Difference between revisions of "CHEM-5181"

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* <span style="color:#ff0000">'''This course WILL be offered in Fall 2011, WILL NOT be offered in Fall 2012, and will ''likely'' be offered again in Fall 2013 '''</span>
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* This is the new home for the CU-Boulder Graduate Course <b>CHEM-5181: Mass Spectrometry, Chromatography, and Research Methods</b> (note new name in Fall 2013). ''A shortcut to this page is [http://tinyurl.com/CHEM-5181 http://tinyurl.com/CHEM-5181].''
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* This is the new home for the CU-Boulder Graduate Course CHEM-5181: Mass Spectrometry and Chromatography. A shortcut to this page is [http://tinyurl.com/CHEM-5181 http://tinyurl.com/CHEM-5181].
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* Schedule: <font color="blue">'''This course is being offered in Fall 2013 and will be offered in Fall 2014 (co-taught between Paul Ziemann and Jose-Luis Jimenez).'''</font> ''' <font color="red"> '''It will NOT be offered in Fall 2015 as Jose will be on sabbatical.'''</font> <font color="blue">'''It WILL very likely be offered in Fall 2016.'''</font>
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* The old web page is located [http://www.colorado.edu/chemistry/chem5181/ here], and I'll be gradually move things over to this Wiki page, which is much easier to update.
 
  
 
== Course Information ==
 
== Course Information ==
  
−
* [https://docs.google.com/document/pub?id=15oSpKZHRLBssPAdC23923cPuSHeXjsL4M3txEmk7PIU Fall 2011 Syllabus]
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* [https://docs.google.com/document/pub?id=15oSpKZHRLBssPAdC23923cPuSHeXjsL4M3txEmk7PIU Fall 2013 Syllabus]
  
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* Lectures: Tue & Thu 11:00-12:15, Ekeley W166
+
* Schedule:
−
* Labs: to be determined, based on the student and MS facility schedules (typically three Tue afternoons 1-3 pm)
+
** Lectures: Tue & Thu 11:00-12:15, Ekeley W166
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* Office hours: immediately after class on Tue & Thu
+
** Labs: to be determined, based on the student and MS facility schedules (typically three Tue afternoons 1-3 pm)
 +
** Office hours: immediately after class on Tue & Thu, or TBD after start of the course if that time doesn't work.
  
−
* Textbooks:
+
* Textbooks (reading will be assigned from these):
−
** de Hoffmann & Stroobant. <i>Mass Spectrometry, Principles and Applications</i>, 3rd. Ed. ISBN: 0471485667; Library: QD96.M3 H6413 2007
+
** Required: de Hoffmann & Stroobant [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC ''Mass Spectrometry, Principles and Applications''], 3rd. Ed. ISBN: 0471485667; Library: QD96.M3 H6413 2007
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** McLafferty & Turecek <i>Interpretation of Mass Spectra</i>, 4th Ed., ISBN: 0935702253; Library: QC454.M22 1993;
+
** Required: McLafferty & Turecek [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC ''Interpretation of Mass Spectra''], 4th Ed., ISBN: 0935702253; Library: QC454.M22 1993
 +
** Suggested: Moore et al. [http://app.knovel.com/web/toc.v/cid:kpBSAE0006/viewerType:toc/root_slug:building-scientific-apparatus/url_slug:building-scientific-apparatus/? ''Building Scientific Apparatus''], 4th Ed., 2009. [http://0-library.books24x7.com.libraries.colorado.edu/toc.aspx?bookid=42919 Alt. Link]
 +
** Suggested: Wavemetrics [http://www.lulu.com/spotlight/wavemetrics ''Igor Pro Manuals'']
 +
** Suggested: Press et al. [http://www.nr.com/ ''Numerical Recipes'']
 +
** Suggested: Taylor, [http://www.amazon.com/Introduction-Error-Analysis-Uncertainties-Measurements/dp/093570275X ''An Introduction to Error Analysis''], 2nd Ed., 1996.
  
 
== FAQs about CHEM-5181 ==
 
== FAQs about CHEM-5181 ==
Line 21: Line 24:
 
** Answer: Yes, but you need to register for it as "Audit / No Credit", either as a regular CU student or through the [http://conted.colorado.edu/programs/access/ ACCESS Program]. Auditors typically attend lectures but do not do the labs, homeworks, or exams, unless they want to.
 
** Answer: Yes, but you need to register for it as "Audit / No Credit", either as a regular CU student or through the [http://conted.colorado.edu/programs/access/ ACCESS Program]. Auditors typically attend lectures but do not do the labs, homeworks, or exams, unless they want to.
  
−
* '''But I don't want to register at all. Can I still audit the class?'''
+
* '''But I don't want to register at all. Can you make an exception for me to still audit the class?'''
−
** Answer: No.  
+
** Answer: This is not possible for people in industry. For CU postdocs we can sometimes make an exception, if there are at least 8 students registered for the class. Otherwise the Dean may cancel the class due to being too small, and in those cases we need all auditors to register as "Audit / No Credit".  
  
 
* '''I work in industry and use MS and chromatography in my work, can I take the class?'''
 
* '''I work in industry and use MS and chromatography in my work, can I take the class?'''
 
** Answer: Yes, registering through the [http://conted.colorado.edu/programs/access/ ACCESS Program]. You will have the option to take the class as "for grade", "Pass/Fail", and "Audit / No Credit." In making the choice, some things to think about are: (a) you need to have the relevant background or be willing to work to gain the background, especially if you want to take the class for credit. (b) This is a class for 1st year graduate students in Anaytical & Environmental Chemistry, and it takes quite a bit of work to take the class for credit. If you don't have much time for the class due to your work responsibilities, you should register as "Audit / No Credit".
 
** Answer: Yes, registering through the [http://conted.colorado.edu/programs/access/ ACCESS Program]. You will have the option to take the class as "for grade", "Pass/Fail", and "Audit / No Credit." In making the choice, some things to think about are: (a) you need to have the relevant background or be willing to work to gain the background, especially if you want to take the class for credit. (b) This is a class for 1st year graduate students in Anaytical & Environmental Chemistry, and it takes quite a bit of work to take the class for credit. If you don't have much time for the class due to your work responsibilities, you should register as "Audit / No Credit".
 +
 +
* '''I am an undergraduate at CU, can I take the class?'''
 +
** Answer: Yes, if you have the prerequisites. Contact Jose in case of doubt. However you need to take into account that this class takes more work than a typical undergraduate course.
 +
 +
* '''Do I need a laptop for this class?'''
 +
** Yes, as we will do a lot of work using Igor and Labview. A PC is much preferable as Labview does not work well on Macs. If you already have a Mac, we strongly recommend that you install a Windows partition using e.g. [http://www.apple.com/support/bootcamp/ Bootcamp]. You will find it useful well beyond the class, as much research-related software does not run on Macs.
  
 
* '''Do I need a background in computer programming or on Igor to take the class?'''
 
