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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].''
 
* 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].''
* 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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* Schedule: <font color="blue">'''This course will be offered in Fall 2017 by Jose.'''</font>  
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<span style="color:#FFFF00; background:#00C000">================================================<br>THIS WEB PAGE HAS MOVED to [http://tinyurl.com/Main5181 http://tinyurl.com/Main5181]. PLEASE FOLLOW THAT LINK FOR THE UPDATED MATERIAL<br>================================================</span>
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== Course Information & Organization ==
 
== Course Information & Organization ==
  
* [https://docs.google.com/document/pub?id=15oSpKZHRLBssPAdC23923cPuSHeXjsL4M3txEmk7PIU Fall 2013 Syllabus]
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* [http://tinyurl.com/CHEM-5181-Syll Syllabus: http://tinyurl.com/CHEM-5181-Syll]
  
* Schedule:
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* 3 Key Electronic Resources for the Course
** Lectures: Tue & Thu 11:00-12:15, Ekeley W166
+
** This Wiki page [http://tinyurl.com/CHEM-5181 http://tinyurl.com/CHEM-5181]: readings and class slides
** Labs: to be determined, based on the student and MS facility schedules (typically three Tue afternoons 1-3 pm)
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** [https://piazza.com/class/j6wrqna1p7w13s Piazza bulletin board]: for Q&A & email list
** Office hours: immediately after class on Tue & Thu, or TBD after start of the course if that time doesn't work.
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** [http://tinyurl.com/hw-5181 Homeworks]
 +
 
 +
* Other Resources:
 +
** [https://docs.google.com/spreadsheets/d/1ZiYkjswI7UD1D1V5JiS7EQeg_-yACUp6vRnuDd_erlI/edit#gid=0 Spreadsheet for time conflicts]
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** [https://docs.google.com/spreadsheets/d/1QlPkrmRnmxyQjDAZmcsf4YdyhUsxXMW3xX3kBJ5ak6Q/edit#gid=895878608 Course schedule] (to be updated)
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 +
== Introduction & Review of Fundamentals ==
 +
 
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_1_Review_Fundamentals.pdf Organization, Introduction & Review of Fundamentals]
 +
 
 +
* Readings:
 +
** 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)]
 +
** Probability and Statistics:
 +
*** 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)]
  
 
* Textbooks (reading will be assigned from these):
 
* Textbooks (reading will be assigned from these):
 
** 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
 
** 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
 
** 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
 
** 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]
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** Required: Wavemetrics [http://www.lulu.com/spotlight/wavemetrics ''Igor Pro Manuals''] (available as PDFs inside Igor, but printed version recommended)
** Suggested: Wavemetrics [http://www.lulu.com/spotlight/wavemetrics ''Igor Pro Manuals'']
+
** Suggested: Travis & Kring, [http://www.amazon.com/LabVIEW-Everyone-Graphical-Programming-Edition/dp/0131856723 Labview for Everyone] /  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. / 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: 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.
+
** ''For all the readings that include a simulation, you are required to use the simulation for a range of parameters.''
 +
 
 +
** 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)])
 +
 
 +
** Complete this [https://docs.google.com/forms/d/1oL2N908rzAnkYC3-bvGX7MEeWS6OghNH0DZUZwjCZFs/viewform Reading Quiz] by 9am on Thu.
 +
 
 +
* [http://tinyurl.com/hw-5181 HW for Thu 28-Aug-2014]
 +
 
 +
== Intro to Igor & MS Resolution ==
 +
 
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_Igor.pdf Intro to Igor]
 +
 
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_Igor.pdf Intro to Igor] & [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol.pdf MS Resolution]
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 +
* 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 for Tue 2-Sep-2014 (Required unless marked otherwise)
 +
** On Mass Spectrometer Resolution
 +
*** [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)
 +
*** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac022010j Scaling MS Plateaus with High-Resolution FT-ICRMS]. A. G. Marshall, C. L. Henderickson, and S. D.-H. Shi <i>A. Chem</i>, 74(9), 252A (2002)
 +
** On Igor
 +
*** 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)
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*** [http://payam.minoofar.com/igor/ Unofficial Igor Programming Manual]
 +
*** [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]
 +
*** [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]
 +
 
 +
* For you to do:
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** Complete this [https://docs.google.com/forms/d/1oL2N908rzAnkYC3-bvGX7MEeWS6OghNH0DZUZwjCZFs/viewform Reading Quiz] by 9am on class day.
 +
** [http://tinyurl.com/hw-5181 HW2] due Tue 2-Sep-2014
 +
 
 +
== MS Analyzers: TOFMS ==
 +
 
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOF.pdf Time-of-Flight]
 +
 
 +
* Reading for next class:
 +
** Required: [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.4 (start) and 2.4.1 of de Hoffman & Stroobant on linear 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, Intro: [http://www.rmjordan.com/Resources/Tutorial.pdf Tutorial on TOFMS] (from RM Jordan, manufacturer of custom MS)
 +
** Suggested, Intro: [http://en.wikipedia.org/wiki/Time-of-flight_mass_spectrometry TOFMS in Wikipedia]
 +
** Suggested, Historical: [http://www.asms.org/docs/history-posters/bendix-tof.pdf?sfvrsn=2 ASMS poster on the Bendix TOFMS] (first commercial TOFMS)
 +
** Suggested, Intro: [http://www.chem.agilent.com/temp/radF998C/00045384.pdf Agilent's Tutorial on Time-of-Flight Mass Spectrometry]
 +
** Suggested, Intro: [http://www3.interscience.wiley.com/cgi-bin/abstract/110464657/ABSTRACT Tutorial. Principles and instrumentation in time-of-flight mass spectrometry. Physical and instrumental concepts]. M. Guilhaus, <i>J. Mass. Spec.</i>, Volume 30: 1519-1532, 1995. [http://www.colorado.edu/chemistry/chem5181/Restricted/Guilhaus_ToFRev_JMS1995.PDF (pdf)]
 +
* For you to do
 +
** [http://tinyurl.com/hw-5181 HW3]
 +
** [https://docs.google.com/forms/d/17zQGXhIKpJot_-RZbhu3TLqBdPOTxMrLW8hbwIVEPcQ/viewform Reading Quiz] (needs to be completed at least 2 hrs before the start of class)
 +
 
