MS links, "web diamonds"

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IonSource MS links
Web Diamonds

Table of Contents

Web Based Calculations
Mass Spectrometry Consultants and Contract Labs
Databases and Tools
Definitions (MS), Dictionaries, and Reference Materials
Employment Listings
History
Mass Spectrometry Interest Groups
Metabolism
Journals
Pharmacokinetics
Proteomics
Proteomic Search Engines
Societies and Meetings
Tables
Tutorials
Universities, Institutes and Government MS Labs
Vendors (LC)
Vendors (MS)
Links to More Links and Resources

Surfing Hints:
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Sometimes a link will appear dead, try hitting the refresh button on your browser. Periodically we check our links and if the link is dead we often leave it up and label it (dead link). Please try the link to see if it is still dead, it may be that their server was down at the time of the check. Our procedure is to go back and check the status of the link at a later time and if the link is still dead we will remove it.

Web Based Calculations

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.

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.

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.

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

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 mattsweeney@earthlink.net

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.

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

The Lipid Library A site dedicated entirely to.... lipids. This site has a great introduction to lipids, lipid protocols, MS of lipids, EI spectral libraries, and lipid NMR data.

mMass - Open Source Mass Spectrometry Tool, mMass presents an open source and multi-platform package of many
tools for mass spectrometric data analysis, mainly in proteomics. (This program has yet to be reviewed by IonSource)

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

SEQUEST MS/MS database searching tool by Jimmy Eng/John Yates.

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

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

List of MS definitions

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

Employment Listings

Visit The Employment Links at IonSource.Com

History

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

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

History of Chemistry.

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

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

Google Mass Spectrometry Interest Group

The Mass Spectrometry Interest Group of the National Cancer Institute at Frederick, MD (link dead 121607)

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 (link dead 121607)

Journals

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.

Metabolism

Metabolism Basics at IonSource

Metabolism Articles and Resource Links at IonSource

Pharmacokinetics

http://www.bioanalytical.com

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.

Proteomics

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.

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

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

Tables

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

Tutorials

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.

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

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

"Introduzione alla Apettrometria di Massa" An beautiful introduction to mass spectrometry in Italian, by Prof. Carlo Mauizio Camaggi. (Link found dead 12/16/07, we will check back)

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

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.

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

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 Bioanalytical Research 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 (Link found dead 12/16/07, we will check back)

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

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"

Vendors (LC)

Agilent They sell the new 1200™ 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. (trouble connecting 051607)

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

Cohesive Technologies 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.

Mico-Tech Scientific Inc, 760-597-9088, Located in Vista, California, 2330 Cousteau Court, 92081, USA. They sell splitless capillary HPLCs along with a large selection of capillary HPLC columns and supplies. We have been using their columns since 1991 and have never had a bad column. Column selection page. The company founder and president is Frank Yang a long time expert in the field of capillary chromatography. Contact Frank if you need help with a specialized proteomics application.

Rheodyne L.P. 707-588-2000, 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 508-478-2000, 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. Maybe best known as an HPLC injection valve manufacturer. The products page. They 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.

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.

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

Thermo 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

BioPortfolio.Com Sort of like a Bio Search engine.

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

dmoz.org Open Directory - Mass Spectrometry

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...?"

BioWorks ® is a registered trademark of Thermo Electron Corporation

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