* '''Do I need a background in computer programming or on Igor to take the class?'''
−
** Answer: No. We cover those topics but we assume that people have no background when they start the class. We strongly recommend donwloading a [http://www.wavemetrics.com/support/demos.htm demo version of Igor] and going through the [http://www.wavemetrics.com/products/igorpro/manual.htm Getting Started section of the manual] and the [http://www.wavemetrics.com/products/igorpro/videotutorials.htm Video tutorials] before the class starts.
+
** Answer: We cover those topics but we assume that people have no strong background when they start the class. However we progress quickly, and any prior work that you can do in this area will be very useful in the course. If you do NOT have a background on computer programming (i.e. you don't know how to use FOR loops, DO-WHILE loops, IF-ELSE statements etc.), we strongly recommend downloading a [http://www.wavemetrics.com/support/demos.htm demo version of Igor] and going through the [http://www.wavemetrics.com/products/igorpro/manual.htm Getting Started section of the manual] and the [http://www.wavemetrics.com/products/igorpro/videotutorials.htm Video tutorials] before the class starts, as well as doing some of the [http://tinyurl.com/hw-5181 first homeworks from previous years].
 +
 
 +
* '''Could I use a programming language different than Igor for this class?'''
 +
** Answer: No. It is important to be able to project the screen and discuss code from all students in class, during office hours and HW help sessions, in Piazza etc. That is facilitated by using a single programming language, and would be very confusing if we were to use multiple languages, especially since typically 2/3 of the students in the class have very limited to no previous programming experience. The choice of Igor instead of other equally capable languages such as IDL or Matlab is due to the fact that most groups in our Analytical Chemistry program, as well as many collaborators and future employers, use Igor heavily and they do not use the alternatives. Thus research is made more efficient because one can ask Igor questions from dozens of people in our program. Our groups also use large data analysis packages that are available only in Igor.
 +
 
 +
== Introduction and Tools ==
 +
 
 +
=== Introduction & Review of Fundamentals ===
 +
 
 +
Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_1_Review_Fundamentals.pdf Organization, Introduction & Review of Fundamentals]
 +
* Organizational items
 +
** [http://doodle.com/tb4nf9p2mix452cf Doodle poll for office hrs & labs] / [https://piazza.com/colorado/fall2013/chem5181/home Piazza bulletin board for Q&A] / [https://plus.google.com/communities/100585967223170475855 Google+ Literature Community for class] / [http://www.ni.com/labview/ Labview data acquisition software] / [http://tinyurl.com/hw-5181 Homeworks] / [https://docs.google.com/spreadsheet/pub?key=0Arne3B66AUZCdHVxWHNRTnFGVEJ2WmRQMHpQa25DNWc&output=html Scoring]
 +
 
 +
* Reading on math & statistics (required unless marked otherwise):
 +
** ''For all the readings that include a simulation, you are required to use the simulation for a range of parameters.''
 +
** Basic Statistics: [http://onlinestatbook.com/stat_sim/sampling_dist/ Statistics Demo] / [http://www.chem.uoa.gr/applets/AppletCentralLimit/Appl_CentralLimit2.html Central Limit Theorem]
 +
** Suggested: [https://www.khanacademy.org/math/probability Probability & Statistics (KhA)]
 +
** Linear Regression: [http://www.vias.org/simulations/simusoft_linregr.html Regression] / [http://www.chem.uoa.gr/applets/AppletTheil/Appl_Theil2.html Non-Parametric Regression] /  [http://www.chem.uoa.gr/applets/AppletPoly/Appl_Poly2.html Least Squares Polynomial Approximation] / [http://apps.nrbook.com/c/index.html Numerical Recipes] (pages 656-662 of chapter 15) / [http://www.nlreg.com/orthogonal.htm Intro to Orthogonal Distance Regression] (for 10-Sep) / [http://www.wavemetrics.net/doc/igorman/III-08%20Curve%20Fitting.pdf Orthogonal Distance Regression in Igor Manual] (pages III-208 to III-212) (for 10-Sep)
 +
** Fourier Analysis: [http://www.chem.uoa.gr/applets/AppletFourAnal/Appl_FourAnal2.html Fourier Analysis] /  [http://www.chem.uoa.gr/applets/AppletFourier/Appl_Fourier2.html Fourier Synthesis] /
 +
** Differential Equations:
 +
*** [http://en.wikipedia.org/wiki/Differential_equation DEs (W)]
 +
*** Suggested: [https://www.khanacademy.org/math/differential-equations DE Videos (KhA)]
 +
*** Suggested: [http://dspace.mit.edu/handle/1721.1/70961 DE Videos (MIT OCW)]
 +
 
 +
* Reading on basic physical chemistry, physics, fluids (required unless marked otherwise):
 +
** Kinetic Theory and Gas Properties: [http://celiah.usc.edu/collide/1/ Kinetic Theory of Gases] / [http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/menfre.html Mean Free Path] / [http://phet.colorado.edu/en/simulation/gas-properties Ideal Gas Law, Diffusion] / (Suggested: [http://en.wikipedia.org/wiki/Mean_free_path MFP (W)])
 +
** Reynolds Number & laminar turbulent / flow (for 5-Sep): [https://www.youtube.com/watch?v=XOLl2KeDiOg video demo of the transition] / [http://udel.edu/~inamdar/EGTE215/Laminar_turbulent.pdf Laminar & Turbulent flows] (up to page 6) / [http://en.wikipedia.org/wiki/Reynolds_number Reynolds number (W)] (until "Flow in a wide duct")
 +
** Electric and Magnetic Fields & Forces:
 +
*** [http://srikant.org/core/node8.html Electric & Magnetic Fields] / [http://hyperphysics.phy-astr.gsu.edu/hbase/magnetic/magfie.html#c1 Magnetic Fields & Forces]
 +
*** Suggested: [http://en.wikipedia.org/wiki/Electrostatics Electrostatics (W)]
 +
 
 +
=== Computer Programming & Igor Pro ===
 +
 
 +
* Basic info:
 +
** [http://www.wavemetrics.com/products/igorpro/igorpro.htm Igor Pro graphing and programming software]
 +
** [https://www.wavemetrics.com/order/order_coursework.htm Limitations of Igor Coursework License] that we will use in the class
 +
 
 +
* Reading (required unless marked otherwise):
 +
** Igor: [http://www.wavemetrics.com/products/igorpro/manual.htm "Getting Started" section of the manual]
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/IgorProgConv_v3.ipf Igor Programming Conventions] (v3, 24-Sep-2013)
 +
** [http://cires.colorado.edu/jimenez-group/wiki/index.php/Igor_Quick_Reference Igor Quick Reference Page] / [http://www.wavemetrics.com/products/igorpro/videotutorials.htm Video Tutorials]
 +
** Suggested: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2_Intro_Igor.pdf Intro to Igor Pro] (2011 lecture slides)
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/Read/2013-10_Igor_Reading_Map.pdf Parts of Igor that we will use and not]. We have excluded some topics, either because they are too advanced, tangential to what we need, or unnecessary / confusing. Often things can be done in multiple ways, and in that case we are trying for the students to only use the simplest / least confusing / most useful method and avoid the others.
 +
** Suggested (very useful if no background): [https://www.khanacademy.org/cs/programming Computer Programming (KhA)]
 +
 
 +
* Reading from Igor Users' Guide I & II (when releant for a corresponding HWs) (required unless marked otherwise):
 +
** [http://www.wavemetrics.net/doc/igorman/II-01%20Getting%20Help.pdf Getting Help]
 +
** [http://www.wavemetrics.net/doc/igorman/II-02%20Command%20Window.pdf The Command Window]
 +
** Suggested: [http://www.wavemetrics.net/doc/igorman/II-03%20Expts%20Files%20Folders.pdf Experiments, Files, and Folders]
 +
** [http://www.wavemetrics.net/doc/igorman/II-05%20Waves.pdf Waves]
 +
** Suggested: [http://www.wavemetrics.net/doc/igorman/II-08%20Data%20Folders.pdf Data Folders]
 +
** [http://www.wavemetrics.net/doc/igorman/II-11%20Tables.pdf Tables]
 +
** [http://www.wavemetrics.net/doc/igorman/II-12%20Graphs.pdf Graphs]
 +
** [http://www.wavemetrics.net/doc/igorman/II-14%20Contour%20Plots.pdf Contour Plots]
 +
** [http://www.wavemetrics.net/doc/igorman/II-15%20Image%20Plots.pdf Image Plots]
 +
** Suggested: [http://www.wavemetrics.net/doc/igorman/III-01%20Notebooks.pdf Notebooks]
 +
** Suggested: [http://www.wavemetrics.net/doc/igorman/III-02%20Annotations.pdf Annotations]
  