 +
* Reading for 2nd Lecture
 +
** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC All of Sect. 2.4 of de Hoffman & Stroobant on TOFMS]
 +
** Suggested: also the suggested readings for the previous lecture
 +
** Suggested, Advanced: [http://www3.interscience.wiley.com/cgi-bin/abstract/13069/ABSTRACT Perfect Timing: Time-of-flight Mass Spectrometry] M. Guilaus, RCMS, 1997, 951-962
 +
** Suggested, Advanced: [http://www3.interscience.wiley.com/cgi-bin/abstract/10009442/ABSTRACT  Time-of-Flight Mass Spectrometry: State of the Art in Chemical Analysis and Molecular Science] C. Weickhardt, F. Moritz, and J. Grotemeyer. MS Review. 1996, 139-162.
 +
** Suggested, Advanced: [http://jchemed.chem.wisc.edu/Journal/issues/1997/nov/abs1288.html Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Instrumentation and Applications] D. C. Muddiman, R. Bakhtiar, S. A. Hofstadler, and R. D. Smith <i>J. Chem. Ed.</i> 74, 1288, 1997.
 +
** Suggested, Advanced: [http://www3.interscience.wiley.com/cgi-bin/abstract/71004180/ABSTRACT Orthogonal acceleration time-of-flight mass spectrometry]. Guilhaus et al., <i>Mass Spec. Rev.</i>, 19: 65-107, 2000.
 +
** Suggested, Advanced: [http://link.aip.org/link/%3FRSINAK/26/1150/1 Time-of-Flight Mass Spectrometer with Improved Resolution] W. C. Wiley and I. H. McLaren, Rev. Sci. Instrum. 1955, 26(12), 1150-1157.
 +
** Suggested, Advanced: [http://www.ingentaconnect.com/content/els/13873806/2001/00000206/00000003/art00392 Time-of-flight mass spectrometry (concepts, achievements, and prospects)] B. A. Mamyrin, Int J Mass Spec, 2001, 251-266
 +
 
 +
* For you to do
 +
** [http://tinyurl.com/hw-5181 HW4]
 +
** Reading Quiz (needs to be completed at least 2 hrs before the start of class)
 +
 
 +
* Reading for 25-Sep-2014
 +
** [http://en.wikipedia.org/wiki/Euler_method Euler Method]
 +
** [https://www.youtube.com/watch?v=4CqaepeaJHA Euler Method Video]
 +
 
 +
== MS Analyzers: Quadrupole ==
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS3_Quad.pdf Quadrupoles]
 +
** ''Prop: Quadrupole''
 +
 
 +
* Reading for Tue 30-Sep
 +
** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.1 of de Hoffmann & Stroobant]
 +
** Suggested, will use in HW: [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.
 +
** (Will use in HW) [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://cires.colorado.edu/jimenez/CHEM-5181/HW/2013-10-15_Quad_Simulation.ipf IPF of quad simulation] (only needed if PXP is giving you problems)
 +
** [http://www.youtube.com/watch?v=PSFF6JJEFPE&NR=1 Agilent GC/MS Triple Quad Video]
 +
** Suggested: [http://jchemed.chem.wisc.edu/Journal/Issues/1996/Dec/abs1142.html Quadrupole Mass Spectrometers: An Intuitive Look at the Math]. Leary and Schmidt, <i>J. Chem. Ed.</i> 73: 1142-1144, 1996.
 +
** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/mas.20249/abstract Linear Quadrupoles in Mass Spectrometry], D.J. Douglas, <i>Mass Spec. Rev.</i>, 28: 937-960, 2009.
 +
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/85010411/ABSTRACT An introduction to quadrupole–time-of-flight mass spectrometry] I. V. Chernushevich, A. V. Loboda, and B. A. Thomson, JMS, 2001, 849-865
 +
** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-8-Tandems-and-Hybrids.pdf Lecture on MS/MS from Prof. Bob Cotter]
 +
 
 +
== MS Analyzers: Ion Traps, FTICR, Orbitrap ==
 +
 
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf 3d & 2d Quadrupole Ion Traps, FTICR, Orbitrap]
 +
 
 +
* Reading: (all required unless marked otherwise):
 +
** [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]
 +
** 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
 +
** [https://www.youtube.com/watch?v=PYpbKSmOnNc Homemade ion trap with two spons and a wire!]
 +
** [http://www.youtube.com/watch?v=KjUQYuy3msA Orbitrap animation]
 +
** Suggested if you are curious: [https://www.youtube.com/watch?v=8NAFdjfM-ds Short interview of Alexander Makarov] (Orbitrap inventor, very commercial)
 +
** [http://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introductory animation of FTICR]
 +
** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-9888(199704)32:4%3C351::AID-JMS512%3E3.0.CO;2-Y/abstract An Introduction to Quadrupole Ion Trap Mass Spectrometry], R. Mach, <i>J. Mass Spec.</i>, 32: 351-369, 1997.
 +
** Suggested: [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2001/73/i03/abs/ac000973h.html Baseline mass resolution of peptide isobars: A record for molecular mass resolution], He F, Hendrickson CL, Marshall AG, <i>Anal. Chem.</i> 73 (3): 647-650, 2001.
 +
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/24610/ABSTRACT Fourier Transform Mass Spectrometry (Tutorial)] I. J. Amster, JMS, 1996, 1325-1337.  
 +
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/10009487/ABSTRACT Fourier transform ion cyclotron resonance mass spectrometry: A primer]. A.G. Marshall et al., <i>Mass Spec. Rev.</i> 17: 1-35, 1998.
 +
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/110471441/ABSTRACT The Orbitrap: a new mass spectrometer (Perspective)]. R.G. Cooks et al., <i>J Mass Spec.</i> 40: 430-443, 2005.
 +
** [https://docs.google.com/forms/d/1l5AH8QkKPtAaBprvTBOJzEZ-FndScaFShvnCyxyhrUg/viewform Reading Quiz]
  
* Organizational items
+
== Chemical Ionization (CI) ==
** [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]
 
  
== Introduction and Tools ==
+
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz2_CI.pdf Chemical Ionization]
  
=== Introduction & Review of Fundamentals ===
+
* Reading
 +
** de Hoffmann and Stroobant 2007, Sections 1.2, 1.12, 1.13, 1.16
 +
** [http://www.ptrms.com PTRMS Commercial Instrument] (read at least 10 pages on the site, focusing on the most relevant to the fundamentals and the course)
 +
** [http://www.syft.com/about-sift-ms SYFT Commercial Instrument] (same)
 +
** [https://sites.google.com/site/citofms/ ToF-CIMS Commercial Instrument] (same)
 +
** Suggested: [http://www.atmos-meas-tech.net/4/1471/2011/ Bertram. et al. 2011] on Aerodyne ToF-CIMS
 +
** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ja00964a001 Chemical Ionization Mass Spectrometry. I.  General Introduction]. M.S.B. Munson and F.H. Field, <i>J. Am. Chem. Soc.</i>, 2621, 1966. (First paper on CI)
 +
 
