Interpretation of Mass SpectraInterpretation of Mass Spectra

Short Course designed for Chemists and Laboratory personnel with no formal training in mass spectrometry, and Chromatographers who are using mass selective detectors or ion traps as chromatography detectors

Date: May 6 – 7, 2003 Germantown, Maryland

Course Description: The Mass Spectrometry Discussion Group of the Greater Washington-Baltimore Area will present a short course on “Interpretation of Mass Spectra.” This introductory level course on the qualitative interpretation of mass spectra of small organic, biochemical and environmental compounds will be taught by solving practical examples.

Registrants should be familiar with basic principles of organic chemistry. Extensive problem-solving time will be augmented by lectures to illustrate the principles of interpretation. Emphasis will be placed on the interpretation of electron ionization (EI) mass spectra. The workshop format and a high instructor-to-student ratio are designed to benefit those with little or no experience, but who wish to expand their interpretation skills.

Format: A workshop format and limited class size will ensure the participants ample
opportunity to interact with the instructors.

Who Should Attend: Chemists and Laboratory Personnel with no formal training in mass spectrometry,
and Chromatographers who are using mass selective detectors or ion traps as chromatography detectors. A knowledge of basic organic chemistry will be assumed.

Date: May 6 and 7, 2003 — 8:30 a.m. to 5:00 p.m. (ample free parking available)

Place: Agilent Technologies, 20403 Century Blvd., Germantown, MD 20874. Directions:
Take I-270 to Exit 16 and head towards Germantown, turn left onto Crystal Rock Dr.,
left on to Clover Leaf Center Dr., and left onto Century Blvd., building is on left.

Registration: Course enrollment will be limited to 24 students to ensure a high instructor-to- student
ratio. Registration fee includes textbooks, course materials, lunches Register early space is limited!

To register, complete and return the Registration Form in the attached
CEU’s Course rated as 1.3 Continuing Education Units

Contact: Ms. Janet Cunningham, Course Manager
Barr Enterprises, P.O. Box 279, Walkersville, Maryland 21793
Phone 301-668-6001; Fax 301-668-4312; e-mail…

2003 Washington-Baltimore MSDG Young Investigator Travel Award2003 Washington-Baltimore MSDG Young Investigator Travel Award

The MSDG will be awarding a single $1000 award to an outstanding young investigator to support travel to the 2003 ASMS meeting in Montreal, Quebec, Canada. As in the past, the award is open to senior graduate students and postdoctoral associates in laboratories and institutions traditionally associated with the MSDG (approximate boundaries: Richmond and Charlottesville on the south and Newark, Delaware on the north). Applicants for the award should expect to receive their degree by May 2005 or have received their degree no earlier than May 2001. Applicants should submit an electronic copy (PDF or Word format preferred) of their ASMS abstract, an additional two page summary of their research project (figures can be included), a CV and a letter of recommendation from their advisor to John Callahan, CFSAN, Food and Drug Administration, (5100 Paint Branch Parkway, College Park, MD 20740, 301-436-2039). Applications should be submitted no later than May 12, 2003. The award will be announced at the May 19, 2003 MSDG meeting. The successful applicant will be expected to present a 20-30 minute talk at the post-ASMS poster session in June.…

2002 Nobel Prize in Chemistry Awarded to Professor John Fenn of Virginia Commonwealth University and Dr. Koichi Tanaka of Shimadzu Corporation2002 Nobel Prize in Chemistry Awarded to Professor John Fenn of Virginia Commonwealth University and Dr. Koichi Tanaka of Shimadzu Corporation

Congratulations to Professor John Fenn of VCU for the 2002 Nobel Prize in Chemistry, shared with Koichi Tanaka and Kurt Wuthrich. Professors Fenn and Tanaka were specifically recognized for their contributions to the development of soft ionization techniques (electrospray and laser desorption, respectively) for mass spectrometric analysis of biomolecules. The implications of these discoveries have been obvious to mass spectrometrists since their inception; however, their impact has spread so far as to be almost unimaginable.

