Difference between revisions of "CHEM-5181"

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(Lectures, Reading, and Homeworks)
(Lectures, Reading, and Homeworks)
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* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/1_Intro_Review_Fundamentals.pdf Introduction and Review of Fundamentals]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/1_Intro_Review_Fundamentals.pdf Introduction and Review of Fundamentals]
 
** 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]  
 
** 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://cires.colorado.edu/jimenez/CHEM-5181/HW/HW1_Review_Fund.doc Homework #1 on review of fundamentals]
 
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2_Intro_Igor.pdf Introduction to Igor Pro]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/2_Intro_Igor.pdf Introduction to Igor Pro]
 
** ''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]''
 
** ''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://cires.colorado.edu/jimenez/CHEM-5181/HW/IgorProgrammingConventions_v2.ipf Igor Programming Conventions (v2)]
 
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/IgorProgrammingConventions_v2.ipf Igor Programming Conventions (v2)]
 +
 +
* Homeworks
 +
** [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] (Assigned: 6-Sep-11, due: 15-Sep-11)
 
** [http://cires.colorado.edu/jimenez/CHEM-5181/HW/HW2_Igor_Sector.docx Homework #2 on Igor and Electric Sector MS] (Assigned: 6-Sep-11, due: 15-Sep-11)
  
=== Mass Spectrometers ===
+
=== Mass Analyzers ===
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol_Sector.pdf Intro to MS, Resolution/Accuracy, Sector Mass Spectrometers, and Ion Optics]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS1_Intro_Resol_Sector.pdf Intro to MS, Resolution/Accuracy, Sector Mass Spectrometers, and Ion Optics]
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** ''Suggested Reading: [http://www.asms.org/Publications/Historical/HistoryofMassbrSpectrometryandASMS/tabid/94/Default.aspx ASMS Posters on the History of MS]''
 
** ''Suggested Reading: [http://www.asms.org/Publications/Historical/HistoryofMassbrSpectrometryandASMS/tabid/94/Default.aspx ASMS Posters on the History of MS]''
 
** 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]
 
** 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]
** HW on electric sector is already part of HW2
 
** [http://cires.colorado.edu/CHEM-5181/HW/HW_Ion_Optics_Simul.docx HW: Ion Optics Simulation Part 1] (not in 2011)
 
** [http://cires.colorado.edu/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/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/Lect/MS2_TOFMS.pdf Time-of-Flight MS]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS2_TOFMS.pdf Time-of-Flight MS]
 
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 2.4''
 
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 2.4''
** [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/Lect/MS3_Quad.pdf Quadrupoles]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS3_Quad.pdf Quadrupoles]
 
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 2.1''
 
** ''Required Reading: de Hoffmann and Stroobant 2007, Section 2.1''
** [http://www.youtube.com/watch?v=PSFF6JJEFPE&NR=1 Video of Agilent GC/MS Triple Quad]
+
** 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]
** [http://www.chem.agilent.com/en-US/Products/Instruments/ms/6100SeriesQuadrupoleLCMSSystems/Pages/6100_video.aspx Video of Agilent LC/MS Quad]
 
** [http://www.chem.agilent.com/en-US/Products/Instruments/ms/6410triplequadrupolelcms/pages/gp56595.aspx Video of Agilent LC/MS Triple Quad]
 
 
** ''Prop: Quadrupole''
 
** ''Prop: Quadrupole''
** [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]
 
  
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf Ion Traps, FTICR, Orbitrap]
 
* [http://cires.colorado.edu/jimenez/CHEM-5181/Lect/MS4_IT_FTICR_Orbitrap.pdf Ion Traps, FTICR, Orbitrap]
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** 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]
 
** 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://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introd. animation of FTICR]
 
** [http://www.youtube.com/watch?v=a5aLlm9q-Xc&feature=related Introd. animation of FTICR]
 +
 +
* Homeworks on Mass Analyzers
 +
** [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/CHEM-5181/HW/HW_Ion_Optics_Simul.docx HW: Ion Optics Simulation Part 1] (not in 2011)
 +
** [http://cires.colorado.edu/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 ===
 
=== Ionization Sources ===

Revision as of 13:47, 18 October 2011

  • This course WILL be offered in Fall 2011, WILL NOT be offered in Fall 2012, and will likely be offered again in Fall 2013
  • 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.
  • The old web page is located here, and I'll be gradually move things over to this Wiki page, which is much easier to update.

Course Information

  • 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
  • Textbooks:
    • de Hoffmann & Stroobant. Mass Spectrometry, Principles and Applications, 3rd. Ed. ISBN: 0471485667; Library: QD96.M3 H6413 2007
    • McLafferty & Turecek Interpretation of Mass Spectra, 4th Ed., ISBN: 0935702253; Library: QC454.M22 1993;

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 I still audit the class?
    • Answer: No.
  • 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".

Lectures, Reading, and Homeworks

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.

Introduction, Review, Igor

Mass Analyzers

Ionization Sources


  • -------------- Material below this line is from the previous offering of the course ------------------


MS Detectors, Data Acquisition, Vacuum

  • Vacuum Technology
    • Props: turbo pump, diaphragm pump

MS Interpretation

  • Interpretation of Mass Spectra III (The Molecular Ion)
    • Required Reading: McLafferty and Turecek 1993, Chapters 3 and 5
  • Interpretation of Mass Spectra IV (Fragmentation Mechanisms)
    • Required Reading: McLafferty and Turecek 1993, Chapters 4, and skim 9

Chromatography and Chemical Separations

  • Gas Chromatography
    • Prop: GC column
  • LC and HPLC
  • Ion Chromatography & Thin Layer Chromatography
  • Chromatographic Detectors

Presentations

Reference material for presentations

Labs

Lab 1: MALDI-TOFMS

Lab 2: Electrospray MS

Lab 3: GC-MS of mixtures

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

MS Interpretation

Chromatography: General

Electric Field Driven Separations

LC, GC, and IC

Award for the Best Performance in CHEM-5181

  • 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 MS Content

Analytical Chemistry Journals

Mass Spectrometry Journals

Chromatography and Analytical Separations Journals