog.
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Arman Chowdhury
ReplyDeleteAssignment 3A
0.Knew: MALDI-MS is used for the analysis of endogenous biological species directly from tissue.
1. Learned: Applications of Imaging MALDI–MS include spatial determination of differential protein expression in disease versus control tissue, characterization of tumor and adjacent non-tumor tissue, and mapping the localization of drug and metabolite distribution in targeted tissue or in the context of whole-body animals. It is challenging to discern which signals correspond to lipid versus peptidic analytes in the absence of IM-separation. 3D data set can be obtained at each pixel location in an imaging experiment by adding post-ionization structural separations with ion mobility prior to mass analysis. Structural separation (X) can be used to illustrate the attenuation/ rejection of chemical noise (lipids and peptides) using IM-separation.
2. Pressing ?: Two problems that the research addresses are: IM resolution vs. IM separation optimization, and extremely large file size generation when full IM-MS spectra are attempted to be saved for analysis. Since tackling these issues would mean adding a lot of cost, can we save money by combing IM-MALDI imaging with other imaging techniques (like MRI), rather than trying to improve IM-MALDI on its own?
3. Presentation: Clear presentation of experimental procedure, results and discussion, and benefits of IM-MALDI imaging over MALDI imaging.
4. Thoughts: Very interesting paper which is explaining moving from the traditional 2D mass spectroscopy imaging to 3D and even 5D. A significant breakthrough is being able to discern lipid and peptidic analytes using this technique which was previously very difficult with 2D MALDI imaging.
Selene van der Walt
ReplyDeleteAssignment 3A
0. Knew: about imaging mass spectrometry and its applications, although not a lot about using it to image whole tissue samples.
1. Learned: The mechanics of MALDI, as well as mass spectrometry applications for imaging tissue samples. I also learned about the struggle to balance data acquisition rates and IM resolution and the benefits IM-MS provides for imaging complex tissue including suppression of chemical noise and high mass measurement accuracy.
2. Pressing ?: When each piece of the sample contains so many analytes, how possible is it to note small but significant changes, say a change in a single peptide in diseased vs. healthy tissue?
3. Presentation: Ion mobility-mass spectrometry and its applications for imaging tissue samples
4. Thoughts: This seems like very promising technology that could benefit various fields of study with the ability to accurately image complex tissue samples. It is clearly successful in distinguishing between lipid and peptide analytes however I wonder how successfully it can distinguish individual peptides or lipids or small changes between samples.
Tim Lee
ReplyDeleteAssignment 3A
0. Knew: The existence of methods to image endogenous biological species.
1. Learned: The details of how the known IMS method provided many advantages in characterizing protein expression and drug and metabolite distribution.I also learned the disadvantages of IMS and how IM-MS looked to counter those disadvantages. I learned the specific unique advantages IM-MS has over IMS that were outlined in the conclusion.
2. Pressing: Although the data produced from IM-MS is more selective, it still seems as though the issue of the extremely large volume of data is still present. Are the present methods of data handling and processing efficient and practical enough to deal with the immense volume of IM-MS data?
3. Presentation: Research and outline of the advantages of IM-MS over IMS applications.
4. Thoughts: We're getting to such a microscale level of evaluating each detail of a cell, so it seems like the issue of an extremely high volume of data is inevitable. It is fascinating to see how this recent technology has the power to differentiate minute details and we do need it to understand complex biological mechanisms, but is there efforts being made to be able to process this immense amount of data?
Kendra Oliver A03/ Profiling and imaging of tissues by imaging ion mobility-mass spectrometry
ReplyDeleteJohn A. McLean, Whitney B. Ridenour, and Richard M. Capiolo
0. Knew: Mass spectrometry is a technique that is used to determine the amount and the type of chemicals present in a sample. Determining the mass-to-charge ration and the peak of the ion determines and the amount of the ion respectively from the mass spectrum.
1. Learned: Imaging IM-MS has several advantages including separation of lipids versus peptides or the ability to separates sub-populations. Also, reduction of ion suppression effects in the source of the TOFMS, by temporal IM separation of analysts. Finally and most importantly, potential utility for nearly simultaneous IM-MS/MS of all analytes at a particular pixel coordinate.
2. Pressing ?: What about the issues with identification of spectra for unknown metabolites? Unknown/Non-validated samples?
