- Rapid, exhaustive sequencing and characterization of proteins & protein complexes
- Sequence/validate known monoclonal antibodies and protein therapeutics
- De novo sequencing of unknown monoclonal antibodies
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:
- custom sequences
- known post-translational modifications
- unknown post-translational modifications (blind search)
- known single nucleotide polymorphisms (SNPs)
- unknown amino acid point substitutions
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.
- protein solubilization and extraction based on sample type
- clean-up, if necessary, typically via the “filter-assisted sample prep” (FASP) method or SDS-PAGE to isolate heavy and light chains
- enzymatic digestion, protein-dependent, typically with trypsin, Lys-C, chymotrypsin, Glu-C, Asp-N, aLP
- peptide desalting via reversed phase stop-and-go extraction (STAGE) tips
- 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 is searched by up to three tandem mass spectrometry protein identification algorithms, including X!Tandem, OMSSA and K-score, and by X!Hunter if a spectral library is available.
- We support all available protein sequence libraries, including any custom FASTA library or RNA-seq-derived library, at no additional charge.
- Search results are combined and may be viewed online to inspect the protein composition of the sample, identified peptides, matching tandem mass spectra, and much more.
- Quantitation via MS1 peak area measurement.
- Samples or groups of samples are compared, generating fold-change values for every measured protein.
- Your data is stored securely and indefinitely. Samples are organized by project. Additional samples can be added to a project.
- All data is hosted and delivered using our web-based portal, Proteome Cluster
- One-click to download raw data files (mzML format), peak list files (MGF format), search parameters (XML format) and search outputs (mzIdentML format)
- View data reports online or download as Excel files
- Data reports include:
- protein table: protein identifications and intensity of all possible isoforms
- parsimony table: proteins grouped to minimum set supported by data
- peptide table: peptide identifications and intensity, including PTM annotation
- protein sequence coverage: peptides mapped to individual protein sequence
- tandem MS spectrum viewer: see fragment ion assignments for all identified peptides
- quantitation summaries: for both proteins and peptides; see intensities for every protein/peptide across all samples in the project
- comparisons: define samples or groups to compare, view fold-change values for all proteins and peptides
- For de novo protein assembly, the reports refer to searches of the proposed final sequence(s)
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.