We have been distinctly fortunate to have Professor Fenn in our own backyard for many years now. He has been an attendee at our Discussion Group meetings, and he has honored us by making presentations to the group over the years. His most recent presentation to the group was in 1995, when the title of his talk was “How Ions are Formed from Charged Droplets – A Blend of Fact, Fancy, Fiction and Faith”. John is well known for his entertaining and enlightening presentations; few who were there can forget the talk he gave on the Old Testament and New Testament of Ionization in 1989 at the first Sanibel Conference. Those of us who have been fortunate enough to hear and know Professor Fenn over the years can attest to the clarity and depth of his scientific insight, the extent of his vision, his persistence, and most of all, his humility and humanity. As anyone attending an ASMS meeting knows, there are few scientists more accessible and more willing to discuss ideas. It has indeed been a privilege and an honor to work in a field led by such a scientist.

Koichi Tanaka was recognized for his role in the development of soft laser ionization. At the Joint Japan-China Mass Spectrometry Meeting in 1987 in Takarazuka, Japan he presented perhaps the first very high mass spectra of proteins using a pulsed nitrogen laser and a cobalt powder/glycerol matrix. While both electrospray and the MALDI method of Franz Hillenkamp and Michael Karas were being developed at the time, the spectacular results in the 70 kDa and above range provided considerable impetus to mass spectroscopists to extend their mass ranges. Dr. Tanaka is a senior engineer with the Shimadzu Corporation in Kyoto, and has recently been responsible for the development of a combined ion trap/time-of-flight (QitTOF) tandem instrument at the Shimadzu Research Laboratories in Manchester, UK.
Once again, congratulations to Professor Fenn and Dr. Tanaka.…

Thermo Finnigan Presents:Thermo Finnigan Presents:

A Free Proteomics Seminar, Including Two In-Depth Workshops at:

The National Cancer Institute, Fort Detrick, Maryland, March 4th and 5th, 2002

Conference Center, Building 549

(Register for Free Workshops at Bottom)

Monday, March 4, 2002 AGENDA

8:00 – 8:30 Sign-In Refreshments Provided

8:30 – 9:00 Dr. Timothy Veenstra Introduction


9:00 – 10:00 Dr. Jim Stevenson Ion Trap Theory

Research Triangle Institute

10:00 – 10:15 Morning Break Refreshments Provided

10:15 – 11:00 Dr. Leo Bonilla- Thermo Finnigan’s New Bioworks 3.0

Thermo Finnigan

11:00 – 11:45 Dr. Shiaw-Lin Wu- The use of Differential Quantitation in Targeted Proteomics:

Thermo Finnigan Quantitation of ATP receptor (P2X3) in human embryonic kidney cells using Thermo Finnigan New Proteome X with Bioworks 3.0 software and ICAT reagents.

11:45 – 1:00 Lunch – Provided Lunch-Time Seminar (12:15): Dr. Eric Stover, Thermo Hypersil

Interface of Different LC Modes to MS

1:00 2:00 Dr. Jeffrey Kowalak 2DLC/MS Application.

National Institute of Mental Health

2:00 3:00 Dr. Donald Hunt Analysis of Differential Gene Expression by Mass Spectrometry

University of Virginia

3:00 3:15 Afternoon Break Refreshments Provided

3:15 4:00 Andreas Huhmer Femtomole Detection Sensitivity of an Automated Sample

Thermo Finnigan Presentation Technique for Peptides and Proteins Using Nanospray Ion-trap Mass Spectrometry.

4:00 4:45 Dr. Shiaw-Lin Wu Using MALDI with the Power of an MSn Ion-trap to Quickly

Thermo Finnigan Determine Multiple Peptide’s Sequences and Modification Sites

4:45 – 5:30 Dr. Gary Paul Quantitative and Qualitative Applications of a Novel High

Thermo Finnigan Resolution Triple Quadrupole Mass Spectrometer

5:30 – 6:00 Reception On-Site, Refreshments Provided

Tuesday, March 5, 2002 AGENDA

10:00 – 12:00 Workshop 1 Proteomics using the DecaXP – Dr. Leo Bonilla

12:00 – 1:00 Lunch Provided

1:00 – 3:00 Workshop 2 ICAT Analysis Using Bioworks 3.0 – Dr. Leo Bonilla


In order to provide an accurate amount of refreshments and to register for a workshop on March 5, 2002,

please send an email specifying which workshop (or both) is desired and who will be attending each day to:


The use of Differential Quantitation in Targeted Proteomics: The quantitation of ATP receptor (P2X3) in human embryonic kidney cells by Proteome X with Bioworks software and ICAT reagent.

