Mass Spectrometry – Protocols

Protocols and Useful Links

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
UCB (Formerly OGS-Proteome)

Database Search

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

Protocols and Notes

In-Gel Trypsin Digest
Ziptip Cleanup Instructions
Ziptip Product Notes

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 HEPES, MOPS, Tris, NH4OAc, Octyl glucoside
Solvents and chemicals that should be avoided:
glycerol, sodium azide, DMSO, SDS, phosphate, NaCl, 2M Urea, 2M guanidine

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