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Protocols and Useful Links

Mass Spec Resources

General Mass Spectrometry web pages:

Base Peak, Mass Spec Resource from Wiley: http://www.wiley.com/wileychi/ms/
American Society of Mass Spectrometry    http://www.asms.org/Default.aspx?tabid=80
IonSource:  http://www.ionsource.com/

MS Tools:

Spectral Database for Organic Compounds, SDBS.  http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi
Chemical composition finder:                             http://www.chemcalc.org/MFFinder.html
Isotope Distribution Calculator and Mass Spec Plotter: http://www2.sisweb.com/mstools/isotope.htm
Molecular weight calculation                                     http://www.chemie.fu-berlin.de/cgi-bin/molform
Nucleic acid mass calculation: http://library.med.utah.edu/masspec/mongo.htm
Peptide mass finder: http://www.colby.edu/chemistry/NMR/scripts/peptide.html

Websites of Mass Spectrometer Manufactures and Supplies

Waters-Micromass: http://www.micromass.co.uk/
Applied Biosystems, http://www.appliedbiosystems.com/
Shimadzu: http://www.shimadzu.com/
Agilent:  http://www.home.agilent.com/agilent/home.jspx?cc=US&lc=eng&cmpid=4533
Millipore : http://www.millipore.com/
OGS-Proteome Technologies: http://www.ogs.com/proteome/home.html
A guide to HPLC: http://kerouac.pharm.uky.edu/ASRG/HPLC/hplcmytry.html

Database Search:

EMBL Protein and Peptide Search:  http://www.mann.embl-heidelberg.de/GroupPages/PageLink/peptidesearchpage.html
Mascot Search: http://www.matrixscience.com/cgi/index.pl?page=/search_form_select.html
Pepfrag: http://prowl1.rockefeller.edu/PROWL/pepfrag-java.html
Protein Prospector: http://prospector.ucsf.edu/ (including MS-Tag, MS-Fit, MS-Edman, MS-Seq...)
ExPASy: http://expasy.org/

Protocols and notes

Ziptip cleanup http://www.millipore.com/publications.nsf/docs/tn072
In-gel trypsin digest:  http://www.nature.com/nprot/journal/v1/n6/full/nprot.2006.468.html l

Special note for sample preparation for MALDI analysis

(from Applied Biosystems Manual Book):
Solvents and chemicals that generally pose no interference:   TFA, formic acid, β-mercaptoethanol, DTT, volatile organic solvents, HCL, NH4OH, acetic acid
Solvents and chemicals that are generally tolerable at <50 mM:
HEPES, MOPS, Tris, NH4OAc, Octyl glucoside
Solvents and chemicals that should be avoided:
glycerol, sodium azide, DMSO, SDS, phosphate, NaCl, 2M Urea, 2M guanidine