Protocols and Useful Links

Mass Spec Resources

General Mass Spectrometry web pages:

Base Peak, Mass Spec Resource from Wiley:
American Society of Mass Spectrometry

MS Tools:

Spectral Database for Organic Compounds, SDBS.
Chemical composition finder:                   
Isotope Distribution Calculator and Mass Spec Plotter:
Molecular weight calculation                           
Nucleic acid mass calculation:
Peptide mass finder:

Websites of Mass Spectrometer Manufactures and Supplies

Applied Biosystems,
Millipore :
OGS-Proteome Technologies:
A guide to HPLC:

Database Search:

EMBL Protein and Peptide Search:
Mascot Search:
Protein Prospector: (including MS-Tag, MS-Fit, MS-Edman, MS-Seq...)

Protocols and notes

Ziptip cleanup
In-gel trypsin digest: 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