3. Presentation: What are the practical methods by which imaging IM-MS be used in a system biology organ-on-chips setting?
4. Thoughts: MS is a great technique for detecting things that we already know the m/z ratio and spectral characterization of but what about things that we do not know the MS spectra or the metabolites? What techniques would we be able to use to identify the individual components?
James Pino
ReplyDeleteAssignment 3A
0:Knew: Principle of mass spec.
1:Learned: Purpose and principles of imaging IM-MS. Its advantages. How it can go beyond previous methods and separate based on structural features. The storage required to save high resolution scans.
2: Pressing: What type of data is stored? How many proteins can it distinguish and what is the level of resolution that we are at right now? Can a single cell be analyzed?
3:Presentations: Application and principles of imaging IM-MS.
4:Thoughts: I am curious what type of data this brings and how to utilize it.
Chuck Herring
ReplyDeleteAssignment 3A
0:Knew: Applications of MS outside of imaging, CyTOF for instance.
1:Learned: Pretty much everything about IM-MS was new to me.
2: Pressing: How does the slide prep effect the samples? Are the structural conformations of proteins effected?
3:Presentations: The imaging of tissues using ion mobility-mass spectrometry.
4:Thoughts: Could this method aid in cell segmentation?
Kate Jones
ReplyDeleteAssignment 3A Article 03
0. Knew: I knew of mass spectroscopy using a mass-charge ratio and washing techniques to minimize background and contamination. I honestly did not know much about the topic of the article.
1. Learned: I learned of the limitations in imaging MALDI-MS such as a congested spectra. I also learned that data handling and processing are still challenges.
2. Pressing ?: Does the ethanol washing cause any loss of product or affect the results in another negative way? For example, the article mentions that it is difficult to discern which signals correspond to lipid or peptidic analyses.
3. Presentations: Other possible separation techniques and why this one prevails. Also the remaining challenges to overcome.
4. I did not consider the challenges of separating and characterizing cellular products and other compounds in the fluid passing out of the organ on a chip.
Shuaipeng "Jimmy" Zhang
ReplyDeleteAssignment 3A
0. Knew: Mass spectrometry is widely used in biology and medical research. IM-MS provides 2D separation based on molecular structure and m/z.
1. Learned: The steps used in the preparation of samples, and the mechanism of the IM-MS instrument. The large file sizes associated with each image (full IM-MS spectra image of 3500 pixels takes up 70 GB). The three primary benefits of IM-MS; suppression of chemical noise, qualitative identification of the analyte molecular class, and potential for high mass measurement accuracy by using internal calibrants.
2. Pressing ?: The section describing the IM-MS operations was very convoluted and confusing for me. For example, what are the positive ion mode and reflectron mode? What is the smallest scale that IM-MS can operate at? Is there any way to reduce the enormous amount of storage used per image without sacrificing quality?
3. Presentation: IM-MS costs and comparisons with other techniques. A clearer walk-through of the methodology behind sample preparation and IM-MS functions.
4. Thoughts: MS provides a great tool to characterize compounds. How cost effective is it compared to other techniques?
Juan Gnecco
ReplyDeleteAsgn 3A/ Mclean article
Knew: IM-MS gets its power and data from separating ions based on size,geometry, confromation and size - so two degrees of separation. This allows to identify more types of molecules - lipids and proteins while reducing background. Disadvantages - more expensive and not readily available
Learned: The use of IM-MS for imaging and determining differences between tissues of normal or pathologic. Also learned about power and concept of Im-MS. Spatial use for lipid and protein determination.
Pressing: How is this technology applicable and most importantly available for use. How complex is it to manage such large quantities of data? Is this the only applicable analytic tool for RTA?
Presentation: The potential use of IM-MS for imaging that could offer potential as a highly analytical tool.
Thoughts: A little over my head in terms of the technology because I am not very familiar with this technique and how it can be used to comprehend large complex networks. Not entirely clear on the technical difference between MS/IM-MS/MS-MS
Mark Vander Roest
ReplyDeleteAssignment 3A - JMS Paper, McLean
0. Knew: Really not much about this topic. The basic concept of desoption/ionization for sorting by charge/mass is familiar, but the actual mechanisms are very foreign.
1. Learned: More of the basics of these techniques, the capability of Imaging IM-MS to identify different compounds and how selective it can be for specific compounds, even sorting by structure differences within one species.
