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Table of Contents

Web Based Calculations

Mass Spectrometry Consultants and Contract Labs
Databases and Tools
Definitions (MS),  Dictionaries, and Reference Materials
Employment Listings
Mass Spectrometry Interest Groups
Search Engines
Societies and Meetings
Universities, Institutes and Government MS Labs
Vendors (LC)
Vendors (MS)
Links to More Links and Resources

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Web Based Calculations 

Phenyx A software platform for the identification and characterization of proteins and peptides from mass spectrometry data. Developed by GeneBio in collaboration with the Swiss Institute of Bioinformatics (SIB).

Proteomic Tools from the Institute for Systems Biology:  peptide fragment calculator, protein digester, DNA translator, composition calculator.

ChemCalc - a chemical calculator written entirely in Java by Michal Krompiec. Calculates isotopic distribution, elemental composition, molecular mass, exact mass and molecular formula.

Buffers for pH control. Use a java calculator to design a buffer with specified pH, concentration, and ionic strength.

SearchXLinks  SearchXLinks, a program for analyzing mass spectrometric experiments carried out on modified, cross-linked and digested proteins.  This includes identification of peptides linked via disulfide bridges.  They provide a fully functional free web based version and they also sell a standalone version.

MS-Bridge linked peptide search of MS data at the UCSF Protein Prospector web site.  Useful in identifying disulfide lined peptides.

Sheffield ChemPuter  Isotope patterns, element percentages, reaction yields, oxidation state, electron accountancy, VSPER, MLXZ.

Mass Spectrometry Consultants and Contract Labs 

Bay Bioanalytical Laboratory, Inc.  They do electrospray, APCI, HPLC, GC, CE, Spectroscopy, Method Validation.  Visit their services page for more detail. (GLP/cGMP compliant)

M-Scan Mass Spectrometry Consultants and Analysts. "Areas of specialist expertise include Biotechnology and Environmental/Petroleum Analysis. In addition to mass spectrometry, other analytical services such as GC, HPLC, gas phase sequencing, amino acid analysis, carbohydrate composition and linkage analysis are routinely available." 

Matt Sweeney    Mass Spec Consulting Training/Operations/Consulting/Method Development LC/MS Pharmacokinetics, Peptides, Proteins, Metabolism, Maintenance Classes, Specialist in Finnigan Equipment and Software.  IonSource is proud to host  Matt's Perl for Proteomics Page on our web site.
E-mail Matt at

Novatia Corporation   Novatia is a mass spectrometry consulting company with Mark Hail as the chief consultant   The Novatia web site provides an open forum to help people get answers in the areas of LC/MS, bio-MS, and high-throughput pharmaceutical applications of MS.  The web site contains hot topics like; which mass spectrometer system is best for proteomics and tips for using SEQUEST.

Pheonix International Life Sciences, Inc. now MDS Pharma Services,  They do it all from lead drug candidate ID through all phases of clinical trials.  (GLP/cGMP compliant)

Stanford University Mass Spectrometry Core Facility  This lab provides rapid protein identification from 1D and 2D SDS PAGE gels. This lab also provides quality detailed peptide mapping  in conjunction with post-translational modification identification.  There is also the availability of experienced mass spectrometry and proteomics consultation.  This is a quality contract laboratory.

Taylor Technology, Inc.  "Is a privately held contract analytical laboratory focused on quantitative bioanalytical mass spectrometry services for the pharmaceutical industry. Their services are utilized across the spectrum of the drug development process from early discovery to phases III and IV." (GLP/cGMP compliant)

Databases and Tools   

Baktron Search a bacterial database to identify bacteria by mass.

Biology Links Page. Harvard University Dept of Molecular and Cellular Biology. Many good database links.

Proteome Analysis @ EBI Fine collection of protein databases; human, yeast, drosophila and many more.

Entrez-PubMed National Center for Biotechnology Information. Literature databases.  National Library of Medicine. 

