Protein Characterization

All services include UPLC-MS/MS on Q-Exactive Orbitrap via unbiased, data-dependent acquisition, inclusive of sample preparation and parallel multi-enzyme digestions using six enzymes, sequence library searching, relative quantitation and reporting via Proteome Cluster.

Protein characterization services can include searches of:


Service 131 – $1,000 Add to cart

Protein Characterization 50k
Six-enzyme digestion, UPLC-MS/MS, up to 50,000 sequencing events, 50 cm column, 90 min gradient
Sample types:
Ideal for in-depth characterization of a single protein or low complexity mixture of proteins, including post-translational modifications. Often used for characterization of histones, therapeutic proteins and monoclonal antibodies.
At least 10 micrograms of the target protein.

Service 132 – $5,000 Add to cart

De novo Protein Assembly 150k
Six-enzyme digestion, UPLC-MS/MS, up to 150,000 sequencing events, 50 cm column, 90 min gradient
Sample types:
Sequence a purified protein with no reference sequence required. Greater than 95% sequence coverage is typical. Often used to determine monoclonal antibody sequences.
At least 100 micrograms of the target protein. Protein should be pure, contamination can result in a failed analysis.


Samples are processed upon arrival and placed in a queue for UPLC-MS/MS. Samples are analyzed on a first-come, first-served basis. Typical turn-around time is two to three weeks. Samples undergoing custom preparations, utilizing custom LC-MS methods and/or data analyses may require additional time.

Sample Preparation


Thermo Easy-nLC 1000
C18 reversed phase 50 cm (length) by 75 micron (inner diameter) with integrated nanoelectrospray tip, heated to 50 C
determined by assay (90 min or 4 hours) at 300 nL/min
Thermo Easy Spray
Thermo Q-Exactive quadrupole-Orbitrap mass spectrometer

Data Analysis



Send at least 10 micrograms for standard protein characterization. Send at least 100 micrograms for de novo assembly. De novo sequencing requires that the protein be pure. Contamination can result in a failed analysis.

Please send in the smallest volume possible.

Any species with an available sequence library (FASTA file) can be assayed. If a sequence library is not available for a species or if the library is limited in scope, we can attempt to search a library of related species to search for homologous proteins. There is no extra charge for searching a custom sequence library. We support all UniProt libraries by default. Search UniProt taxonomies to see if your organism is present.