−
== Lectures, Reading, and Homeworks ==
+
* Required reading from Igor Programming Manual (along with corresponding HWs) (required unless marked otherwise):
 +
** [http://www.wavemetrics.net/doc/igorman/IV-01%20Commands.pdf Working with Commands]
 +
** [http://www.wavemetrics.net/doc/igorman/IV-02%20Prog%20Overview.pdf Programming Overview]
 +
** [http://www.wavemetrics.net/doc/igorman/IV-03%20User%20Functions.pdf User-Defined Functions]
 +
** [http://www.wavemetrics.net/doc/igorman/IV-08%20Debugging.pdf Debugging]
  
−
These lectures are updated every year that the course is offered, so you should not print them ahead of time as they will likely changed for the present year. Relevant printouts will be distributed at the start of every lecture.
+
== Mass Analyzers ==
  
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=== Introduction, Review, Igor ===
+
=== Mass Analyzers I: Electric & Magnetic Sector, Resolution & Accuracy, Ion Optics ===
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol_Sector.pdf Intro to MS, Sector MS, Resolution/Accuracy, Ion Optics]
 +
** Resources we may use in class: [http://www.vias.org/simulations/simusoft_msscope.html MS Oscilloscope Simulator] /  [http://www.vias.org/simulations/simusoft_ms_sectorfield.html Magnetic Sector MS Simulator] / [http://www.vias.org/simulations/simusoft_ionoptics.html Ion Optics Simulator]
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/1_Intro_Review_Fundamentals.pdf Introduction and Review of Fundamentals]
+
* Required Reading:
−
** Resources used in class: [http://www.chem.uoa.gr/applets/AppletCentralLimit/Appl_CentralLimit2.html Central Limit Theorem] /  [http://www.chem.uoa.gr/applets/AppletFourAnal/Appl_FourAnal2.html Fourier Analysis] /  [http://www.chem.uoa.gr/applets/AppletFourier/Appl_Fourier2.html Fourier Synthesis] / [http://www.vias.org/simulations/simusoft_linregr.html Regression] / [http://www.chem.uoa.gr/applets/AppletTheil/Appl_Theil2.html Non-Parametric Regression] /  [http://www.chem.uoa.gr/applets/AppletPoly/Appl_Poly2.html Least Squares Polynomial Approximation] / [http://celiah.usc.edu/collide/1/ Kinetic Theory of Gases] / [http://phet.colorado.edu/en/simulation/gas-properties Ideal Gas Law, Diffusion]
+
** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Introduction Chapter & Sect. 2.5.1 & 2.5.2 of de Hoffman & Stroobant] (for 12-Sep)
 +
** [http://en.wikipedia.org/wiki/Euler_method Euler Method] (for 12-Sep, with HW)
 +
** [https://www.youtube.com/watch?v=4CqaepeaJHA Euler Method Video]
 +
** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Intro to Chapter 2 (p. 85-90), section 2.5.3 (p. 145-146), and Appendix 1.1 & 1.2 (p. 437-438) of de Hoffman & Stroobant] (for 19-Sep)
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/Read/2004_Resol_Acc_MS_v2.pdf Debating Resolution and Mass Accuracy in Mass Spectrometry] (for 19-Sep)
 +
** [http://apps.nrbook.com/c/index.html NR Ch 9: 9.0 Intro and 9.1 Bracketing & Bisection] (p.347-354) (for 24-Sep)
 +
** [https://www.youtube.com/watch?v=DGmNbs5Cywo&list=TLzb5ziJ1Ft_E Bisection method (Video)] & [https://www.youtube.com/watch?v=ErmB2v80tnA Its advantages & disadvantages (Video)] (for 24-Sep)
 +
** [http://www.asms.org/docs/history-posters/evolution-of-ms-1910-to-1940-2010.pdf The Early History of MS]
 +
** [http://www.asms.org/docs/history-posters/thomson's-vision-commercialization-2009.pdf The Commercialization of MS]
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2_Intro_Igor.pdf Introduction to Igor Pro]
+
* ''Suggested Reading:
−
** ''Required Reading: [http://www.wavemetrics.com/products/igorpro/manual.htm "Getting Started" section of the manual] and the [http://www.wavemetrics.com/products/igorpro/videotutorials.htm Video tutorials]''
+
** [http://www.chemheritage.org/research/policy-center/oral-history-program/projects/critical-mass/index.aspx Critical Mass: a History of MS]
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/IgorProgrammingConventions_v2.ipf Igor Programming Conventions (v2)]
+
** [http://www.asms.org/publications/historical/history-posters ASMS Posters on the History of MS]'' (for 19-Sep)
 +
** [http://mass-spec.lsu.edu/msterms/index.php/Resolution_(mass_spectrometry) More details on the definitions] (Not everyone uses the same definitions, and there is an active debate on this topic. Thus you should always be clear about which definition YOU are using). (for 19-Sep)
  
−
* Homeworks
+
* 2011 and earlier materials, for reference
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW1_Review_Fund.doc Homework #1 on review of fundamentals]
 
 
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW2_Igor_Sector.docx Homework #2 on Igor and Electric Sector MS]
 
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW2_Igor_Sector.docx Homework #2 on Igor and Electric Sector MS]
  
−
=== Mass Analyzers ===
+
=== Mass Analyzers II: Time-of-Flight MS ===
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOFMS.pdf Time-of-Flight MS]
 +
 
 +
* Reading for Tue 1-Oct.
 +
** Required: [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.4 of de Hoffman & Stroobant on TOFMS]
 +
** Required: Agilent videos: [https://www.youtube.com/watch?v=iF21xzaY07w ESI TOFMS] & [https://www.youtube.com/watch?v=BFuZaIi-zDk ESI Q-TOFMS w/ MW/MS]
 +
** Suggested: [http://www.rmjordan.com/Resources/Tutorial.pdf Tutorial on TOFMS] (from RM Jordan, manufacturer of custom MS)
 +
** Suggested: [http://en.wikipedia.org/wiki/Time-of-flight_mass_spectrometry TOFMS in Wikipedia]
 +
** Suggested: [http://www.asms.org/docs/history-posters/bendix-tof.pdf?sfvrsn=2 ASMS poster on the Bendix TOFMS] (first commercial TOFMS)
 +
** [https://docs.google.com/forms/d/17zQGXhIKpJot_-RZbhu3TLqBdPOTxMrLW8hbwIVEPcQ/viewform Reading Quiz] (needs to be completed at least 90 min before the start of class)
 +
 