ExPASy Molecular Biology Server  with links to SWISS-PROT and TrEMBL "Annotated protein sequence database" and FTP: SWISS-PROT + TrEMBL download a non-redundant database and PeptIdent "PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data."  There is so much more, here is a list of links to ExPASy.

National Center for Biotechnology Information,   "NCBI creates public databases."

Oxford Glycobiology Institute  Many good proteomics and valuable database links.

Protein Data Bank, PDB, "The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR."

SEQUEST MS/MS database searching tool by Jimmy Eng/John Yates.  This link originates at The Scripps Research Institute

  Human, Yeast, and nonredundant Protein and DNA databases.   Link to Sequest resource.

The UCSF Mass Spectrometry Page, Alma L. Burlingame, PhD, Director.  The web home of "Protein Prospector." Tools include  search by peptide mass, search with peptide ms/ms data, search with Edman data, etc.. "Protein Prospector" is one of the best database searching tools.

 ChemFinder  Free search by chemical name, CAS number, molecular formula, or molecular weight.

  NIST, Chemistry WebBook.  Search a chemical database. Chemical information including mass spectra

Atomic Weights and Isotopic Compositions, NIST, Physics Laboratory

The Enzyme Manual. A searchable database of enzymes at Worthington Biochemical Corporation Each enzyme record includes digest methods and  ample references. One of the best sites on the web.


Definitions (MS), Dictionaries and Reference Materials   

List of MS definitions 

General Glossary at The Electrophoresis Society

Genetics Glossary The University of Edinburgh, School of Biology

The Dictionary of Cell and Molecular Biology at The University of Edinburgh.

HPLC Glossary  from Upchurch Scientific

Biochemical Society Interest Groups, Glossary of terms

Glossary of terms used in theoretical organic chemistry at the IUPAC web site.

IUPAC Nomenclature Home Page.  

IUPAC  Periodic Table. Atomic weights out to five significant figures. 

IUPAC Commission on Atomic Weights and Isotopic Abundances 1995   Atomic Weights of the Elements 1995.

IUPAC Commission on Atomic Weights and Isotopic Abundances 1997 no change has been made to the 1995 atomic weights except for a footnote for lithium. Isotopic reports on non-terrestrial data added.

IUPAC Subcommittee for Isotopic Abundance Measurements. Isotopic Compositions of the Elements 1997

Acronyms and Abbreviations  handy for those pesky acronyms. 


Invitrogen.  The new seller of Novex line of electrophoresis products.

Employment Listings   

 Visit The Employment Links at IonSource.Com


Atomic Structure "sometimes it is worth returning to high school"  They also present papers on the isotopes and atomic weight, explore.   

A History of Mass Spectrometry: The Scripps Research Institute in La Jolla, CA Description:  Mass spectrometry historical retrospective.

Who Won the Nobel Prize for the Invention of the Ion Trap? You should know, try looking here. 

History of Chemistry. 

History of Chemistry  Presented by Woodrow Wilson Summer Institute.  Excellent monographs on chemists from the past.  

History of Electrochemistry  

History of the Pharmaceutical Industry 

History of Xenobiotic Metabolism

Classic Papers from the History of Chemistry Classic papers posted at Diamond Bar High School 

Mass Spectrometry Interest Groups    

American Society for Mass Spectrometry (ASMS)  Topics: Analytical Laboratory Managers | Biological Macromolecules | Computer Applications | Desorption Ionization | Elemental & Isotopic | Environmental Applications | Flavor, Fragrance & Foodstuffs | Fourier Transform MS | Fundamentals | History of Mass Spectrometry | Hydrocarbon & Chemical Processes | Ion Trap Mass Spectrometry | LC/MS & Related Topics | Metal Ion Coordination Chemistry | Pharmaceuticals | Polymeric Materials | Quantitation | Surface Science | Time-of-Flight MS | Young Mass Spectrometrists 

The Association of Biomolecular Resource Facilities Electronic Discussion Group (ABRF)

British Mass Spectrometry Society Special Interest Groups (BMSS)  Topics:  Combinatorial Chemistry | Environmental Food and Nutrition | Fundamentals | Interface 2000 | LC/MS | Miniaturization | MS/MS | Non-covalent interactions | Trapped Ions

  Google Mass Spectrometry Interest Group  

  The Mass Spectrometry Interest Group of the National Cancer Institute at Frederick, MD

NIH Mass Spectrometry Discussion Group

List of Regional Discussion Groups at the NCI at Frederick Web Site


Journal of The American Society for Mass Spectrometry   JASMS is accessible on-line for members of ASMS and Chem-Web.