 +
== Electrospray Ionization (ESI) & Ambient Ionization Sources ==
  
Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_1_Review_Fundamentals.pdf Organization, Introduction & Review of Fundamentals]
+
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz3_ESI.pdf Electrospray and its Ion Chemistry]
 +
** ''Prop: ESI Source''
 +
 
 +
* Reading on ESI (suggested unless marked otherwise)
 +
** Required: de Hoffmann and Stroobant 2007, Section 1.11
 +
** [http://www3.interscience.wiley.com/journal/122463140/abstract Electrospray: From ions in solution to ions in the gas phase, what we know now]. P. Kebarle and U.H. Verkerk, <i>Mass Spec. Rev.</i> doi: 10.1002/mas.20247, 2009.
 +
** [http://www3.interscience.wiley.com/cgi-bin/abstract/72512664/ABSTRACT  A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry] P. Kebarle, <i>J.Mass Spec.</i>,804-817, 2000.
 +
** [http://www.pnas.org/cgi/content/abstract/91/24/11290 The Emergence of Mass Spectrometry in Biochemical Research] G. Siuzdak, <i>Proc. Natl. Acad. Sci. USA</i>, 91(24), 11290, 1994.
 +
** [http://nobelprize.org/nobel_prizes/chemistry/laureates/2002/chemadv02.pdf Mass spectrometry and nuclear magnetic resonance applied to biological macromolecules.] Advanced Information on the Nobel Prize in Chemistry 2002.
 +
** [http://www3.interscience.wiley.com/cgi-bin/abstract/93518527/ABSTRACT Practical implications of some recent studies in electrospray ionization fundamentals]. Cech and Enke, <i>Mass Spec. Rev.</i>, 20: 362-387, 2002.
 +
** [http://www3.interscience.wiley.com/cgi-bin/abstract/72512616/ABSTRACT Some tenets pertaining to ESI-MS] R. B. Cole, <i>J. Mass Spec.</i>,763-772,2000. 
 +
** [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/1996/68/i01/abs/ac9509519.html Analytical Properties of the Nanoelectrospray Ion Source] M. Wilm and M. Mann, <i>A. Chem.</i>, 1-8, 1996.
 +
 
 +
* Reading on Ambient Sources
 +
** Required: [http://www3.interscience.wiley.com/journal/122518620/abstract Atmospheric Pressure Ion Sources]. <i>Mass Spec. Rev.</i>, doi: 10.1002/mas.20246, 2009.
 +
** [http://www3.interscience.wiley.com/cgi-bin/abstract/112126895/ABSTRACT Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology] Z. Takats, J. M. Wiseman, and R. G. Cooks, <i>J. Mass Spec.</i>,1261-1275, 2005.
 +
** [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i08/abs/ac050162j.html Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions] R. B. Cody, J. A. Laramee, H. D. Durst, <i>A. Chem.</i>, 2297-2303, 2005.
 +
 
 +
= Old Materials from Here Down, for Reference =
 +
 
 +
== Introduction & Review of Fundamentals ==
  
 
* Reading on math & statistics (required unless marked otherwise):  
 
* 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)
 
** 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] /  
 
** 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] /  
Line 40: Line 190:
  
 
* Reading on basic physical chemistry, physics, fluids (required unless marked otherwise):
 
* 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")
 
** 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 ===
+
* Info for Student Presentations
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_presentations.pdf Tips for Student Presentations]
 +
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/JournalSkim_Template.doc Template for Journal Skims (.doc)]
 +
** Required reading: [http://cires.colorado.edu/jimenez/CHEM-5181/Read/Advice_Beginning_Speakers.pdf Advice to Beginning Physics Speakers], by James C. Garland, Physics Today, July 1991.
 +
 
 +
== Computer Programming, Igor Pro, and Labview ==
  
* Basic info:
+
=== Igor Pro ===
** [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):
 
* 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)
 
** 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.  
 
** [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)]
 
** Suggested (very useful if no background): [https://www.khanacademy.org/cs/programming Computer Programming (KhA)]
 
** Suggested: [http://lists.info-igor.org/listinfo.cgi/info-igor-info-igor.org Sign up for Igor email list] (Strongly suggested for people who will use Igor in their research. Suggest "daily digest" mode to reduce the number of messages you get)
 
** Suggested: [http://lists.info-igor.org/listinfo.cgi/info-igor-info-igor.org Sign up for Igor email list] (Strongly suggested for people who will use Igor in their research. Suggest "daily digest" mode to reduce the number of messages you get)
 +
** Suggested: [http://payam.minoofar.com/wp-content/uploads/2007/07/introduction_to_igor_programming.pdf Intro to Igor Programming]
  
 
* Reading from Igor Users' Guide I & II (when releant for a corresponding HWs) (required unless marked otherwise):
 
* Reading from Igor Users' Guide I & II (when releant for a corresponding HWs) (required unless marked otherwise):
Line 74: Line 221:
 
** Suggested: [http://www.wavemetrics.net/doc/igorman/III-02%20Annotations.pdf Annotations]
 
** Suggested: [http://www.wavemetrics.net/doc/igorman/III-02%20Annotations.pdf Annotations]
  
* Required reading from Igor Programming Manual (along with corresponding HWs) (required unless marked otherwise):
+
=== Data Acquisition using Labview ===
** [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]
+
* Lecture Materials:
** [http://www.wavemetrics.net/doc/igorman/IV-03%20User%20Functions.pdf User-Defined Functions]
+
** [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/LV_Class_2_PID.pdf Intro to PID control]
** [http://www.wavemetrics.net/doc/igorman/IV-08%20Debugging.pdf Debugging]
+
 
 +
* Reading:
 +
** [http://www.ni.com/labview/skills-guide/en/ Labview Skills Guide]
 +
** [http://www.ni.com/gettingstarted/labviewbasics/ Labview Basics]  
 +
** [http://www.ni.com/academic/students/learn-labview/ Learn Labview]
 +
** [http://sine.ni.com/myni/self-paced-training/app/main.xhtml Self-Paced Training]  
 +
** Specific reading items required for each day are listed [https://docs.google.com/document/d/1NZAvXmL43BZHpOleswY6bITdOpdKpzgZt9OzipDvYu8/pub here]
 +
** [http://en.wikipedia.org/wiki/PID_controller Reading on PID]
  
=== Student Presentations ===
+
* Practice Programs:
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Intro_2_presentations.pdf Tips for Student Presentations]
+
** [http://cires.colorado.edu/science/groups/volkamer/wiki/index.php/CHEM5161#Lecture_Schedule Example VIs in the CHEM-5161 page]
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/JournalSkim_Template.doc Template for Journal Skims (.doc)]
+
**  Example:[http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Error_Example.vi Error Example 1] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Error_Example_2.vi Error Example 2] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Error_Example_3.vi Error Example 3] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Global_1.vi Global Example] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Simulated_AI_Data.vi Simulated AI Example] / [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/Simulated_AO_Data.vi Simulated AO Example]
** Required reading: [http://cires.colorado.edu/jimenez/CHEM-5181/Read/Advice_Beginning_Speakers.pdf Advice to Beginning Physics Speakers], by James C. Garland, Physics Today, July 1991.
+
** [http://cires.colorado.edu/jimenez/CHEM-5181/Soft/USB6008_P_controller_w_simulated_data_homework.vi Program for HW #15] (Need the simulated AO, AI, and Global examples)
 +
*** Notes:  you can open just the "6008 Check.vi". If you want to see what a project is like, you can open the "6008 Check.lvproj", but that is not necessary for using the program.
  