2. Pressing: Is 200um resolution good enough for most applications? Coming from a lab that uses live tissue AFM on micron sized patches, 200um sounds a bit large. What's the cost of each scan?
3. Presentation: The concept of imaging IM-MS and how it might be used for high throughput analysis of tissue for various biochemical components.
4. Thoughts: Definitely a lot of unfamiliar stuff in here. I see the potential for it to contribute to a lot of useful analysis, but I wonder what its role in systems biology is.
Cameron Togrye
ReplyDeleteAssignment 3A - JMS Paper, McLean
0. Knew: Laser desorption mass spectrometry (formally known as MALDI) provides the ability to separate molecules based off their m/z, or mass to charge ratio.
1. Learned: Ion Mobility- Mass Spectrometry seems to function by first separating charged biomolecules (ionized by MALDI) according to m/z by an IM-drift cell, and then by separating by cross sectional area via a time of flight MS.
2. Pressing: The paper mentions that it can process data in less than 600 microseconds with the settings they employed. Then why did the paper state that they spent 3 seconds at each spatial location? Is this a measure to ensure a more complete representation of the 300 micrometer location? How homogenized can we expect such a small portion of a tissue to be?
3. A description of how IM-drift cells and time of flight MS separate molecules
4. Thoughts: I think that is pretty amazing that IM-MS can generate a map of a tissue cross section in such a relatively short time. The size of data does seem to represent a major problem to me though, as even the less comprehensive 3D images have file sizes approaching 70 gigs which does not seem feasible for the average lab.
Priyanka Ravichandran
ReplyDeleteAssignment 3A - Mclean article
0. Knew - how basic mass spectrometry works
1. Learned - advantages of IMS, advantages of IM-MS over MS-only techniques
2. Pressing - how to develop new, more efficient data collection methods that can handle the amount of data this method produces
3. Presentation - research paper describing experiment that was done to show how useful IM-MS can be
4. Thoughts - It seems like IM-MS can be quite useful in analyzing complex biological molecules. While the paper showed that it can distinguish between lipids and proteins specifically, what about other classes of molecules?
Cami Johnson
ReplyDeleteAssignment 3A: Article 3
0. Knew: MS is a tool used to separate analytes based on their mass/charge ratio. However, this is mostly unfamiliar material for me, and I knew very little about IM-MS.
1. Learned: Congested spectra are often a problem in biological samples, due to the abundance of analytes. This contributes a great deal of background noise, most of which might not even be of interest. Therefore, IM-MS can be incredibly useful, due to its ability to separate signals structurally, using the collision cross-section, as well as on the basis of m/z ratio. With prior knowledge of the relative collision cross-sections for different molecules, distinctions can be made more easily.
2. Pressing ?: Is the sample consumed faster with a higher resolution (and does this cause problems)? How well known are the relative collision cross-sections for different classes of molecules?
3. Presentation: The basics of IM-MS imaging technology and what makes it different and more advantageous compared to other techniques, along with experimental confirmation of the utility of IM-MS imaging.
4. Thoughts. This is far from my background, so this article was more difficult for me to understand than the previous ones. Although I think I understand the general concepts, the details of the mechanisms behind IM-MS are a little unclear for me. Hopefully, some of the specifics will be cleared up for me in class.
0. Knew: The basic function of MS as a tool to separate substances by mass/charge ratio, time-of-flight measurements.
ReplyDelete1. Learned: Crowded spectra and chemical background noise are often large problems in mass spectrometry. IM-MS is to able to better resolve distinct analytes in crowded spectra by not only selecting by mass/charge ratio, but molecular structure using both ion mobility and time-of-flight mass spectrometry. Analytes are charged using a MALDI laser prior to measurement.
2. Pressing ?: How can data collection be made more efficient? Can file size be reduced by exploiting baseline subtraction for an RTA application? What additional dimensions of characterization could be added to further distinguish analytes? How well would this method translate to microfluidic platforms?
3. Presentation: The presentation of IM-MS as a 2 dimensional method of identifying molecules by class and properties among crowded spectra with high chemical noise.
4. Thoughts: IM-MS seems like an effective analysis tool, but think the data size problem may be a large one for its use in RTA. The quantity of potential molecules of interest and variability of time scales over which a change must be observed would likely result in even larger datasets that would be difficult to analyze.