Shiaw-Lin Wu1, David Barnidge2, Gargi Choudhary1, Leo Bonilla1, Paul Shieh1, and William S. Hancock1

Proteomic Division of ThermoFinnigan1 and Proteomic Division of Neuromics2

The expression level of a given protein in disease state vs the normal state is an important indication in the study of the mechanism and subsequent treatment of the disease. An approach to measuring differential protein expression levels has been published lately by Aebersold et. al. using ICAT reagent with a LCQ ion trap mass spectrometer (Nature Biotechnology Vol 17, pp. 994, 1999). We have demonstrated here a methodology to quantitate the differences of a low level (femtomole) pain-related biomarker protein, ATP receptor (P2X3) in human embryonic kidney cells, by a new LC-MS system (Proteome X) with a new software program (Bioworks) and the ICAT reagent.

Interface of Different LC Modes to MS

Eric Stover

Reversed phase LC/ESI/MS is by far the most popular form of LC/MS techniques because a wide range of moderately complex samples can be analyzed at very low levels without molecular weight restrictions. However, this technique also poses a serious challenge because of a need to control the ionization of solutes to optimize the MS interface efficiency (sensitivity) as well as a need to control retention and separation. Although powerful, not all problems can be addressed by this approach. This presentation will include a review of all modes of LC, including reversed phase, normal phase, adsorption, ion exchange and size exclusion with an assessment of how amenable each might be to interface with the MS and how important each might become for various LC/MS applications. Multiple modes or dimensions through the use of valves and stream switching will be mentioned as an on-line strategy for separation of complex mixtures. HPLC column hardware and interface (plumbing) requirements will also be discussed.

Femtomole Detection Sensitivity of an Automated Sample Presentation Technique for Peptides and Proteins Using Nanospray Ion-trap Mass Spectrometry.

Andreas Hühmer1, Helen Tran1, Sally Swedberg1

1Thermo Finnigan, 255 River Oaks Parkway, San Jose, CA 95134.

Nanospray LC ESI-MS/MSn has become an invaluable analytical tool for ultra-sensitive analysis of complex biological samples. Mandated by ever increasing demands for higher sensitivity and limited sample amounts, mass spectrometry detectors are now routinely coupled to micro and nanoscale LC columns for identification and characterization of peptides and proteins. For low-flow LC, where submicroliter flow rates are typical, efficient sample preparation and presentation techniques are crucial to exploit the high sensitivity of mass spectrometry. For example, peptides recovered from in-gel digests need to be desalted and concentrated prior to introduction to LC-MS. For the best experimental results the combination of a peptide trap in line with a capillary column for the automated removal of electrospray incompatible sample components is superior to off-line sample preparation steps. We present method and data that demonstrate the features and advantages of this sample presentation technique for rapid and accurate peptide characterization. We also discuss experimental approaches for data dependent MSn analysis that exploits the unique capabilities of ion-trap MS for the identification and characterization of post-translational modifications in proteins. Different data-dependent acquisition methods are evaluated to maximize sequence coverage and sequence information for those peptide fragments.

Analysis of Differential Gene Expression by Mass Spectrometry

Donald F. Hunt, Departments of Chemistry and Pathology, University of Virginia, Charlottesville, Virginia 22901

Gene expression in bacteria under environmental pressure can now be measured directly by mass spectrometry. Bacillus subtilis has a genome of 4,300 genes and expresses 1,300-1,500 proteins at any given time. To identify genes differentially expressed in the vegetative and sporulation states of the bacterium, samples of cells in both states were lysed separately, proteins were extracted and digested with trypsin, and the …