 +
* Reading for Thu 3-Oct.
 +
** Required: [http://www.wavemetrics.net/doc/igorman/III-10%20Function%20Analysis.pdf Igor Manual on Solving Ordinary-Differential Equations (ODEs)] (p. III-270 to III-283)
 +
** Required: Runge-Kutta Method: [https://www.youtube.com/watch?v=AT7Olelic8U Part I] & [https://www.youtube.com/watch?v=gzgghqto1Ws Part II]
 +
** Suggested: [http://apps.nrbook.com/c/index.html Numerical Recipes Chapter 16]
 +
** Suggested: [http://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods Wikipedia on Runge-Kutta]
 +
** [https://docs.google.com/forms/d/1PHZToo88a9IA4i4eAny4YCtyqiLUTQx5oxMbclAJcrU/viewform Reading Quiz] (needs to be completed at least 90 min before the start of class)
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol_Sector.pdf Intro to MS, Resolution/Accuracy, Sector Mass Spectrometers, and Ion Optics]
+
* Reading for Thu 10-Oct. (Required unless marked otherwise)
−
** ''Required Reading: de Hoffmann and Stroobant 2007: Introduction & Section 2.5''
+
** [http://www.wavemetrics.net/doc/igorman/III-07%20Analysis.pdf Histograms in Igor] (p. III-128 to III-136)
−
** ''Suggested Reading: [http://www.asms.org/Publications/Historical/HistoryofMassbrSpectrometryandASMS/tabid/94/Default.aspx ASMS Posters on the History of MS]''
+
** [https://piazza.com/class/hiy250ehses10l?cid=93 Piazza post on responses to the last reading]
−
** Resources used in class: [http://www.vias.org/simulations/simusoft_msscope.html MS Oscilloscope Simulator] /  [http://www.vias.org/simulations/simusoft_ms_sectorfield.html Magnetic Sector MS Simulator] / [http://www.vias.org/simulations/simusoft_ionoptics.html Ion Optics Simulator]
+
** [https://plus.google.com/u/0/communities/100585967223170475855 Posts from your classmates in G+] (need to +1 one and only one of the 2)
 +
*** Suggested: look at the articles after reading the posts, and reading the abstract and looking at the rest of the figures (i.e. skimming the paper, a critical skill in drinking from the research literature firehose!)
 +
** [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC Ch. 6 of McLafferty] (p. 103-114)
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/Labs/Voyager_Biospectrometry_user_guide.pdf Appendix E of Voyager MALDI-TOFMS User's Guide]  
 +
*** Chapter 1 of the same guide is suggested if you have time
 +
** [https://docs.google.com/forms/d/1hjnnT3YQvY7UYBge1SZwgHbYvq-j1QPl51YG06fSj2A/viewform Reading Quiz]
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOFMS.pdf Time-of-Flight MS]
+
* Reading for Thu 17-Oct. (Required)
−
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 2.4''
+
** Required (for HW): [http://www.wavemetrics.net/doc/igorman/III-08%20Curve%20Fitting.pdf Curve Fitting in Igor] (III-158 to 182, rest of the chapter is suggested as needed for HW)
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS3_Quad.pdf Quadrupoles]
+
=== Mass Analyzers III: Quadrupole MS ===
−
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 2.1''
+
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS3_Quad.pdf Quadrupoles]  
−
** Videos from Agilent: [http://www.youtube.com/watch?v=PSFF6JJEFPE&NR=1 GC/MS Triple Quad] / [http://www.chem.agilent.com/en-US/Products/Instruments/ms/6100SeriesQuadrupoleLCMSSystems/Pages/6100_video.aspx LC/MS Quad] / [http://www.chem.agilent.com/en-US/Products/Instruments/ms/6410triplequadrupolelcms/pages/gp56595.aspx LC/MS Triple Quad]
 
 
** ''Prop: Quadrupole''
 
** ''Prop: Quadrupole''
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf Ion Traps, FTICR, Orbitrap]
+
* Reading for Tue 22-Oct (all required):
−
** ''Required Reading: de Hoffmann and Stroobant 2007, Sections 2.2, 2.3, 2.6''
+
** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.1 of de Hoffmann & Stroobant]
−
** Ion trap movies: [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/1_dampinggas.exe geometry + buffer gas], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/2_trappingmsms.exe trapping], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/3_scanning_ms.exe scanning], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/5_esilcq.exe ESI-IT overview], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_1_elimination.exe MS/MS elimination], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_2_capture.exe capture], and [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_3_collision.exe collision-induced dissociation]
+
** [http://cires.colorado.edu/jimenez/CHEM-5181/Read/1998_JCE_Steel_Quad_Simul.pdf Understanding the Quadrupole Mass Filter through Computer Simulation], Steel and Henchman, <i>J. Chem. Ed.</i> 75:1049-1054, 1998.
−
** [http://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introd. animation of FTICR]
+
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/2013-10-15_Quad_Simulation.pxp Quad Simulation in Igor] following Steel and Henchman. Need to understand the code and be ready answer questions about it and about how it would be modified. Investigations using the code will be the next HW.
 +
** [http://www.youtube.com/watch?v=PSFF6JJEFPE&NR=1 Agilent GC/MS Triple Quad Video]
 +
 
 +
=== Mass Analyzers IV: Ion Traps ===
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf 3d & 2d Quadrupole Ion Traps, FTICR, Orbitrap]
 +
 
 +
* Reading:
 +
** Required [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC: Sect. 2.2, 2.3, 2.6 & 2.7 of de Hoffmann and Stroobant 2007]
 +
** Required: Ion trap movies: [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/1_dampinggas.exe geometry + buffer gas], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/2_trappingmsms.exe trapping], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/3_scanning_ms.exe scanning], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/5_esilcq.exe ESI-IT overview], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_1_elimination.exe MS/MS elimination], [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_2_capture.exe capture], and [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/MSMS_3_collision.exe collision-induced dissociation]
 +
*** Note: IT movies only work on PCs, find a PC to watch them if you have a Mac
 +
** Required: [https://www.youtube.com/watch?v=PYpbKSmOnNc Homemade ion trap with two spons and a wire!]
 +
** Required: [http://planetorbitrap.com/about-the-technology#.Ukuv_4bks_c Orbitrap animation]
 +
** Required: [http://planetorbitrap.com/orbitrap-velos-pro#.UkuxOobks_c animation of auxiliary components to Orbitrap]
 +
** Suggested if you are curious: [https://www.youtube.com/watch?v=8NAFdjfM-ds Interview of Makarov] (Orbitrap inventor, very commercial)
 +
** Required: [http://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introductory animation of FTICR]
 +
 
 +
== MS Interpretation ==
 +
 
 +
=== Interp. I: Intro & Elemental Composition ===
 +
 
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp1_Intro_Elem.pdf Introduction to MS Interpretation & Elemental Composition 1]
 +
 
 +
** ''Prop: Offline NIST database''
 +
 
 +
* Reading for Tue 8-Oct
 +
** Required: [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC Ch. 1 and Sect. 2.1-2.4 of McLafferty & Turecek]
 +
** Required: [http://webbook.nist.gov NIST Chemistry WebBook]
 +
** Suggested: [http://www.atmos-chem-phys.net/9/6633/2009/acp-9-6633-2009-supplement.pdf Example of ions in high-resolution MS of Ambient Aerosols (Fig. S-18)]
 +
 
