General Mass Spectrometry Web Pages

American Society of Mass Spectrometry
IonSource

MS Tools

Spectral Database for Organic Compounds (SDBS)
Chemical Composition Finder
Isotope Distribution Calculator and Mass Spec Plotter
Nucleic Acid Mass Calculation
Peptide Mass Finder
PeptideCutter
Peptide Fragment Ion Calculator
Ion Source

Websites of Mass Spectrometer Manufactures and Supplies

Waters-Micromass
ThermoFisher Scientific
Bruker
Sciex
Shimadzu
Agilent
Millipore
Matrix Science

HPLC

A Practical Guide to HPLC Detection – ScienceDirect
The LC Handbook – Agilent Technologies

Database Search

EMBL Bioinformatics Services
Mascot Search
Pepfrag
Protein Prospector (including MS-Tag, MS-Fit, MS-Edman, MS-Seq)
ExPASy
MaxQuant
MaxQuant documentation

Protocols and Notes

Ziptip Cleanup Instructions
Ziptip Product Notes
In-Gel Trypsin Digest

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