Mass Spectrometry Proteomics Core

Overview of Services

Mass Spectrometry Proteomics Core provided a broad range of services with beginning-to-end support that includes project evaluation and design, sample processing and biochemical purifications, mass spectrometry measurements, data processing, and bioinformatics analysis performed by the experienced core personnel.

Please email us at  msproteomicscore@bcm.edu to set up a consultation! All inquiries receive a free consultation.

Consultation and Project Design

The core directors provide advice on usage of mass spectrometry as a discovery technique and upfront assistance in experimental design of the projects. We consult users on suitability of methodologies, feasibility, detailed protocols and optimization routines, sample preparation, and evaluation of necessities for biological and technical replicates. Consultation and Project Design are included with all major project packages.

365 Proteome Profiling (Label-Free or TMT-Based)

Our “365” proteome profiling service allows identification and quantification of over 6,000 proteins from as little as 100,000 cells or 10-20 micrograms of tissue extract. This profiling protocol is based on a dual-pH reverse phase fractionation of the total digested cellular proteome. The sample preparation method is coupled with sequencing on Thermo Scientific Orbitrap Lumos Tribrid or Exploris 480 Orbitrap mass spectrometers – the two most sensitive core instrument configurations. With such workflow, we can obtain an average of ~125,000 peptide spectra in 12 hours of sequencing time. These spectrometry data routinely identifies 6,000 proteins in each experiment. The sensitivity of the profiling methodology is suitable for the cost effective analysis of small scale or clinical samples. The label-free mass spectrometry-based protein quantification is standard with this service and can be effectively used for differential protein expression analysis.

Phosphoproteome & Proteome Profiling (TMT-Based)

The core offers combined phosphoproteome and proteome profiling based on a CPTAC TMT10/11 harmonized protocol. This profiling protocol includes extensive off-line basic pH reverse phase fractionation of the total digested cellular proteome. The sample preparation method is coupled with sequencing on Thermo Scientific Orbitrap Lumos Tribrid or Exploris 480 Orbitrap mass spectrometers – the two most sensitive core instrument configurations.

Affinity-Based Interactome Analysis

1. Protein Complex Identification:

Isolation and identification of extended protein complex networks is a featured expertise of the Core. At heart of this service is the knowledge base accumulated by our personnel over the past 12 years of research (Jung SY, 2005, PMID: 16051665; and Malovannaya, 2010, PMID: 20133760). We have built custom algorithms to analyze IP/MS data and compiled a reference database of more than 5,000 endogenous protein complexes from ~4,000 IP/MS performed here at BCM (Malovannaya; 2011, PMID: 21620140). This is the most extensive endogenous human protein complex interaction dataset to date.

We start with ~20mg of total protein lysates, use a short affinity enrichment protocol, resolve protein complexes on SDS-PAGE, and analyze protein complex components on Thermo Orbitrap Fusion mass spectrometer. The core offers options for antibody characterization, optimization of protein extraction, and cellular pre-fractionation in cases where interacting partners are sought for specific cellular compartments (e.g. nuclear or cytosolic). The staff is also versatile in many variations of affinity-based protocols, including endogenous protein complex immunoprecipitations (IP/MS), affinity purification of tagged antigens (AP/MS), affinity enrichment (AE/MS), and cross-linked protocols (XL-IP/MS) for highest retention of transient interactors and membrane complexes.

Having established a protein complexome, we provide filtering of non-specific identifications, annotation of true interacting partners, and mapping of interacting proteins onto reference protein complex networks as a standard part of our IP/MS project packages.

2. Protein-DNA Interactions

3. Protein-Small Molecule Interactions

Post-Translational Modification (PTM) Verification

Our core provides PTM (post-translational modification) analysis of affinity purified endogenous or ectopically expressed single recombinant proteins. PTMs that are readily analyzed include phosphorylation (on serine, threonine and tyrosine), ubiquitinylation (on lysine), and acetylation (on lysine). To identify modifications, raw data are searched against a modified protein database containing corresponding modification-specific mass changes. Trained core personnel manually validate all protein-specific PTM spectral matches to address heightened false discovery rates that are inherent to the automated PTM matching algorithms.

Single-Run LC-MS/MS Profiling

Our core performs routine sequencing of proteins samples for protein identification and verification purposes. This service is generally reserved for simple samples such as, for example, a specific band of the SDS-PAGE gel-purified proteins.

Data Analysis

The raw spectral data are analyzed in Proteome Discoverer software (Thermo Scientific) with the Mascot search engine (Matrix Science). The assigned peptide spectra and peptide peak quantification are then processed through a gene-centric protein inference algorithm gpGrouper that accounts for distribution of shared peptide quantities (Saltzman/Malovannaya; 2018, PMID: 30093420).

To evaluate specificity of interacting partners, we rely on referencing our complexome study database and algorithms that were established by this work. The results are annotated and provided back as specific candidate lists and in align! data mining application or spreadsheet export. Quality control, normalization and primary analysis of differential expression and interactions are included as a package with the MS technology platforms. The Core can also perform batch correction, standard clustering analysis (hierarchical, K-means), PCA, volcano plots, and GSEA enrichment analyses as needed.

The services are provided with full “beginning-to-end” support that includes project evaluation and design, biochemical purifications, mass spectrometry sequencing, and data analysis performed within the core and by the experienced core personnel. The Proteomics Core considers, on case-by-case basis, special R&D agreements for collaborative initiatives than include method and informatics development.

Leadership

Academic Director: Anna Malovannaya, Ph.D.
Laboratory Director: Antrix Jain, M.S.

Emailmsproteomicscore@bcm.edu

Location and Hours of Operation

Location

 Hours

ACMD Proteomics and Metabolomics Core Labs
Jones Building, 107-113C
Baylor College of Medicine
One Baylor Plaza
Houston, TX 77030

9 a.m. - 5 p.m., Monday to Friday

Consultation: By appointment

Links and Resources

  • Core website: https://www.bcm.edu/research/atc-core-labs/mass-spectrometry-proteomics-core

Getting Started

  • BCM Users:  Click the link in the upper right corner to login or register for an iLab account using valid BCM credentials.
  • Non-BCM Users:  Click the appropriate link in the upper right corner to login with your approved iLab credentials or to sign up for an iLab account.

Contacts

Name Role Phone Email Location
MSPC Team
Directors and Personnel
 

 
msproteomicscore@bcm.edu
 
108C-113C (Cullen Bldg)
 
Anna Malovannaya
Academic Director
 

 
malovann@bcm.edu
 
108CB (Cullen Bldg)
 
Antrix Jain
Technical Director
 

 
antrixj@bcm.edu
 
108CA (Cullen Bldg)
 

Core Services


Search available services: View: by category alphabetically
MASS SPECTROMETRY Services (9)