 +
* Reading & HW for Tue 15-Oct (required unless noted otherwise)
 +
** HW 8, due Tue: work through the 6 remaining group questions in the handouts from last time. We will discuss in class.
 +
** [http://books.google.com/books/about/Interpretation_of_Mass_Spectra.html?id=xQWk5WQfMQAC Sect. 2.5-2.8 McLafferty & Turecek]
 +
** [http://las.perkinelmer.com/Content/TechnicalInfo/TCH_ICPMSThirtyMinuteGuide.pdf Periodic Table of the Isotopes (only)] (the rest of this document is only suggested)
 +
** [http://en.wikibooks.org/wiki/Probability/Combinatorics Combinatorics] (combinations w/ replacement is what applies for isotopes)
 +
** Suggested: [https://www.khanacademy.org/math/probability/probability-and-combinatorics-topic/permutations_and_combinations/v/combinations Combinations videos (KA)]
 +
** Suggested: [http://www.science.uottawa.ca/eih/ch1/ch1.htm Use of isotopes for environmental studies] (the "small" isotopic fractionations that we discussed in class)
 +
** Suggested: [http://en.wikipedia.org/wiki/Isotope_fractionation Isotopic Fractionation (W)]. See the links these, those are the processes that cause the deviations studied by stable isotope research.
 +
** Software Tools:
 +
*** [http://www.chemcalc.org/ ChemCalc Isotopic Distribution] (Online) (play with the different functions)
 +
*** [http://www.sisweb.com/mstools/isotope.htm Isotopic Calculator (SIS)] (same)
 +
*** [http://sites.google.com/site/isoproms/ IsoPro Isotopic Distribution] (PC Download, install, play with)
 +
*** [http://chemdata.nist.gov/ MS Tools from NIST] (if website is back up)
 +
*** Suggested: [http://www.mmass.org/ NMass] (very powerful, but note that it has a lot of proteomics functions that are not relevant to us)
 +
** [https://docs.google.com/forms/d/13OZ1kkzLXyvTPU_jGFTFbMfJmJI7y9VwuFMrrqqxMHI/viewform Reading Quiz]
 +
 
 +
=== Interp. II: The Molecular Ion ===
 +
 
 +
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp3_Molec_Ion.pdf Interpretation III: The Molecular Ion]
 +
** ''Required Reading: McLafferty and Turecek 1993, Chapter 3''
 +
** [http://www.chem.ucla.edu/harding/ec_tutorials/tutorial28.pdf Tutorial on interpretation] (there is a question in the reading from this document, which one of your classmates found clearer than the book)
 +
 
 +
=== Interp. III: Fragmentation Mechanisms ===
 +
 
 +
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp4_Frag_Mech.pdf Interpretation IV: Fragmentation Mechanisms]
 +
** ''Required Reading: McLafferty and Turecek 1993, Chapters 4, and skim 7 & 8''
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/ART_MS_Invited.pdf Autoresonant MS (ART-MS)] (Invited Lecture by Jeff Rathbone, Brooks Inc.)
+
=== Interp. IV: Postulation of Molecular Structures ===
−
** [http://www.brooks.com/documents.cfm?documentID=5413 IJMS paper on ART-MS]
+
 
−
** [http://www.brooks.com/pages/4209_simplicity_solutions_830_vqm_mass_spectrometer.cfm Web page on ART-MS product] with additional information
+
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp5_Molec_Struct.pdf Interpretation V: Postulation of Molecular Structures]
 +
** ''Required Reading: McLafferty and Turecek 1993, Chapter 5''
 +
 
 +
* Old Homeworks & Additional Practice on interpretation
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/Unknowns_Lee.pdf Additional Practice Problems] & [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/Solutions_Lee.pdf  Their Solutions]
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp1_Elemental_Comp.doc HW Int1 (elemental composition)]
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp2_2011.pdf HW Int2]
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp3_2011.pdf HW Int3]
  
−
* Homeworks on Mass Analyzers
+
== Ionization Sources & Detectors ==
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW3_TOFMS.docx HW3: Resolution & Simulation of Laboratory #1 on MALDI-TOFMS]
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/Raw_TOFAMS_Spec_only.itx TOFMS spectrum for Problem #1] (Igor Text File, save and double-click to open in Igor)
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_MS_Resolution.docx HW 3.1: mass spec resolution and accuracy]
 
−
** [http://cires.colorado.edu/jimenez-group/AMSsd/L_OTH_Q_001_diiodomethane.pxp Quadrupole MS for donwload] (Igor PXP format)
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/VLSPYDLTHK.xlsx Orbitrap MS for download] (Excel format)
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Ion_Optics_Simul.docx HW: Ion Optics Simulation Part 1] (not in 2011)
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Ion_Optics_Simul_2.docx HW: Ion Optics Simulation Part 2] (not in 2011)
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW4_Quad_Simul.docx HW4: Quadrupole MS simulation]
 
−
*** [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/1998_JCE_Steel_Quad_Simul.pdf Understanding the Quadrupole Mass Filter through Computer Simulation], Steel and Henchman, <i>J. Chem. Ed.</i> 75:1049-1054, 1998.
 
−
*** [http://en.wikipedia.org/wiki/Runge-Kutta 4th order Runge-Kutta Integration Method]
 
  
−
=== Ionization Sources ===
+
=== Ion Sources ===
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz1_EI.pdf Introduction and Electron Ionization]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz1_EI.pdf Introduction and Electron Ionization]
Line 93: Line 243:
 
** [http://www.ptrms.com PTRMS Commercial Instrument]
 
** [http://www.ptrms.com PTRMS Commercial Instrument]
 
** [http://www.syft.com SYFT Commercial Instrument]
 
** [http://www.syft.com SYFT Commercial Instrument]
 +
** [http://www.atmos-meas-tech.net/4/1471/2011/ Aerodyne CIMS Commercial Instrument]
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz3_ESI.pdf Electrospray and its Ion Chemistry (from Invited Lecturer Dr. Shuji Kato)]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz3_ESI.pdf Electrospray and its Ion Chemistry (from Invited Lecturer Dr. Shuji Kato)]
Line 99: Line 250:
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz4_Others.pdf Ionization IV: Bombardment, MALDI and Elemental]  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz4_Others.pdf Ionization IV: Bombardment, MALDI and Elemental]  
−
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 1.4, 1.7, 1.8, 1.9, 1.14, 1.15 ''
+
** Required Reading:  
 +
*** de Hoffmann and Stroobant 2007, Section 1.4, 1.7, 1.8, 1.9, 1.14, 1.15
 +
*** [http://www.spectroscopyonline.com/spectroscopy/data/articlestandard//spectroscopy/052002/8458/article.pdf A beginner's guide to ICPMS]
 +
*** [http://las.perkinelmer.com/content/TechnicalInfo/tch_icpmsthirtyminuteguide.pdf The 30-minute guide to ICPMS]
 +
 
 
** [http://instaar.colorado.edu/~marchitt//lab.html ICP-MS Facility at CU-Boulder]
 
** [http://instaar.colorado.edu/~marchitt//lab.html ICP-MS Facility at CU-Boulder]
 
** ''Prop: MALDI plate''
 
** ''Prop: MALDI plate''
Line 105: Line 260:
 
* Homeworks on Ionization:
 
* Homeworks on Ionization:
 
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_ESI_Charge_States.docx HW5.1: ESI charge states]
 
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_ESI_Charge_States.docx HW5.1: ESI charge states]
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_EI_Source.docx HW5.2: EI Source]
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_EI_Spectrum_MonteCarlo.docx HW5.3: Montecarlo simulation of methane spectrum]
 
  
 
=== MS Detectors, Data Acquisition, Vacuum ===
 
=== MS Detectors, Data Acquisition, Vacuum ===
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS_Detectors_AD_SNR.pdf MS Detectors, A/D, Signal-to-Noise]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS_Detectors_AD_SNR.pdf MS Detectors, A/D, Signal-to-Noise]
−
** ''Required Reading: de Hoffmann and Stroobant 2007, Chapter 3''
+
 
