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. The Proteomics Core considers, on case-by-case basis, special R&D agreements for collaborative initiatives than include method and informatics development.

Please email us at msproteomicscore@bcm.edu to set up a consultation or initiate a project request.

Consultation and Project Design

We offer a 45-minute free consultation via Microsoft Teams to all users. 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.

Grant Application Assistance: Letter of Support and Technical Writing

The core assists in technical writing for grant aims that include proteomics, as well as providing letters of support, facilities and equipment documentation, and data management plans.

Multiomic Project Support

The core provides comprehensive assistance for integrated multiomic studies, including sample splitting, OCT block handling, tissue pulverization, and coordinated project setup to streamline downstream proteomic, transcriptomic, and metabolomic analyses.

TMT Proteome Profiling

Instrumentation: Thermo Scientific Exploris 480 or Eclipse mass spectrometers

Our proteome profiling service allows identification and quantification of over 10,000 proteins from as little as 100,000 cells or 10-20 micrograms of tissue extract. This TMT 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 Exploris 480 or Eclipse mass spectrometers – the two most sensitive core instrument configurations. The data processing pipeline provides quantitation at MS1- level (iBAQ approach). The standard data analysis includes recovery metrics, PCA analysis, hierarchical and k-means clustering, data normalization, differential expression (volcano plots), and GSEA pathway analysis.

DIA Profiling

Instrumentation: Bruker timsTOF Ultra 2 mass spectrometer

The single run DIA based profiling service is offered for mid-coverage level and low complexity samples- biofluids, conditioned media, specialized population of cells, samples- organelle preparations, extracellular matrix, etc. The samples are measured on the current state-of-the-art Bruker timsTOF Ultra2 system which can identify over 6,500 proteins from a 20ng diluted Hela protein digest mixture.

Post-Translational Modification (PTM) Profiling (TMT-Based)

Instrumentation: Thermo Scientific Exploris 480 or Eclipse mass spectrometers

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 performed on Agilent Infinity 1260 HPLC system. A small portion of these fractions is measured directly for global proteome profiling while the remaining fraction is processed for phosphopeptide enrichment using immobilized metal affinity chromatography (IMAC). The sample preparation method is coupled with sequencing on Thermo Scientific Orbitrap Exploris 480 or Eclipse mass spectrometers – the two most sensitive core instrument configurations. The data processing pipeline provides quantitation at MS1- level (iBAQ approach). The standard data analysis includes recovery metrics, PCA analysis, hierarchical and k-means clustering, data normalization, differential expression (volcano plots), phosphosite level quantification and GSEA pathway analysis.

Protein Interactome Analysis

Instrumentation: Thermo Scientific Lumos or Fusion mass spectrometers

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 ~5-20mg of total protein lysates, use a short affinity enrichment protocol, resolve protein complexes on SDS-PAGE, and analyze protein complex components on Thermo Orbitrap 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.

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.

Protein-DNA Interactions
Protein-Small Molecule Interactions

Protein Identification

Instrumentation: Thermo Scientific Lumos or Fusion mass spectrometers

Our core performs routine sequencing of proteins samples for protein identification and verification purposes. This singleshot DDA run is generally reserved for simple samples such as, for example, a specific band of the SDS-PAGE gel, recombinant proteins, PTM analysis on a particular protein, knock-out verification, etc.

Targeted Assay Design

This service is mostly suited for targeted assays or cases that involve customization of sample processing pipeline or MS instrument method design. It includes systematic evaluation of best responders (peptides) for use in a Parallel Reaction Monitoring assay for proteins of interest as well as targeted analysis using Skyline software.

Manual Spectral Analysis

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), acetylation (on lysine), and methylation (on arginine). 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.

Leadership

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

Email: msproteomicscore@bcm.edu

Location and Hours of Operation

Location	Hours
ATC Proteomics and Metabolomics Core Labs Cullen 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.

Visit the Customer Help Manual for further guidance using iLab's Core Facility Services.