 
== Mass Analyzers ==
 
== Mass Analyzers ==
Line 93: Line 248:
 
* Required Reading:  
 
* Required Reading:  
 
** [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://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://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)
 
** [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)
 
** [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/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://www.asms.org/docs/history-posters/thomson's-vision-commercialization-2009.pdf The Commercialization of MS]
** [http://pubs.acs.org/doi/abs/10.1021/ac022010j Scaling MS Plateaus with High-Resolution FT-ICRMS]. A. G. Marshall, C. L. Henderickson, and S. D.-H. Shi <i>A. Chem</i>, 74(9), 252A (2002)
 
  
 
* Suggested Reading:
 
* Suggested Reading:
 +
** [http://www.nature.com/nmeth/journal/v8/n8/abs/nmeth.1659.html A century of mass spectrometry: from atoms to proteomes], Yates, Nature Methods 2011.
 
** [http://www.chemheritage.org/research/policy-center/oral-history-program/projects/critical-mass/index.aspx Critical Mass: a History of MS]
 
** [http://www.chemheritage.org/research/policy-center/oral-history-program/projects/critical-mass/index.aspx Critical Mass: a History of MS]
 
** [http://www.asms.org/publications/historical/history-posters ASMS Posters on the History of MS]'' (for 19-Sep)
 
** [http://www.asms.org/publications/historical/history-posters ASMS Posters on the History of MS]'' (for 19-Sep)
Line 120: Line 272:
 
=== Time-of-Flight (TOFMS) ===
 
=== Time-of-Flight (TOFMS) ===
 
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOFMS.pdf 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)
 
** Suggested: [http://www.chem.agilent.com/temp/radF998C/00045384.pdf Agilent's Tutorial on Time-of-Flight Mass Spectrometry]
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/110464657/ABSTRACT Tutorial. Principles and instrumentation in time-of-flight mass spectrometry. Physical and instrumental concepts]. M. Guilhaus, <i>J. Mass. Spec.</i>, Volume 30: 1519-1532, 1995. [http://www.colorado.edu/chemistry/chem5181/Restricted/Guilhaus_ToFRev_JMS1995.PDF (pdf)]
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/13069/ABSTRACT Perfect Timing: Time-of-flight Mass Spectrometry] M. Guilaus, RCMS, 1997, 951-962
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/10009442/ABSTRACT  Time-of-Flight Mass Spectrometry: State of the Art in Chemical Analysis and Molecular Science] C. Weickhardt, F. Moritz, and J. Grotemeyer. MS Review. 1996, 139-162.
 
** Suggested: [http://jchemed.chem.wisc.edu/Journal/issues/1997/nov/abs1288.html Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Instrumentation and Applications] D. C. Muddiman, R. Bakhtiar, S. A. Hofstadler, and R. D. Smith <i>J. Chem. Ed.</i> 74, 1288, 1997.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/71004180/ABSTRACT Orthogonal acceleration time-of-flight mass spectrometry]. Guilhaus et al., <i>Mass Spec. Rev.</i>, 19: 65-107, 2000.
 
** Suggested: [http://link.aip.org/link/%3FRSINAK/26/1150/1 Time-of-Flight Mass Spectrometer with Improved Resolution] W. C. Wiley and I. H. McLaren, Rev. Sci. Instrum. 1955, 26(12), 1150-1157.
 
** Suggested: [http://www.ingentaconnect.com/content/els/13873806/2001/00000206/00000003/art00392 Time-of-flight mass spectrometry (concepts, achievements, and prospects)] B. A. Mamyrin, Int J Mass Spec, 2001, 251-266
 
** [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.
 
* Reading for Thu 3-Oct.
Line 157: Line 293:
 
** 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)
 
** 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)
  
=== Quadrupole ===
 
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS3_Quad.pdf Quadrupoles]
 
** ''Prop: Quadrupole''
 
 
* Reading for Thu 24-Oct (Required unless marked otherwise):
 
** [http://books.google.com/books/about/Mass_Spectrometry.html?id=pqhr5XQZDtUC Sect. 2.1 of de Hoffmann & Stroobant]
 
** [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://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://cires.colorado.edu/jimenez/CHEM-5181/HW/2013-10-15_Quad_Simulation.ipf IPF of quad simulation] (only needed if PXP is giving you problems)
 
** [http://www.youtube.com/watch?v=PSFF6JJEFPE&NR=1 Agilent GC/MS Triple Quad Video]
 
** Suggested: [http://jchemed.chem.wisc.edu/Journal/Issues/1996/Dec/abs1142.html Quadrupole Mass Spectrometers: An Intuitive Look at the Math]. Leary and Schmidt, <i>J. Chem. Ed.</i> 73: 1142-1144, 1996.
 
** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/mas.20249/abstract Linear Quadrupoles in Mass Spectrometry], D.J. Douglas, <i>Mass Spec. Rev.</i>, 28: 937-960, 2009.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/85010411/ABSTRACT An introduction to quadrupole–time-of-flight mass spectrometry] I. V. Chernushevich, A. V. Loboda, and B. A. Thomson, JMS, 2001, 849-865
 
** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-8-Tandems-and-Hybrids.pdf Lecture on MS/MS from Prof. Bob Cotter]
 
 
=== Ion Traps, FTICR, Orbitrap ===
 
 
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf 3d & 2d Quadrupole Ion Traps, FTICR, Orbitrap]
 
 
* Reading for Thu 31-Oct (all required unless marked otherwise):
 
** [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]
 
** 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
 
** [https://www.youtube.com/watch?v=PYpbKSmOnNc Homemade ion trap with two spons and a wire!]
 
** [http://planetorbitrap.com/about-the-technology#.Ukuv_4bks_c Orbitrap animation]
 
** [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 Short interview of Alexander Makarov] (Orbitrap inventor, very commercial)
 
** [http://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introductory animation of FTICR]
 
** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-9888(199704)32:4%3C351::AID-JMS512%3E3.0.CO;2-Y/abstract An Introduction to Quadrupole Ion Trap Mass Spectrometry], R. Mach, <i>J. Mass Spec.</i>, 32: 351-369, 1997.
 