European Mass Spectrometry.  Free abstracts available.  Must have an account to get .pdf articles 

Electrophoresis, Publisher Wiley-VCH

Rapid Communications in Mass Spectrometry , Publisher Wiley InterScience.

The Company of Biologists Limited Is a non-profit organization. They have three journals; Development, Journal of Cell Science, Journal of Experimental Biology.  Abstracts are available for all articles and entire pdf versions for older articles.


Research Group of Dwight E. Matthews,  Ph.D. at the University of Vermont (UVM)  Their motto: "We Do Stable Isotopes Better"  Dwight is Director of the Mass Spectrometry Facility in the General Clinical Research Center, University of Vermont College of Medicine, Burlington, Vermont. 


Visit the proteomics page at IonSource

Search Engines   

BiotechFind More than just a search engine, a resource for the biotechnology industry.


Kart00 A search engine that generates internet maps.  Try searching Mass Spectrometry.

(check each societies web site for meeting details and deadlines)

American Society for Mass Spectrometry

American Chemical Society 

  The British Mass Spectrometry Society  

 Canadian Society for Mass Spectrometry  CSMS, Yearly  Tandem Mass Spectrometry Workshop in Lake Louise, Alberta at the The Fairmont Chateau Lake Louise (December 1 - 4, 2004).

The Electrophoresis Society "Promoting  scientific advancement in electrophoretic theory and applications."  Joint 19th Annual Meeting of The Electrophoresis Society (AES) and American Institute of Chemical Engineers (AIChE). Indianapolis Convention Center Indianapolis, IN Nov.3-8, 2002

The 5th Harsh-Environment Mass Spectrometry Workshop and The 2nd Miniature Vacuum Pump  Workshop Presented by the JPL, Pasadena, CA, Fall, 2005

The International Mass Spectrometry Society  IMSS,  The next IMSC in 2003 in Edinburgh.

  The Italian Home page   Contains links to mass spectrometry meetings in Italy and the world.

  Montreux Symposium on Liquid Chromatography Mass Spectrometry and Short Course in Montreux, Switzerland, Nov. 10-12,2004

  Nederlandse Vereniging voor Massaspectrometrie  NVMS Dutch Society for Mass Spectrometry

List of Mass Spectrometry Societies  Links made available through anzsms

  The San Francisco Bay Area Mass Spectrometry (BAMS) discussion group  

 Swiss Group for Mass Spectrometry


Atomic Weights and Isotopic Compositions, NIST, Physics Laboratory

  Exact Masses and Isotopic Abundances of the Elements at SIS Table of the elements with exact mass and isotopic distribution.

Periodic Table of the Elements  Faculty of Chemical Technology, Split, Croatia


A Science Primer from NCBI, includes primers on: bioinformatics, genome mapping, molecular modeling, SNPs. ESTs, microarray technology, molecular genetics, phamacogenomics, phylogenetics.

The University of New Mexico.  Many good mass spectrometry mini tutorials: Nominal mass determinations, Exact mass (150-1000 Da), High mass accuracy of peptides, ESI of oligonucleotides, ESI of proteins, Multiply charged ions, ESI data on the QTof.

Buffers for pH control. Use a java calculator to design a buffer with specified pH, concentration, and ionic strength.

Carboxyl-Terminal Sequencing Methods, by John E. Shively at the ABRF web site.

What is Mass Spectrometry? (An Introduction to Organic Mass Spectrometry) by
John H Lamb, MRC Toxicology Unit Web edition prepared by Fred Mellon, Institute of Food Research

Basic Mass Spectroscopy By Paul R. Young, University of Illinois at Chicago, 1996.