−
** [http://www.vias.org/simulations/simusoft_emultiplier.html Simulation of an Electron Multiplier]
+
* Reading:
−
** [http://www.vias.org/simulations/simusoft_adconversion.html Simulation of an Analog-to-Digital Converter]
+
** Required: de Hoffmann and Stroobant 2007, Chapter 3
−
** [http://cires.colorado.edu/jimenez-group/QAMSResources/Docs/PCI-6110E.pdf Manual and specifications of a typical analog-to-digital converter]
+
** Required: [http://www.vias.org/simulations/simusoft_emultiplier.html Simulation of an Electron Multiplier]
 +
** Required: [http://www.vias.org/simulations/simusoft_adconversion.html Simulation of an Analog-to-Digital Converter]
 +
** Required: [http://cires.colorado.edu/jimenez-group/QAMSResources/Docs/PCI-6110E.pdf Manual and specifications of a typical analog-to-digital converter]
 +
** Required: [http://www.wavemetrics.net/doc/igorman/III-09%20Signal%20Processing.pdf Igor Manual on FFT] (p. III-237 to III-241) (Rest of the chapter is 'suggested')
 +
** Suggested: [http://apps.nrbook.com/c/index.html Numerical Recipes Chapter 12.0-12.2 on FFT]
 
** ''Props: EMs, MCP, EM in vacuum mount''
 
** ''Props: EMs, MCP, EM in vacuum mount''
  
Line 120: Line 277:
 
** ''Props: turbo pump, diaphragm pump''
 
** ''Props: turbo pump, diaphragm pump''
  
−
=== MS Interpretation ===
+
== Data Acquisition using Labview ==
−
 
 
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp1_Intro.pdf Introduction to MS Interpretation]
 
−
** ''Required Reading: McLafferty and Turecek 1993, Chapters 1 and 6''
 
−
** [http://webbook.nist.gov NIST Chemistry WebBook]
 
−
** [http://www.atmos-chem-phys.net/9/6633/2009/acp-9-6633-2009-supplement.pdf Example of ions in high-resolution MS of Ambient Aerosols (Fig. S-18)]
 
−
** [http://chemdata.nist.gov/ MS Tools from NIST]
 
−
** ''Prop: Offline NIST database''
 
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp2_Elem.pdf Using Elemental Composition in Interpretation]
+
* Reading:
−
** ''Required Reading: McLafferty and Turecek 1993, Chapter 2''
+
** [http://www.ni.com/labview/skills-guide/en/ Labview Skills Guide]
−
** [http://sites.google.com/site/isoproms/ IsoPro Isotopic Distribution] (PC Download)
+
** Required: [http://www.ni.com/gettingstarted/labviewbasics/ Labview Basics] (Sections TBD)
−
** [http://www.chemcalc.org/ ChemCalc Isotopic Distribution] (Online)
+
** Required: [http://sine.ni.com/myni/self-paced-training/app/main.xhtml Self-Paced Training] (sections TBD).
−
** [http://las.perkinelmer.com/Content/TechnicalInfo/TCH_ICPMSThirtyMinuteGuide.pdf Periodic Table of the Isotopes]
+
*** You will need the license number of the CU Academic License of Labview, which will be provided via Piazza.
  
−
* -------------- Material below this line is from the previous offering of the course ------------------
+
== MS Applications ==
  
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp3_Molec_Ion.pdf Interpretation III: The Molecular Ion]
+
=== Specific Implementations or Applications of MS ===
−
** ''Required Reading: McLafferty and Turecek 1993, Chapter 3''
 
−
 
 
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp4_Frag_Mech.pdf Interpretation IV: Fragmentation Mechanisms]
 
−
** ''Required Reading: McLafferty and Turecek 1993, Chapters 4, and skim 7 & 8''
 
−
 
 
−
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Interp5_Molec_Struct.pdf Interpretation V: Postulation of Molecular Structures]
 
−
** ''Required Reading: McLafferty and Turecek 1993, Chapter 5''
 
−
 
 
−
* Homeworks on interpretation
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/Interp_Checklist_v2.doc Checklist for interpretation HW]
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp1_Elemental_Comp.doc HW Int1 (elemental composition)]
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp2_2011.pdf HW Int2]
 
−
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW_Interp3_2011.pdf HW Int3]
 
−
 
 
−
=== Specific Applications of MS ===
 
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Protein_Peptides_W_Old.pdf Mass Spectrometry of Peptides and Proteins] by Prof. W. Old (2011)
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Protein_Peptides_W_Old.pdf Mass Spectrometry of Peptides and Proteins] by Prof. W. Old (2011)
Line 159: Line 294:
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/L_dePuy_Flowing_Afterglow.pdf The Flowing Afterglow and its application to Astrochemistry] by Prof. Chuck dePuy (2010)
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/L_dePuy_Flowing_Afterglow.pdf The Flowing Afterglow and its application to Astrochemistry] by Prof. Chuck dePuy (2010)
 +
 +
* [http://cires.colorado.edu/jimenez/CHEM-5181/Restricted/ART_MS_Invited.pdf Autoresonant MS (ART-MS)] (Invited Lecture by Jeff Rathbone, Brooks Inc., Fall 2012)
 +
** [http://www.brooks.com/documents.cfm?documentID=5413 IJMS paper on ART-MS]
 +
** [http://www.brooks.com/pages/4209_simplicity_solutions_830_vqm_mass_spectrometer.cfm Web page on ART-MS product] with additional information
  
 
* [http://cires.colorado.edu/jimenez/Papers/2010-09_IAC_Aerosol_MS_Tutorial.pdf Aerosol Mass Spectrometry] by J.L. Jimenez (2010)
 
* [http://cires.colorado.edu/jimenez/Papers/2010-09_IAC_Aerosol_MS_Tutorial.pdf Aerosol Mass Spectrometry] by J.L. Jimenez (2010)
 +
** [https://www.youtube.com/watch?v=kmZHwCBJHO8 Video tutorial on AMS]
  
−
=== Chromatography and Chemical Separations ===
+
== Chromatography and Analytical Separations ==
  
−
* Introduction and Theory of Chromatography: [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C1_Intro_Theory.pdf Lecture 1] & [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C2_Intro_Theory.pdf Lecture 2]
+
* [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C1_Intro_Theory.pdf Introduction and Theory of Chromatography I]  
 +
* [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C2_Intro_Theory.pdf Theory of Chromatography II]
 
** [http://www.chem.uoa.gr/applets/AppletChrom/Appl_Chrom2.html Chromatographic Separation Demo] (Web)
 
** [http://www.chem.uoa.gr/applets/AppletChrom/Appl_Chrom2.html Chromatographic Separation Demo] (Web)
 +
** [http://sciencecases.lib.buffalo.edu/cs/collection/detail.asp?case_id=386&id=386 A Play about the Van Deemter equation]
  
 
* [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C3_IMS_CE.pdf Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis]
 
* [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C3_IMS_CE.pdf Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis]
Line 224: Line 366:
 
*(General, Reference) [http://www.msterms.com/wiki/index.php?title=Main_Page MS Terms and Definitions Project]  
 
*(General, Reference) [http://www.msterms.com/wiki/index.php?title=Main_Page MS Terms and Definitions Project]  
 
*(General, Reference) [http://pubs3.acs.org/acs/journals/toc.page?incoden=chreay&indecade=0&involume=101&inissue=2 "Frontiers in Mass Spectrometry"] ,Special issue <i>Chem. Rev.</i> 101(2), 2001.  
 