** Suggested: [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2001/73/i03/abs/ac000973h.html Baseline mass resolution of peptide isobars: A record for molecular mass resolution], He F, Hendrickson CL, Marshall AG, <i>Anal. Chem.</i> 73 (3): 647-650, 2001.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/24610/ABSTRACT Fourier Transform Mass Spectrometry (Tutorial)] I. J. Amster, JMS, 1996, 1325-1337.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/10009487/ABSTRACT Fourier transform ion cyclotron resonance mass spectrometry: A primer]. A.G. Marshall et al., <i>Mass Spec. Rev.</i> 17: 1-35, 1998.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/110471441/ABSTRACT The Orbitrap: a new mass spectrometer (Perspective)]. R.G. Cooks et al., <i>J Mass Spec.</i> 40: 430-443, 2005.
 
** [https://docs.google.com/forms/d/1l5AH8QkKPtAaBprvTBOJzEZ-FndScaFShvnCyxyhrUg/viewform Reading Quiz]
 
  
 
== MS Interpretation ==
 
== MS Interpretation ==
Line 272: Line 374:
 
** Reference: [http://books.google.com/books?id=TA5N2svGCK4C&lpg=PA1&ots=VkoweozDrO&dq=Fundamental%20Electron%20Interactions%20with%20Plasma%20Processing%20Gases Fundamentals of Electron Interactions with Plasma Processing Gases], by L.G. Christophorou, J.K. Olthoff, Springer, 2004.
 
** Reference: [http://books.google.com/books?id=TA5N2svGCK4C&lpg=PA1&ots=VkoweozDrO&dq=Fundamental%20Electron%20Interactions%20with%20Plasma%20Processing%20Gases Fundamentals of Electron Interactions with Plasma Processing Gases], by L.G. Christophorou, J.K. Olthoff, Springer, 2004.
 
** [https://docs.google.com/forms/d/1zoYhXLCokDL7H_BadoT5CCXXArJps6RuTvcTblgTGA4/viewform Reading Quiz]
 
** [https://docs.google.com/forms/d/1zoYhXLCokDL7H_BadoT5CCXXArJps6RuTvcTblgTGA4/viewform Reading Quiz]
 
=== Chemical Ionization (CI) ===
 
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz2_CI.pdf Chemical Ionization]
 
 
* Reading for Tue 5-Nov
 
** de Hoffmann and Stroobant 2007, Section 1.2, 1.12, 1.13, 1.16
 
** [http://www.ptrms.com PTRMS Commercial Instrument] (read at least 10 pages on the site, focusing on the most relevant to the fundamentals and the course)
 
** [http://www.syft.com/about-sift-ms SYFT Commercial Instrument] (same)
 
** [https://sites.google.com/site/citofms/ ToF-CIMS Commercial Instrument] (same)
 
** Suggested: [http://www.atmos-meas-tech.net/4/1471/2011/ Bertram. et al. 2011] on Aerodyne ToF-CIMS
 
** Suggested: [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1966/88/i12/pdf/ja00964a001.pdf Chemical Ionization Mass Spectrometry. I.  General Introduction]. M.S.B. Munson and F.H. Field, <i>J. Am. Chem. Soc.</i>, 2621, 1966. (First paper on CI)
 
 
=== Electrospray Ionization (ESI) & Ambient Ionization Sources ===
 
 
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Ioniz3_ESI.pdf Electrospray and its Ion Chemistry] (from Invited Lecturer Dr. Shuji Kato)
 
** ''Prop: ESI Source''
 
 
* Reading on ESI (not yet assigned)
 
** de Hoffmann and Stroobant 2007, Section 1.11
 
** [http://www3.interscience.wiley.com/cgi-bin/abstract/72512664/ABSTRACT  A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry] P. Kebarle, <i>J.Mass Spec.</i>,804-817, 2000.
 
** [http://www.pnas.org/cgi/content/abstract/91/24/11290 The Emergence of Mass Spectrometry in Biochemical Research] G. Siuzdak, <i>Proc. Natl. Acad. Sci. USA</i>, 91(24), 11290, 1994.
 
** [http://nobelprize.org/nobel_prizes/chemistry/laureates/2002/chemadv02.pdf Mass spectrometry and nuclear magnetic resonance applied to biological macromolecules.] Advanced Information on the Nobel Prize in Chemistry 2002.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/93518527/ABSTRACT Practical implications of some recent studies in electrospray ionization fundamentals]. Cech and Enke, <i>Mass Spec. Rev.</i>, 20: 362-387, 2002.
 
** Suggested: [http://www3.interscience.wiley.com/journal/122463140/abstract Electrospray: From ions in solution to ions in the gas phase, what we know now]. P. Kebarle and U.H. Verkerk, <i>Mass Spec. Rev.</i> doi: 10.1002/mas.20247, 2009.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/72512616/ABSTRACT Some tenets pertaining to ESI-MS] R. B. Cole, <i>J. Mass Spec.</i>,763-772,2000. 
 
** Suggested: [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/1996/68/i01/abs/ac9509519.html Analytical Properties of the Nanoelectrospray Ion Source] M. Wilm and M. Mann, <i>A. Chem.</i>, 1-8, 1996.
 
 
* Reading on Ambient Sources (not yet assigned)
 
** [http://www3.interscience.wiley.com/journal/122518620/abstract Atmospheric Pressure Ion Sources]. <i>Mass Spec. Rev.</i>, doi: 10.1002/mas.20246, 2009.
 
** Suggested: [http://www3.interscience.wiley.com/cgi-bin/abstract/112126895/ABSTRACT Ambient mass spectrometry using desorption electrospray ionization (DESI): instrumentation, mechanisms and applications in forensics, chemistry, and biology] Z. Takats, J. M. Wiseman, and R. G. Cooks, <i>J. Mass Spec.</i>,1261-1275, 2005.
 
** [http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i08/abs/ac050162j.html Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions] R. B. Cody, J. A. Laramee, H. D. Durst, <i>A. Chem.</i>, 2297-2303, 2005.
 