  Mass Spectrometry, Vanderbilt University, Mass Spectrometry Research Center, by Richard Caprioli and Marc Sutter, revised by Markus Stoeckli.  Detailed tutorial in slide form. 

  Theory of mass spectrometry  One of the best tutorials, recommended. Presented at the University of Cambridge, Department of Chemistry by Paul Gates.  Topics Covered-  Ionization: EI, FAB & LSIMS, ESI, MALDI, Mass Analysis: Sector, TOF Quadrupole, FT-ICR, Ion Trap.

  "Introduzione alla Apettrometria di Massa" An beautiful introduction to mass spectrometry in Italian, by Prof. Carlo Mauizio Camaggi. 

  Mass Spectrometry On-line Tutorial  Under construction and provided by Kamel Harrata at Iowa State University.

"Instrument and Ionization Methods Tutorial" Washington University Center for Biomedical and Bioorganic Mass Spectrometry: A NIH-Supported Resource Center.

Mass Spectrometry Accuracy and Resolution from Matrix Science Ltd

An Introduction to Fourier Transform Mass Spectrometry IonSpec Corporation

Introduction to Enzymes, at Worthington Biochemical Corporation

HPLC Introduction at Upchurch Scientific. 

Visit the Chem Team for many great chemistry tutorials and chem. history. 

What is Microdialysis? and how can it be used in pharmacokinetics? 

Universities, Institutes and Government MS Labs

Stanford University Mass Spectrometry Core Facility  This lab provides rapid protein identification from 1D and 2D SDS PAGE gels. This lab also provides quality detailed peptide mapping  in conjunction with post-translational modification identification.  There is also the availability of experienced mass spectrometry and proteomics consultation.  This is a quality contract laboratory.

PAF :  Protein Analysis Facility at The University of Lausanne.  They provide protein MS ID services, as well as education, collaborations and plan to provide new technology which will benefit the scientific community. 

The University of New Mexico,  Mass Spectrometry in the Department of Chemistry.  Many good mass spectrometry mini tutorials: Nominal mass determinations, Exact mass (150-1000 Da), High mass accuracy of peptides, ESI of oligonucleotides, ESI of proteins, Multiply charged ions, ESI data on the QTof.

University Utrecht, Department of Biomolecular Mass Spectrometry   The group in Utrecht applies mass spectrometry primarily to proteomics and studies into biomolecular interactions, such as protein-protein interactions. Here is a short list of the research projects that they are currently involved with: Assembly and function of flavoproteins, B-cell activation, New drug-targets in for instance asthma and cancer, Enzyme-inhibitor studies on for instance Glyoxalase I and tyrosine kinases, Protein-membrane interactions and Antibiotics function (vancomycin, nisin and colicin).   

Dwight E. Matthews Research Group,  Ph.D. at the University of Vermont (UVM)  Their motto: "We Do Stable Isotopes Better"  Dwight is Director of the Mass Spectrometry Facility in the General Clinical Research Center, University of Vermont College of Medicine, Burlington, Vermont.

EMBL Protein and Peptide Group, group leader is Matthias Wilm.  Great resource for mass spectrometry, lots of protein and peptide related software in addition they have a core facility doing ms and n-term sequencing. Original home of the program Peptide Search 

Michael MacCoss' Home Page at the University of Washington

Middle Atlantic Mass Spectrometry Lab The Johns Hopkins University, Peptides and proteins and post-translation modification, DNA sequencing by MS.

Oak Ridge National Laboratory "ORNL is a multiprogram science and technology laboratory managed for the U.S. Department of Energy by UT-Battelle, LLC. Scientists and engineers at ORNL conduct basic and applied research and development to create scientific knowledge and technological solutions that strengthen the nation's leadership in key areas of science."

Rega institute for Medical Research, Belgium. Katholieke Universiteit Leuven, Medicinal Chemistry molecular mass calculator, oligonucleotide mass calculator, peptide mass calculator, PEPSEQ interprets, MS/MS data.

