Description:

Identify proteins in solution or in excised gel bands using nanoLC-MS/MS. This service can be used to:

• Confirm the presence of a known protein in a sample.
• Identify unknown proteins from organisms with available protein sequence databases.

User provides:

• Peptide samples prepared according to our in-solution or in-gel digestion protocol.
• The species from which the sample was derived (unknown protein identification) OR Uniprot ID (known protein).
• Typically, 0.05–2 µg of peptides is sufficient for protein identification, although the optimal amount depends on sample complexity and experimental goals.

Service performed:

Peptide samples are analyzed by nanoLC-MS/MS on a Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer. MS/MS spectra are searched against the appropriate protein sequence database to identify proteins and their corresponding peptides.

Report details:

Results are provided as a Proteome Discoverer report and typically include:

• Identified protein(s)
• Peptide sequences
• Peptide-Spectrum Matches (PSMs)
• Protein sequence coverage
• Protein confidence metrics
• Identified peptide modifications (when applicable)

SAMPLE REPORT

Cost:

• $150/sample (NC State Internal rate)
• $228/sample (External academic or federally funded clients rate)
• $750/sample (Commercial rate)

Description:

Determine the accurate molecular mass of intact proteins using high-resolution LC-MS. This service can be used to:

• Characterize glycoform distributions and other mass variants of antibodies and glycoproteins.
• Confirm the molecular weight of recombinant or purified proteins.
• Assess protein heterogeneity.
• Determine the drug-to-antibody ratio (DAR) for antibody-drug conjugates (ADCs).

User provides:

• A purified protein solution. Recommended protein concentration: 1–20 mg/mL.
• Samples should be free of nonvolatile contaminants and surfactants (e.g., SDS, Triton X-100, NP-40, Tween-20/80, PEG, and similar detergents), which interfere with mass spectrometric analysis.
• Recommended sample purity: ≥70%, as assessed by SDS-PAGE or an equivalent method.

Service performed:

Samples are analyzed by reversed-phase UHPLC coupled to high-resolution mass spectrometry using a Thermo Scientific Vanquish Horizon UHPLC and an Orbitrap Exploris 480 mass spectrometer. 

Report details:

• Measured intact molecular mass
• Mass accuracy (mass error)
• Charge state distribution
• Deconvoluted mass spectrum
• Relative abundance of detected mass species
• Drug-to-antibody ratio (DAR), when applicable
• Relative abundance of different glycoforms and other protein variants, when applicable

SAMPLE REPORT

Cost:

Intact protein mass analysis:

• $100/sample (NC State Internal rate)
• $152/sample (External academic or federally funded clients rate)
• $500/sample (Commercial rate).

Top-down protein sequencing:

• $125/sample (NC State Internal rate)
• $190/sample (External academic or federally funded clients rate)
• $600/sample (Commercial rate).

Description:

Identify protein binding partners from affinity purification (AP-MS) or co-immunoprecipitation (Co-IP) experiments using quantitative LC-MS/MS. This service is designed to characterize protein-protein interactions by identifying proteins specifically enriched with a target (bait) protein.

User provides:

• Samples prepared according to our sample submission guidelines.
• Appropriate negative controls (required) to distinguish specific interactors from nonspecific background. Examples include:

• IgG isotype control
• Tag-only control
• EGFP-tag control
• Other appropriate experimental controls

• The species from which the samples were derived or, if applicable, a custom protein sequence database (FASTA format).
• The amino acid sequence or accession number of the bait protein, if it is not present in the reference database.

Service performed:

Samples are analyzed by nanoLC-MS/MS using a Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer. Protein identification is performed using Proteome Discoverer with database searching against the appropriate protein sequence database. Quantitative comparison of experimental and control samples is used to identify proteins that are significantly enriched with the bait protein, generating a list of candidate binding partners. 

Report details:

• Identified proteins
• Peptide sequences
• Peptide-spectrum matches (PSMs)
• Protein sequence coverage
• Relative protein abundance across experimental and control samples
• Statistical enrichment analysis of proteins in bait versus control samples
• List of candidate binding partners

SAMPLE REPORT AVAILABLE UPON REQUEST

Cost:

Exploratory Analysis: (one experimental & one control sample; not publishable)

• $350 / experiment (NC State Internal rate)
• $532 / experiment (External academic or federally funded clients rate)
• $1750 / experiment (Commercial rate).

Full Analysis: (three experimental & three control samples; generally suitable for publication)

• $1000 / experiment (NC State Internal rate)
• $1520 /experiment (External academic or federally funded clients rate)
• $5000/ experiment (Commercial rate).

Description:

Compare protein abundance across biological samples using state-of-the-art label-free quantitative LC-MS/MS (LFQ). This service enables the high-throughput identification and quantification of thousands of proteins, allowing investigators to pinpoint differentially expressed proteins between distinct experimental conditions.

⚠️ Experimental Design Note: For statistically robust data, we require a minimum of three (3) biological replicates per experimental group.

User provides:

• Protein Samples: 5–10 µg of purified protein per sample, prepared according to our Sample Preparation Guidelines.
• Experimental Metadata: A detailed description of the experimental design, including sample groups, control groups, and biological replicates.
• Sequence Database: The specific species of origin or a custom protein sequence database in FASTA format (if applicable).

Service performed:

• Mass Spectrometry: Peptides are analyzed via nanoLC-MS/MS on a Thermo Scientific™ Orbitrap Eclipse™ Tribrid™ mass spectrometer using Data-Independent Acquisition (DIA).
• Data Processing: Protein identification and label-free quantification (LFQ) are performed using Proteome Discoverer™.
• Statistical Analysis: Differential abundance is calculated using tailored statistical methods (e.g., pairwise comparisons or multi-group ANOVA) based on your experimental design.

Report details:

• Differential Expression Analysis: Fold-changes between experimental groups alongside statistical significance metrics (adjusted p-values and False Discovery Rate).
• Protein Identification & Coverage: Lists of identified proteins, sequence coverage, and peptide-spectrum matches (PSMs).
• Quantification Data: Relative protein abundances across all samples, including identified peptide modifications where applicable.

SAMPLE REPORT AVAILABLE UPON REQUEST

Cost:

Exploratory Analysis: (one experimental & one control sample; not publishable)

• $500 / experiment (NC State Internal rate)
• $760 / experiment (External academic or federally funded clients rate)
• $2500/ experiment (Commercial rate).

Full Analysis: (three experimental & three control samples; generally suitable for publication)

• $1500 / experiment (NC State Internal rate)
• $2280 /experiment (External academic or federally funded clients rate)
• $7500/ experiment (Commercial rate).