*(General, Reference) [http://pubs3.acs.org/acs/journals/toc.page?incoden=chreay&indecade=0&involume=101&inissue=2 "Frontiers in Mass Spectrometry"] ,Special issue <i>Chem. Rev.</i> 101(2), 2001.  
−
*(General, Reference) The 'Thompson'. A Suggested Unit for Mass Spectroscopists. R. G. Cooks RG and A. L. Rockwood, <i>Rap. Comm. Mass Spec.</i> 5, 93, 1991. [http://www.colorado.edu/chemistry/chem5181/Restricted/Cooks_Thompson.pdf (pdf)]  
+
*(General, Reference) The 'Thomson'. A Suggested Unit for Mass Spectroscopists. R. G. Cooks RG and A. L. Rockwood, <i>Rap. Comm. Mass Spec.</i> 5, 93, 1991. [http://www.colorado.edu/chemistry/chem5181/Restricted/Cooks_Thompson.pdf (pdf)]
 +
* (History, Reference) [http://www.chemheritage.org/research/policy-center/oral-history-program/projects/critical-mass/index.aspx Critical Mass: A History of MS]
 
*(Ion Optics, Advanced) [http://www3.interscience.wiley.com/cgi-bin/abstract/66001221/ABSTRACT Ion Optics in Mass Spectrometry]. H. Wollnik, <i>J. Mass. Spec.</i>, 34: 991-1006, 1999.
 
*(Ion Optics, Advanced) [http://www3.interscience.wiley.com/cgi-bin/abstract/66001221/ABSTRACT Ion Optics in Mass Spectrometry]. H. Wollnik, <i>J. Mass. Spec.</i>, 34: 991-1006, 1999.
 
*(Vacuum, Reference) [http://www.colorado.edu/chemistry/chem5181/Restricted/MooreDavisCoplan_Chap3.pdf Vacuum Technology], Davis, Moore, and Coplan
 
*(Vacuum, Reference) [http://www.colorado.edu/chemistry/chem5181/Restricted/MooreDavisCoplan_Chap3.pdf Vacuum Technology], Davis, Moore, and Coplan
Line 301: Line 444:
 
*(Aerosol, Link to references) [http://mae.ucdavis.edu/wexler/spa_refs.html A List of Publications in Single Particle Mass Spectrometry], maintained by Prof. Tony Wexler.
 
*(Aerosol, Link to references) [http://mae.ucdavis.edu/wexler/spa_refs.html A List of Publications in Single Particle Mass Spectrometry], maintained by Prof. Tony Wexler.
 
*(Aerosol, Link to references) [http://www.udel.edu/chem/johnston/SPMSdbase.html Another List of Publications in Single Particle Mass Spectrometry], this one maintained by Prof. Murray Johnston.
 
*(Aerosol, Link to references) [http://www.udel.edu/chem/johnston/SPMSdbase.html Another List of Publications in Single Particle Mass Spectrometry], this one maintained by Prof. Murray Johnston.
 +
 +
=== Applications: Other ===
 +
 +
* (IRMS, suggested) [http://rsi.aip.org/resource/1/rsinak/v84/i1/p011101_s1?TRACK=RSIJAN13 Isotope-Ratio MS]
  
 
===MS Interpretation===
 
===MS Interpretation===
Line 349: Line 496:
 
=== GCxGC ===
 
=== GCxGC ===
  
−
*(GCxGC,) [http://www.j-chrom-sci.com/index.php?option=com_virtuemart&page=shop.product_details&flypage=flypage.tpl&product_id=2127 Using Comprehensive Two-Dimensional Gas Chromatography to Study the Atmosphere], J.F. Hamilton, <i>Journal of Chromatographic Science</i>, 48, 274-282, 2010.  
+
*(GCxGC, Advanced) [http://www.j-chrom-sci.com/index.php?option=com_virtuemart&page=shop.product_details&flypage=flypage.tpl&product_id=2127 Using Comprehensive Two-Dimensional Gas Chromatography to Study the Atmosphere], J.F. Hamilton, <i>Journal of Chromatographic Science</i>, 48, 274-282, 2010.  
−
*(GCxGC,) [http://dx.doi.org/10.1016/S0021-9673(03)00242-5 Comprehensive two-dimensional gas chromatography: a powerful and versatile analytical tool], J. Dalluge, J. Beens, and U.A.T. Brinkman, <i>Journal of Chromatography A</i>, 1000, 69-108, 2003.  
+
*(GCxGC, Suggested) [http://dx.doi.org/10.1016/S0021-9673(03)00242-5 Comprehensive two-dimensional gas chromatography: a powerful and versatile analytical tool], J. Dalluge, J. Beens, and U.A.T. Brinkman, <i>Journal of Chromatography A</i>, 1000, 69-108, 2003.  
−
*(GCxGC,) [http://dx.doi.org/10.1021/ac041549+ GC x GC], J.M.D. Dimandja, <i>Anal. Chem.</i>, 76, 167A - 174A, 2004.
+
*(GCxGC, Suggested) [http://dx.doi.org/10.1021/ac041549+ GC x GC], J.M.D. Dimandja, <i>Anal. Chem.</i>, 76, 167A - 174A, 2004.
−
*(GCxGC,) [http://dx.doi.org/10.1080/10826070600574762 Recent advances in comprehensive two-dimensional gas chromatography (GC x GC)], T. Gorecki, O. Panic, and N. Oldridge, <i>Journal of Liquid Chromatography & Related Technologies</i>, 29(7-8), 1077-1104, 2006.
+
*(GCxGC, Advanced) [http://dx.doi.org/10.1080/10826070600574762 Recent advances in comprehensive two-dimensional gas chromatography (GC x GC)], T. Gorecki, O. Panic, and N. Oldridge, <i>Journal of Liquid Chromatography & Related Technologies</i>, 29(7-8), 1077-1104, 2006.
  
 
==Award for the Best Performance in CHEM-5181==
 
==Award for the Best Performance in CHEM-5181==
  
−
*Fall 2010: Brett Palm (PhD Chemistry, Jimenez group)
+
* Fall 2011: Rui Li (PhD Atmospheric Sciences, de Gouw group)
−
*Fall 2009: Eleanor Waxman (PhD Chemistry, Volkamer group)
+
* Fall 2010: Brett Palm (PhD Chemistry, Jimenez group)
−
*Fall 2007: Sean Coburn (PhD Chemistry, Volkamer group)
+
* Fall 2009: Eleanor Waxman (PhD Chemistry, Volkamer group)
−
*Fall 2006: Jesse Marcum (PhD Chemistry, Weber group)
+
* Fall 2007: Sean Coburn (PhD Chemistry, Volkamer group)
−
*Fall 2004: Steve Dutton (PhD Mechanical Engineering, Hannigan group)
+
* Fall 2006: Jesse Marcum (PhD Chemistry, Weber group)
−
*Fall 2003: Melinda Beaver (PhD Chemistry, Tolbert group)
+
* Fall 2004: Steve Dutton (PhD Mechanical Engineering, Hannigan group)
−
*Fall 2002: Aaron Appel (PhD Chemistry, Rakowski-Dubois group)
+
* Fall 2003: Melinda Beaver (PhD Chemistry, Tolbert group)
 +
* Fall 2002: Aaron Appel (PhD Chemistry, Rakowski-Dubois group)
  
 
== Other MS and Chrom. Resources ==
 
== Other MS and Chrom. Resources ==
Line 402: Line 550:
 
*[http://www.sciencedirect.com/science?_ob=JournalURL&_issn=13873806&_auth=y&_acct=C000047944&_version=1&_urlVersion=0&_userid=918210&md5=a040de59a240c21a86c8e27e7ca55b39 International Journal of Mass Spectrometry] (Norlin Basement, QC451.I54)
 
*[http://www.sciencedirect.com/science?_ob=JournalURL&_issn=13873806&_auth=y&_acct=C000047944&_version=1&_urlVersion=0&_userid=918210&md5=a040de59a240c21a86c8e27e7ca55b39 International Journal of Mass Spectrometry] (Norlin Basement, QC451.I54)
 