Rockefeller University. Prowl Contents: ProteinInfo, ProFound, PepFrag, Software, Amino acids, Peptides, Protocols, Contaminants, Links.

Vanderbilt University Medical Center in Nashville, Mass Spectrometry Research Center (MSRC). "The MSRC is part of the School of Medicine, with faculty and staff having appointments in the Departments of Biochemistry, Pharmacology, and Chemistry." "Prof. Richard M. Caprioli's mass spectrometry group with the focus on measurement of biological samples."  

The UCSF Mass Spectrometry Page, Alma L. Burlingame, PhD, Director.  The web home of "Protein Prospector"

Washington University Center for Biomedical and Bioorganic Mass Spectrometry. Will perform MS for a fee.  Services include; EI, CI, FAB, ESI-ion trap, LC/MS, MALDI, exact mass, MS/MS, GC, isotope ratio.

Vendors (LC)

Agilent They sell the 1100™ standard and capillary HPLC's.

Alltech Associates, Inc. 800-255-8324,   "Specialists in Chromatography"  They sell: Instruments,GC, Sample Prep, Vials, Standards, TLC, HPLC, LC Accessories, IC.

Bodman  800-241-8774, They sell chromatography systems and chromatography supplies.

  Cohesive Technologies  Specializing in systems for chromatographic solutions for pharmacokinetic analysis.

LC Packings  415-552-1855,  They sell capillary HPLCs,  columns and capillary UV flow cells and much more. Visit their capillary applications section. 

Michrom BioResources, Inc.  (530) 888-6498,  Michrom sells the MAGIC 2002™ HPLC plus columns traps and other HPLC and LC/MS supplies and accessories. The company founder and president is Kerry Nugent a well respected and knowledgeable chromatographer..

Mico-Tech Scientific Inc.  408-730-8324,  Located in Sunnyvale, California.  They sell capillary HPLCs along with a large selection of capillary HPLC columns and supplies. Column selection page.
The company founder and president is Frank Yang a long time expert in the field of capillary chromatography.

Rheodyne L.P.   707-588-2016, Best known as an HPLC injection valve manufacturer.  Lots of information here on trouble shooting HPLC injection valves.

ThermoFinnigan They sell the Surveyor™ HPLC, and assorted UV detectors as well as autosamplers.

Waters Corporation  508-478-2016, They sell HPLCs, HPLC columns, mass spectrometers and more. 

Upchurch Scientific 800- 426-0191, They sell chromatography products and specialize in HPLC fittings and connections. They have helpful resources like "The HPLC Center"  

Valco Instruments Co. Inc.  Contact Info.  Maybe best known as an HPLC injection valve manufacturer.  The products page.  Fantastic valve applications with Java enabled valves to show you all the positions, great applications and ideas.  Support Page.  Theys sell Injectors, detectors, valves, fittings, syringes and tubing.

Vydac  800-247-0924,  They sell HPLC columns ranging from capillary to preparative. My favorite peptide column is Vydac C8-300A-5 micron.  (recheck this link)

Vendors (MS)  

Agilent, Inc.

Bruker Daltonics They sell ion traps, MALDI TOF, FTMS and more (recheck this link)

Micromass  They sell single and triple quadrupole mass spectrometers, MALDI TOF,  ICP mass spectrometers and more of course.

  New Objective They sell nano-ESI/MS accessories and more. 

  Proxeon  They sell nano-spray attachments, nano-spray needles and other tools for proteomic investigations including software.

Thermo Finnigan Corporation.  They sell ion traps, triple quadrupole mass spectrometers, GC/MS, ICP-MS, FTMS, magnetic sector instruments and more. 


Links to More Links and Resources   

Gene's Now (DB Link) Graduate School of Frontier Sciences, The University of Tokyo

Links to mobile and miniature mass spectrometer

The University of Liverpool Department of Chemistry List over 7350 chemistry internet resources including an index called "Whatever Happened to...?" 

BioPortfolio.Com Sort of like a Bio Search engine.





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Last updated:  Tuesday, January 19, 2016 02:51:35 PM