  
 
=== Other Types of Ionization: SIMS, MALDI, ICP etc. ===
 
=== Other Types of Ionization: SIMS, MALDI, ICP etc. ===
Line 352: Line 422:
 
** Suggested: [http://www.pfeiffer-vacuum.com/cnt/technology.action?chapter=tec1 Introduction to Vacuum Technology] (Pfeiffer)
 
** Suggested: [http://www.pfeiffer-vacuum.com/cnt/technology.action?chapter=tec1 Introduction to Vacuum Technology] (Pfeiffer)
 
** Suggested: [http://www.pfeiffer-vacuum.com/products/vacuum-technology-book/container.action Vacuum Technology Book] (Pfeiffer)
 
** Suggested: [http://www.pfeiffer-vacuum.com/products/vacuum-technology-book/container.action Vacuum Technology Book] (Pfeiffer)
 
=== Data Acquisition using Labview ===
 
 
* Reading:
 
** [http://www.ni.com/labview/skills-guide/en/ Labview Skills Guide]
 
** [http://www.ni.com/gettingstarted/labviewbasics/ Labview Basics] (Sections TBD)
 
** [http://www.ni.com/academic/students/learn-labview/ Learn Labview] (Sections TBD)
 
** [http://sine.ni.com/myni/self-paced-training/app/main.xhtml Self-Paced Training] (sections TBD).
 
*** You will need the license number of the CU Academic License of Labview, which will be provided via Piazza.
 
 
== Specific Implementations or Applications of MS ==
 
 
=== MS of Peptides and Proteins ===
 
 
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Protein_Peptides_W_Old.pdf Mass Spectrometry of Peptides and Proteins] by Prof. W. Old (2011)
 
* Reading:
 
** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20024/abstract Paizs and Suhai: Fragmentation Pathways of Protonated Peptides], Mass Spec. Rev., 24:508-548, 2005.
 
** Suggested: [http://dx.doi.org/10.1016/j.ymeth.2004.08.013 Wysocki, Resing et al., 2005: Mass spectrometry of peptides and proteins]
 
** Suggested: [http://www.colorado.edu/chemistry/chem5181/Restricted/CID_Peptides.pdf The Interpretation of Collision Induced Dissociation Tandem Mass Spectra of Peptides], I.A. Papayannopoulos, <i>Mass Spec. Reviews</i> 14: 49-73, 1995.
 
** Suggested: [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr990076h Mass Spectrometry in Proteomics] R. Aerbersold and D.R. Goodlett, <i>Chem. Rev.</i> 101(2), 269, 2001.
 
** Suggested: [http://www.matrixscience.com/ MASCOT Protein MS Database]
 
 
=== Aerosol Mass Spectrometry ===
 
 
* Lecture Notes: [http://cires.colorado.edu/jimenez/Papers/2010-09_IAC_Aerosol_MS_Tutorial.pdf Aerosol Mass Spectrometry] by J.L. Jimenez (2010)
 
 
* Reading:
 
** [http://www3.interscience.wiley.com/cgi-bin/abstract/72001802/ABSTRACT?CRETRY=1&SRETRY=0 Tutorial: Sampling and analysis of individual particles by aerosol mass spectrometry.], M.V. Johnston, <i>J. Mass Spectrom.</i> 35, 585–595 (2000).
 
** [http://cires.colorado.edu/jimenez/Papers/Canagaratna_Review_Published.pdf Chemical and Microphysical Characterization of Ambient Aerosols with the Aerodyne Aerosol Mass Spectrometer]. Canagaratna et al., <i>Mass Spectrometry Reviews</i>, 2007.
 
** [https://www.youtube.com/watch?v=kmZHwCBJHO8 Video tutorial on AMS]
 
** Suggested: [http://www.aaar.org/ast_abst/v33n12pref.htm Special Issue of AS&T on Aerosol Mass Spectrometry]
 
** Suggested: [http://cires.colorado.edu/jimenez/ams.html Aerosol Mass Spectrometry Web Page]
 
** Reference: [http://cires.colorado.edu/jimenez/ams-papers.html Publications using the Aerodyne Aerosol Mass Spectrometer (AMS)]
 
** Reference: [http://mae.ucdavis.edu/wexler/spa_refs.html A List of Publications in Single Particle Mass Spectrometry], maintained by Prof. Tony Wexler.
 
** Reference: [http://www.udel.edu/chem/johnston/SPMSdbase.html Another List of Publications in Single Particle Mass Spectrometry], this one maintained by Prof. Murray Johnston.
 
 
=== Isotope Ratio MS ===
 
 
* Reading: [http://rsi.aip.org/resource/1/rsinak/v84/i1/p011101_s1?TRACK=RSIJAN13 Isotope Ratio MS]
 
 
=== The Flowing Afterglow ===
 
 
* [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)
 
 
=== Auto-resonant MS ===
 
 
* [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
 
  
 
== Chromatography and Analytical Separations ==
 
== Chromatography and Analytical Separations ==
Line 407: Line 428:
 
* Lecture Notes: [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C3_IMS_CE.pdf Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis]
 
* Lecture Notes: [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C3_IMS_CE.pdf Electric-Field Driven Separations: Ion Mobility, Gel Electrophoresis, and Capillary Electrophoresis]
  
* Reading (required unless noted otherwise)
+
* Reading for Tue 12-Nov
 
** [http://www.sepscience.com/Techniques/MS/Articles/1473-/MS-Solutions-25-Ion-Mobility-Spectrometry-A-Primer Ion Mobility Spectrometry: A Primer]
 
** [http://www.sepscience.com/Techniques/MS/Articles/1473-/MS-Solutions-25-Ion-Mobility-Spectrometry-A-Primer Ion Mobility Spectrometry: A Primer]
 
** [http://www.sepscience.com/Information/Archive/MS-Solutions/1797-/MS-Solutions-26-FAIMSDMS-Applications-Overview FAIMS & DMS Applications Overview]
 
** [http://www.sepscience.com/Information/Archive/MS-Solutions/1797-/MS-Solutions-26-FAIMSDMS-Applications-Overview FAIMS & DMS Applications Overview]
 +
** [http://onlinelibrary.wiley.com/doi/10.1002/jms.1383/pdf Ion Mobility - Mass Spectrometry]
 +
** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac071226o Performance, Resolving Power, and Radial Ion Distributions of a Prototype Nanoelectrospray Ionization Resistive Glass Atmospheric Pressure Ion Mobility Spectrometer], Kwasnik et al., Anal. Chem., 2007.
 +
** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac00222a001 Ion Mobility Spectrometry], Hill et al., Anal. Chem., 1990.
 +
** Suggested: [http://en.wikipedia.org/wiki/Ion-mobility_spectrometry IMS (W)]
 +
** Suggested: [http://www.tofwerk.com/cms/?Products:IMS-TOF Tofwerk IMS-TOF]
 
** Suggested (for all of chromatography): [http://www.lcgcmag.com/lcgc/ LC-GC]. The best industry publication on general chromatographic techniques.
 