*[http://www.interscience.wiley.com/jpages/0951-4198/ Rapid Communications in Mass Spectrometry]  
 
*[http://www.interscience.wiley.com/jpages/0951-4198/ Rapid Communications in Mass Spectrometry]  
−
*[http://www.sciencedirect.com/web-editions?_ob=JournalURL&_issn=10440305&_auth=y&_acct=C000019778&_version=1&_urlVersion=0&_userid=417887&md5=e076e941f0b4e70bcd071fb4f528cbc7 Journal of the American Society for Mass Spectrometry]  
+
*[http://link.springer.com/journal/volumesAndIssues/13361 Journal of the American Society for Mass Spectrometry]  
 
*[http://www.impub.co.uk/abstract.html European Mass Spectrometry Journal]  
 
*[http://www.impub.co.uk/abstract.html European Mass Spectrometry Journal]  
 
*[http://www.interscience.wiley.com/jpages/1076-5174/ Journal of Mass Spectrometry]
 
*[http://www.interscience.wiley.com/jpages/1076-5174/ Journal of Mass Spectrometry]

Revision as of 01:50, 17 October 2013

  • This is the new home for the CU-Boulder Graduate Course CHEM-5181: Mass Spectrometry, Chromatography, and Research Methods (note new name in Fall 2013). A shortcut to this page is http://tinyurl.com/CHEM-5181.
  • Schedule: This course is being offered in Fall 2013 and will be offered in Fall 2014 (co-taught between Paul Ziemann and Jose-Luis Jimenez). It will NOT be offered in Fall 2015 as Jose will be on sabbatical. It WILL very likely be offered in Fall 2016.

Contents

Course Information

  • Schedule:
    • Lectures: Tue & Thu 11:00-12:15, Ekeley W166
    • Labs: to be determined, based on the student and MS facility schedules (typically three Tue afternoons 1-3 pm)
    • Office hours: immediately after class on Tue & Thu, or TBD after start of the course if that time doesn't work.

FAQs about CHEM-5181

  • Can I audit the class?
    • Answer: Yes, but you need to register for it as "Audit / No Credit", either as a regular CU student or through the ACCESS Program. Auditors typically attend lectures but do not do the labs, homeworks, or exams, unless they want to.
  • But I don't want to register at all. Can you make an exception for me to still audit the class?
    • Answer: This is not possible for people in industry. For CU postdocs we can sometimes make an exception, if there are at least 8 students registered for the class. Otherwise the Dean may cancel the class due to being too small, and in those cases we need all auditors to register as "Audit / No Credit".
  • I work in industry and use MS and chromatography in my work, can I take the class?
    • Answer: Yes, registering through the ACCESS Program. You will have the option to take the class as "for grade", "Pass/Fail", and "Audit / No Credit." In making the choice, some things to think about are: (a) you need to have the relevant background or be willing to work to gain the background, especially if you want to take the class for credit. (b) This is a class for 1st year graduate students in Anaytical & Environmental Chemistry, and it takes quite a bit of work to take the class for credit. If you don't have much time for the class due to your work responsibilities, you should register as "Audit / No Credit".
  • I am an undergraduate at CU, can I take the class?
    • Answer: Yes, if you have the prerequisites. Contact Jose in case of doubt. However you need to take into account that this class takes more work than a typical undergraduate course.
  • Do I need a laptop for this class?
    • Yes, as we will do a lot of work using Igor and Labview. A PC is much preferable as Labview does not work well on Macs. If you already have a Mac, we strongly recommend that you install a Windows partition using e.g. Bootcamp. You will find it useful well beyond the class, as much research-related software does not run on Macs.
  • Do I need a background in computer programming or on Igor to take the class?
    • Answer: We cover those topics but we assume that people have no strong background when they start the class. However we progress quickly, and any prior work that you can do in this area will be very useful in the course. If you do NOT have a background on computer programming (i.e. you don't know how to use FOR loops, DO-WHILE loops, IF-ELSE statements etc.), we strongly recommend downloading a demo version of Igor and going through the Getting Started section of the manual and the Video tutorials before the class starts, as well as doing some of the first homeworks from previous years.
  • Could I use a programming language different than Igor for this class?
    • Answer: No. It is important to be able to project the screen and discuss code from all students in class, during office hours and HW help sessions, in Piazza etc. That is facilitated by using a single programming language, and would be very confusing if we were to use multiple languages, especially since typically 2/3 of the students in the class have very limited to no previous programming experience. The choice of Igor instead of other equally capable languages such as IDL or Matlab is due to the fact that most groups in our Analytical Chemistry program, as well as many collaborators and future employers, use Igor heavily and they do not use the alternatives. Thus research is made more efficient because one can ask Igor questions from dozens of people in our program. Our groups also use large data analysis packages that are available only in Igor.

Introduction and Tools

Introduction & Review of Fundamentals

Lecture Notes: Organization, Introduction & Review of Fundamentals

Computer Programming & Igor Pro

Mass Analyzers

Mass Analyzers I: Electric & Magnetic Sector, Resolution & Accuracy, Ion Optics

Mass Analyzers II: Time-of-Flight MS

  • Reading for Thu 17-Oct. (Required)
    • Required (for HW): Curve Fitting in Igor (III-158 to 182, rest of the chapter is suggested as needed for HW)

Mass Analyzers III: Quadrupole MS

Mass Analyzers IV: Ion Traps

MS Interpretation

Interp. I: Intro & Elemental Composition

    • Prop: Offline NIST database

Interp. II: The Molecular Ion

Interp. III: Fragmentation Mechanisms

Interp. IV: Postulation of Molecular Structures

Ionization Sources & Detectors

Ion Sources

MS Detectors, Data Acquisition, Vacuum

  • Vacuum Technology
    • Props: turbo pump, diaphragm pump

Data Acquisition using Labview

MS Applications

Specific Implementations or Applications of MS

Chromatography and Analytical Separations

Student Presentations

Reference material for presentations

Labs

Lab 1: MALDI-TOFMS

Lab 2: Electrospray MS

Lab 3: GC-MS of mixtures

Student Choice Projects

Reference Materials

  • Suggestions Encouraged. Please send links to jose.jimenez at colorado.edu
  • All PDFs are linked to the journal websites, so they need to be access while on the CU campus or when using VPN into CU's network

Introduction to Mass Spectrometry

Ionization Methods

Mass Analyzers

Applications: Aerosols

Applications: Other

MS Interpretation

Chromatography: General

Electric Field Driven Separations

LC, GC, and IC

GCxGC

Award for the Best Performance in CHEM-5181

  • Fall 2011: Rui Li (PhD Atmospheric Sciences, de Gouw group)
  • Fall 2010: Brett Palm (PhD Chemistry, Jimenez group)
  • Fall 2009: Eleanor Waxman (PhD Chemistry, Volkamer group)
  • Fall 2007: Sean Coburn (PhD Chemistry, Volkamer group)
  • Fall 2006: Jesse Marcum (PhD Chemistry, Weber group)
  • Fall 2004: Steve Dutton (PhD Mechanical Engineering, Hannigan group)
  • Fall 2003: Melinda Beaver (PhD Chemistry, Tolbert group)
  • Fall 2002: Aaron Appel (PhD Chemistry, Rakowski-Dubois group)

Other MS and Chrom. Resources

Mass Spectrometry Societies

MS & Chrom. Courses at other Universities

Useful MS Links

Journals with Substantial Mass Spectrometry and Analytical Separations Content

Analytical Chemistry Journals

Mass Spectrometry Journals

Chromatography and Analytical Separations Journals

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