The ABI 4800 is a tandem time-of-flight MS/MS system and is the workhorse of the MBCF workflow. The 4800 offers high accuracy intact mass analysis of all types of samples as well as ms/ms capabilities for fragmentation analysis of peptides and other bio-molecules It’s high accuracy, (<10ppm), speed, and easy sample prep make analyzing your sample so simple, researchers can be trained for walk-up use.

Generally, we start processing samples as soon as they arrive. For intact MW determinations this means you usually get data back within 2 hours of receipt of sample.

For Digest and MassFingerprinting allow 2 days for processing.

For LC-MS/MS results allow for additional 2 days.

Intact Mass Analysis

Concentration: Optimally, 10uM. Samples at 1uM work if they are clean and very low buffer and salt content.

Buffer: Samples presented in water or other volatile solvents are best. If your sample is not compatible with those requirements, then use a low salt buffer (< 50mM). Try to avoid phosphate buffers as they quench the signal on the MALDI. Avoid DMSO or glycerol if possible. If not, keep percentage of glycerol/DMSO to <5%.

Volume: 1-10ul. More is better.

Containers: Eppendorf type tubes, with your initials, sample name and date clearly on tube.

Samples for digest and protein identification:

Amount: Optimally, >500 fmol or >50 ng. We can detect as low as 5 ng of protein but the coverage is not great, and the identification is less likely to work. For post-translation modification searches, it is important to give at least 4-5 pmol of sample.

Stain: Coomasie, Sypro, or other mass spec compatible silver stain. Stay away from silver stain containing gluteraldehydes. Do not over-stain gel.

Controls: Please provide blank portion of gel. For your benefit provide a known, not pre-stained, standard. Controls are not charged.

Containers: Place gel slice in methanol rinsed 1.5ml Eppendorf tube.(No need for additional liquid). Clearly label all tubes with your initials, sample name and date.

Affiliation IntactMALDI Intact ESI Digest+MALDI 

1st sample, +blank,


Digest and MALDI 

Samples 2-n

Digest+MALDI +LCmsms 

1st sample

+blank +control

Digest+MALDI +LCmsms 

Samples 2-n

DFCI $25 $50 $150 $50 $200 $100
Non-DFCI $50 $100 $300 $100 $400 $200