** Suggested (for all of chromatography): [http://www.lcgcmag.com/lcgc/ LC-GC]. The best industry publication on general chromatographic techniques.
 +
** Suggested: [http://www.faims.com/ FAIMS website]
 +
** Suggested: [http://www.nature.com/nchem/journal/v6/n4/full/nchem.1889.html?WT.ec_id=NCHEM-201404 The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics], Lanucara et al., 2014.
  
 
=== Introduction and Theory of Chromatography ===
 
=== Introduction and Theory of Chromatography ===
  
* Lecture Notes: [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C1_Intro_Theory.pdf  Introduction and Part I] & [http://www.colorado.edu/chemistry/chem5181/Lectures07/2007_C2_Intro_Theory.pdf  Part II]
+
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/C1_Intro_Theory.pdf  Introduction and Theory of Chromatography]  
  
* Reading:
+
* Reading for Thu 14-Nov:
 
** [http://www.chem.uoa.gr/applets/AppletChrom/Appl_Chrom2.html Chromatographic Separation Demo]
 
** [http://www.chem.uoa.gr/applets/AppletChrom/Appl_Chrom2.html Chromatographic Separation Demo]
 
** [http://www.colorado.edu/chemistry/chem5181/Restricted/BraithwaiteSmith_Chap1.PDF Introduction to Chromatography], Braithwaite and Smith
 
** [http://www.colorado.edu/chemistry/chem5181/Restricted/BraithwaiteSmith_Chap1.PDF Introduction to Chromatography], Braithwaite and Smith
 
** [http://www.colorado.edu/chemistry/chem5181/Restricted/BraithwaiteSmith_Chap2.PDF Theory of Chromatography], Braithwaite and Smith
 
** [http://www.colorado.edu/chemistry/chem5181/Restricted/BraithwaiteSmith_Chap2.PDF Theory of Chromatography], Braithwaite and Smith
** [http://sciencecases.lib.buffalo.edu/cs/collection/detail.asp?case_id=386&id=386 A Play about the Van Deemter equation]
+
** Suggested: [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/http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ac00255a033 Equations for Calculation of Chromatographic Figures of Merit for Ideal and Skewed Peaks], J.P. Foley and J.G. Dorsey, <i>Anal. Chem.</i>, 55: 730-737, 1983.
+
** Suggested: [http://pubs.acs.org/doi/abs/10.1021/ac00255a033 Equations for Calculation of Chromatographic Figures of Merit for Ideal and Skewed Peaks], J.P. Foley and J.G. Dorsey, <i>Anal. Chem.</i>, 55: 730-737, 1983.
 
** Suggested: [http://www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf Nomenclature for Chromatography (IUPAC Recommendations)], L.S. Etre, <i>Pure & Appl. Chem.</i>, 65(4): 819-872, 1993.
 
** Suggested: [http://www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf Nomenclature for Chromatography (IUPAC Recommendations)], L.S. Etre, <i>Pure & Appl. Chem.</i>, 65(4): 819-872, 1993.
 
** Suggested: [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/462001/2090/article.pdf The Birth of Partition Chromatography], L.S. Ettre, <i>LC-GC North America</i>, 19(5), 2001.
 
** Suggested: [http://www.lcgcmag.com/lcgc/data/articlestandard/lcgc/462001/2090/article.pdf The Birth of Partition Chromatography], L.S. Ettre, <i>LC-GC North America</i>, 19(5), 2001.
Line 466: Line 494:
 
** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-4-Chromatography.pdf Lecture on HPLC and CE from Prof. Bob Cotter]  
 
** Suggested: [http://www.hopkinsmedicine.org/mams/MAMS/middleframe_files/teaching_files/ME330.884/2005/MS2005-Lecture-4-Chromatography.pdf Lecture on HPLC and CE from Prof. Bob Cotter]  
 
** Suggested: [http://www.annualreviews.org/doi/abs/10.1146/annurev.fluid.38.050304.092053 Electrokinetic Flow and Dispersion in Capillary Electrophoresis], S. Ghosal, <i>Ann. Rev. Fluid Mech.</i>, 38: 309-338, 2006.
 
** Suggested: [http://www.annualreviews.org/doi/abs/10.1146/annurev.fluid.38.050304.092053 Electrokinetic Flow and Dispersion in Capillary Electrophoresis], S. Ghosal, <i>Ann. Rev. Fluid Mech.</i>, 38: 309-338, 2006.
 +
 +
 +
== Invited Lectures on Applications of MS & Chrom. ==
 +
 +
=== GCxGC-MS ===
 +
 +
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2013_GCxGC_Handouts.pdf Lecture Notes] by Dr. Lucas Smith, LECO Corp. (2013)
 +
* Reading:
 +
** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20158/abstract Comprehensive two-dimensional gas chromatography-mass spectrometry: A review]. Mondello et al., Mass. Spec. Rev. 2008.
 +
** Suggested: [http://onlinelibrary.wiley.com/doi/10.1002/jssc.200301643/abstract Speciation of nitrogen-containing compounds in diesel fuel by comprehensive two-dimensional gas chromatography]. Wang et al., J. Sep. Sci., 2004.
 +
 +
=== MS of Peptides and Proteins ===
 +
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/Protein_Peptides_W_Old.pdf Mass Spectrometry of Peptides and Proteins] by Prof. W. Old (2011)
 +
* Reading:
 +
** [http://onlinelibrary.wiley.com/doi/10.1002/mas.20024/abstract Paizs and Suhai: Fragmentation Pathways of Protonated Peptides], Mass Spec. Rev., 24:508-548, 2005.
 +
** Suggested: [http://dx.doi.org/10.1016/j.ymeth.2004.08.013 Wysocki, Resing et al., 2005: Mass spectrometry of peptides and proteins]
 +
** Suggested: [http://www.colorado.edu/chemistry/chem5181/Restricted/CID_Peptides.pdf The Interpretation of Collision Induced Dissociation Tandem Mass Spectra of Peptides], I.A. Papayannopoulos, <i>Mass Spec. Reviews</i> 14: 49-73, 1995.
 +
** Suggested: [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr990076h Mass Spectrometry in Proteomics] R. Aerbersold and D.R. Goodlett, <i>Chem. Rev.</i> 101(2), 269, 2001.
 +
** Suggested: [http://www.matrixscience.com/ MASCOT Protein MS Database]
 +
 +
=== Aerosol Mass Spectrometry ===
 +
 +
* Lecture Notes: [http://cires.colorado.edu/jimenez/Papers/2010-09_IAC_Aerosol_MS_Tutorial.pdf Aerosol Mass Spectrometry] by J.L. Jimenez (2010)
 +
 +
* Reading:
 +
** [http://www3.interscience.wiley.com/cgi-bin/abstract/72001802/ABSTRACT?CRETRY=1&SRETRY=0 Tutorial: Sampling and analysis of individual particles by aerosol mass spectrometry.], M.V. Johnston, <i>J. Mass Spectrom.</i> 35, 585–595 (2000).
 +
** [http://cires.colorado.edu/jimenez/Papers/Canagaratna_Review_Published.pdf Chemical and Microphysical Characterization of Ambient Aerosols with the Aerodyne Aerosol Mass Spectrometer]. Canagaratna et al., <i>Mass Spectrometry Reviews</i>, 2007.
 +
** [https://www.youtube.com/watch?v=kmZHwCBJHO8 Video tutorial on AMS]
 +
** Suggested: [http://www.aaar.org/ast_abst/v33n12pref.htm Special Issue of AS&T on Aerosol Mass Spectrometry]
 +
** Suggested: [http://cires.colorado.edu/jimenez/ams.html Aerosol Mass Spectrometry Web Page]
 +
** Reference: [http://cires.colorado.edu/jimenez/ams-papers.html Publications using the Aerodyne Aerosol Mass Spectrometer (AMS)]
 +
** Reference: [http://mae.ucdavis.edu/wexler/spa_refs.html A List of Publications in Single Particle Mass Spectrometry], maintained by Prof. Tony Wexler.
 +
** Reference: [http://www.udel.edu/chem/johnston/SPMSdbase.html Another List of Publications in Single Particle Mass Spectrometry], this one maintained by Prof. Murray Johnston.
 +
 +
=== Isotope Ratio MS ===
 +
 +
* Reading: [http://rsi.aip.org/resource/1/rsinak/v84/i1/p011101_s1?TRACK=RSIJAN13 Isotope Ratio MS]
 +
 +
=== The Flowing Afterglow ===
 +
 +
* [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)
 +
 +
=== Auto-resonant MS ===
 +
 +
* [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
  
