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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
Proteomic Search Engines
Societies and Meetings
Universities, Institutes and Government MS Labs
Vendors (LC)
Vendors (MS)
Links to More Links and Resources

Surfing Hints: 
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Web Based Calculations 

Uhmins Tools. DNA related programs at Osaka University. DNA sequence editing and analysis tools.

GeneAlign はJavaを使ったアライメントエディタです。プログラムによる自動アライメントの結果を手動で編集したいときに便利です (GeneAlign is a program for manually editing the aligned sequence produced by an alignment program. Documentation available only in Japanese, but you might be able to figure it out, try http://translate.google.com/)

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

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

ExPASy Proteomics tools  Find most of the online programs you will need for proteomics

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

Computational Mass Spectrometry at UCSD Provides access to the following programs: MS-Dictionary, MS-Generating Function, MS-Clustering, Spectral Networks, PepNovo, Phosphorylation search.

PepNovo a free de novo sequencing on-line resource designed specifically for ion trap data.  

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

SearchXLinks, (can no longer find server) 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.  The paper.

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

Can't find it on this list, check out the IonSource Freeware/Shareware page

Mass Spectrometry Consultants and Contract Labs 

Bioproximity is a contract research organization specializing in protein analysis, proteomics, and informatics. They offer a wide range of proteomic services customized to the needs of our clients.

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." 

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.

Databases and Tools   

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  There is so much at this site, here is a list of proteomics links at 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."

Protein and DNA databases links page at IonSource

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   

Process Library  Find out what that computer process is, what was that, smss.exe?  

List of MS definitions 

Biochemical Society Interest Groups, Glossary of terms

IUPAC Nomenclature Home Page.  

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


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

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

SPC Tools a Google group  "Open forum for discussing Seattle Proteome Center proteomics tools, asking questions, and suggesting new features."

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 Journal of 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.


SmileMS, small molecule identification software for LC-MS systems

Metabolism Basics at IonSource

Metabolism Articles and Resource Links at IonSource



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

Proteomic Search Engines   

Mascot Search a sequence database with mass spectrometry data, data upload limit 300 spectra.  

Protein Prospector Search a sequence database with mass spectrometry data. 

TheGPM Search a sequence database with mass spectrometry data using the program X!Tandem.  No Upload limit. 

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

Biotechnology Calendar, Incscience meetings, science tradeshows, event publications in the USA

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

The Electrophoresis Society "Promoting  scientific advancement in electrophoretic theory and applications."  

Harsh-Environment Mass Spectrometry  

The International Mass Spectrometry Society  IMSS

 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.

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

Mass Spectrometry Accuracy and Resolution from Matrix Science Ltd

Introduction to Enzymes, at Worthington Biochemical Corporation

Time of Flight / TOF Mass Spectrometer Tutorial  Offered by Time Of Flight Mass Spectrometer Components
, R. M. Jordan Company, Inc.

HPLC Introduction at Upchurch Scientific.   

Universities, Institutes and Government MS Labs

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.

Michael MacCoss' Home Page at the University of Washington  Mike has great free software for the analysis of mass spectrometry data.

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.

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

Vendors (LC)

Agilent They sell the new 1200™ standard and capillary HPLC's.

 Cohesive Technologies (now Thermo) Specializing in systems for chromatographic solutions for pharmacokinetic analysis.

Dionex is the new vendor for the LC Packings capillary HPLC. They sell capillary HPLCs,  columns and capillary UV flow cells and much more.

Eksigent  Important to us, Eksigent specializes in non-splitting NanoLC HPLC Systems They offer 1D and 2D capillary systems.  The 2D systems can handle the most complex 2D submicroliter protreomic separations.  They also offer the ExpressLC™ HPLC Systems for fast capillary chromatography.  With the ExpressLC-800 HPLC system you can increase throughput by as much as 40 times that of conventional HPLC systems – while achieving better quality quantitative data.

Michrom BioResources, Inc.,  530-888-6498,  Michrom sells the MAGIC 2002™ and Paradigm capillary HPLCs 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.  Kerry is always a leader in chromatographic innovation.

Rheodyne L.P.  (now part of Idex)  Best known as an HPLC injection valve manufacturer.  Lots of information here on trouble shooting HPLC injection valves.

Thermo Fisher Scientific    They sell the Accela™ U-HPLC, 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  (now part of Idex), They sell chromatography products and specialize in HPLC fittings and connections. They have helpful resources like "The HPLC Center"  

Valco Instruments Co. Inc.  Maybe best known as an HPLC injection valve manufacturer.  The products page.   They sell Injectors, detectors, valves, fittings, syringes and tubing.

Grace Davison Discovery Sciences. (formally Vydac) They sell HPLC columns ranging from capillary to preparative. 

Vendors (MS)  

Applied Biosystems, Inc. Applied Biosystems is the industry leader in sales of  triple quadrupole mass spectrometers mainly used for quantitation of small molecule drugs and biomarkers. They also sell a hybrid triple quadrupole instrument in which the second quad is used as a linear ion trap, the Q-Trap 4000 and 5000 mass spectrometers.  AB also sells the 4800 TOF-TOF as well as the Q-Star Elite, a quadrupole time of flight mass spectrometer. 

Agilent, Inc. Feb, 2006.  Agilent has augmented their ion trap, single quad and GC line, of mass spectrometers with a new Quadrupole Time of Flight mass spectrometer as well as with a brand new triple quadrupole. 

Bruker Daltonics They sell ion traps, MALDI TOF, FTMS and more  http://www.bruker-daltonik.de/  

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

  Proxeon  (now  part of Thermo) They sell nano-spray attachments, nano-spray needles and other tools for proteomic investigations including software.

Thermo Scientific  800-532-4752  They sell orbitraps, ion traps, triple quadrupole mass spectrometers, GC/MS, ICP-MS, FTMS, magnetic sector instruments and more.    They sell ion traps, triple quadrupole mass spectrometers, GC/MS, ICP-MS, FTMS, magnetic sector instruments and more. 


Links to More Links and Resources   

dmoz.org Open Directory - Mass Spectrometry

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...?" 






BioWorks ® is a registered trademark of Thermo Fisher Scientific

Mascot ® is a registered trademark of Matrix Science Ltd.

SEQUEST ® is a registered trademark of the University of Washington

X!Tandem was created by Craig and Beavis of the Manitoba Proteomics Center


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Last updated:  Tuesday, January 19, 2016 02:51:33 PM