 
== FAQs about CHEM-5181 ==
 
== FAQs about CHEM-5181 ==
Line 471: Line 547:
 
* '''Can I audit the class?'''
 
* '''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 [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.
** Note that postdocs and researchers at CU can register for free using the Staff Tuition Benefit, see more details [http://www.alumniconnections.com/links/link.cgi?l=5070036&h=10104&e=UCBI-20131029125211 here].
+
** Note that postdocs and researchers at CU can register for free using the Staff Tuition Benefit, see more details [http://www.alumniconnections.com/links/link.cgi?l=5070036&h=10104&e=UCBI-20131029125211 here] and [http://www.cu.edu/employee-services/tuition-waiver-benefit-boulder-campus here]. They need to apply for the tuition benefit at least 2 weeks before the start of classes, and then can register the day that classes start.
  
 
* '''But I don't want to register at all. Can you make an exception for me to 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?'''
Line 517: Line 593:
  
 
* [http://www.colorado.edu/chemistry/chem5181/Labs/2007_Final_Project.pdf Final Project Organization]
 
* [http://www.colorado.edu/chemistry/chem5181/Labs/2007_Final_Project.pdf Final Project Organization]
 
==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 ==
 
== Other MS and Chrom. Resources ==

Latest revision as of 17:07, 23 December 2017



  • 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 will be offered in Fall 2017 by Jose.

================================================
THIS WEB PAGE HAS MOVED to http://tinyurl.com/Main5181. PLEASE FOLLOW THAT LINK FOR THE UPDATED MATERIAL
================================================


Contents

Course Information & Organization

Introduction & Review of Fundamentals

    • For all the readings that include a simulation, you are required to use the simulation for a range of parameters.

Intro to Igor & MS Resolution

  • For you to do:

MS Analyzers: TOFMS

  • For you to do
    • HW4
    • Reading Quiz (needs to be completed at least 2 hrs before the start of class)

MS Analyzers: Quadrupole

MS Analyzers: Ion Traps, FTICR, Orbitrap

Chemical Ionization (CI)

Electrospray Ionization (ESI) & Ambient Ionization Sources

Old Materials from Here Down, for Reference

Introduction & Review of Fundamentals

Computer Programming, Igor Pro, and Labview

Igor Pro

  • Reading (required unless marked otherwise):
    • Suggested: Intro to Igor Pro (2011 lecture slides)
    • 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): Computer Programming (KhA)
    • Suggested: Sign up for Igor email list (Strongly suggested for people who will use Igor in their research. Suggest "daily digest" mode to reduce the number of messages you get)
    • Suggested: Intro to Igor Programming

Data Acquisition using Labview

Mass Analyzers

Electric & Magnetic Sector, Resolution & Accuracy, Ion Optics

Time-of-Flight (TOFMS)

  • 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)


MS Interpretation

Intro & Elemental Composition

The Molecular Ion

Fragmentation Mechanisms

Postulation of Molecular Structures

Ionization Sources

Fundamentals & Electron Ionization (EI)

Other Types of Ionization: SIMS, MALDI, ICP etc.

MS Detectors, Data Acquisition, Vacuum

MS Detectors, A/D Conversion, Signal-to-Noise

Vacuum Technology

  • Props: turbo pump, diaphragm pump

Chromatography and Analytical Separations

Ion Mobility Spectrometry

Introduction and Theory of Chromatography

Gas Chromatography

Liquid Chromatographies

Chromatographic Detectors

Capillary Electrophoresis


Invited Lectures on Applications of MS & Chrom.

GCxGC-MS

MS of Peptides and Proteins

Aerosol Mass Spectrometry

Isotope Ratio MS

The Flowing Afterglow

Auto-resonant MS

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.
    • Note that postdocs and researchers at CU can register for free using the Staff Tuition Benefit, see more details here and here. They need to apply for the tuition benefit at least 2 weeks before the start of classes, and then can register the day that classes start.
  • 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 students 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 substantially 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, Labview, and other computer programs. A PC is much preferable as Labview does not work well on Macs, and many other programs, including the NIST MS database only run on PCs. If you already have a Mac laptop, 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. Otherwise it is your responsibility to identify a PC where you can do the assigned homework and readings that only work on PCs.
  • 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.

Labs

Lab 1: MALDI-TOFMS

Lab 2: Electrospray MS

Lab 3: GC-MS of mixtures

Student Choice Projects

Other MS and Chrom. Resources

Mass Spectrometry Societies

MS & Chrom. Courses at other Universities

Journals with Substantial Mass Spectrometry and Analytical Separations Content

Analytical Chemistry Journals

Mass Spectrometry Journals

Chromatography and Analytical Separations Journals