Contacts

Name	Role	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

Name	Description	Price
Affinity Purification - MS		Internal BCM - Special 2 $400.00 lane Internal BCM - Special 1 $460.00 lane Internal BCM $500.00 lane External $800.00 lane External - Special $400.00 lane
Affinity Purification - Pulldown		Internal BCM - Special 2 $300.00 each Internal BCM - Special 1 $300.00 each Internal BCM $350.00 each External $560.00 each External - Special $300.00 each
Manual PTM Spectral Analysis		Internal BCM - Special 2 $90.00 each Internal BCM - Special 1 $100.00 each Internal BCM $150.00 each External $240.00 each External - Special $90.00 each
Multiomic Project Setup		Internal BCM - Special 2 $300.00 each
Multiomic Sample Processing- Frozen		Internal BCM - Special 2 $90.00 Sample
Multiomic Sample Processing- OCT		Internal BCM - Special 2 $370.00 each
Profiling Data Analysis		Internal BCM - Special 2 $1,000.00 Project Internal BCM - Special 1 $1,500.00 Project Internal BCM $1,700.00 Project External $2,720.00 Project External - Special $1,000.00 Project
PTM Profiling- TMT MS		Internal BCM - Special 2 $800.00 each Internal BCM - Special 1 $1,100.00 each Internal BCM $1,300.00 each External $2,080.00 each External - Special $800.00 each
PTM Profiling Data Analysis		Internal BCM - Special 2 $2,000.00 Project Internal BCM - Special 1 $3,000.00 Project Internal BCM $3,300.00 Project External $5,280.00 Project External - Special $2,000.00 Project
Single run DDA		Internal BCM - Special 2 $200.00 Project Internal BCM - Special 1 $230.00 Project Internal BCM $250.00 Project External $400.00 Project External - Special $200.00 Project
Single-Run DIA Profiling		Internal BCM $350.00 each Internal BCM - Special 1 $300.00 each Internal BCM - Special 2 $300.00 each External $560.00 each External - Special $300.00 each
Targeted Assay Design		Internal BCM - Special 2 $120.00 each Internal BCM - Special 1 $150.00 each Internal BCM $170.00 each External $270.00 each External - Special $120.00 each
TMT Proteome Profiling		Internal BCM - Special 2 $600.00 each Internal BCM - Special 1 $750.00 each Internal BCM $800.00 each External - Special $600.00 each External $1,280.00 each

Search available services: View: by category alphabetically

Name	Description	Price
▼ ► MASS SPECTROMETRY Services (13)
Multiomic Project Setup		Internal BCM - Special 2 $300.00 each
Multiomic Sample Processing- Frozen		Internal BCM - Special 2 $90.00 Sample
Multiomic Sample Processing- OCT		Internal BCM - Special 2 $370.00 each
TMT Proteome Profiling		Internal BCM - Special 2 $600.00 each Internal BCM - Special 1 $750.00 each Internal BCM $800.00 each External - Special $600.00 each External $1,280.00 each
Single-Run DIA Profiling		Internal BCM $350.00 each Internal BCM - Special 1 $300.00 each Internal BCM - Special 2 $300.00 each External $560.00 each External - Special $300.00 each
Profiling Data Analysis		Internal BCM - Special 2 $1,000.00 Project Internal BCM - Special 1 $1,500.00 Project Internal BCM $1,700.00 Project External $2,720.00 Project External - Special $1,000.00 Project
PTM Profiling- TMT MS		Internal BCM - Special 2 $800.00 each Internal BCM - Special 1 $1,100.00 each Internal BCM $1,300.00 each External $2,080.00 each External - Special $800.00 each
PTM Profiling Data Analysis		Internal BCM - Special 2 $2,000.00 Project Internal BCM - Special 1 $3,000.00 Project Internal BCM $3,300.00 Project External $5,280.00 Project External - Special $2,000.00 Project
Affinity Purification - Pulldown		Internal BCM - Special 2 $300.00 each Internal BCM - Special 1 $300.00 each Internal BCM $350.00 each External $560.00 each External - Special $300.00 each
Affinity Purification - MS		Internal BCM - Special 2 $400.00 lane Internal BCM - Special 1 $460.00 lane Internal BCM $500.00 lane External $800.00 lane External - Special $400.00 lane
Single run DDA		Internal BCM - Special 2 $200.00 Project Internal BCM - Special 1 $230.00 Project Internal BCM $250.00 Project External $400.00 Project External - Special $200.00 Project
Targeted Assay Design		Internal BCM - Special 2 $120.00 each Internal BCM - Special 1 $150.00 each Internal BCM $170.00 each External $270.00 each External - Special $120.00 each
Manual PTM Spectral Analysis		Internal BCM - Special 2 $90.00 each Internal BCM - Special 1 $100.00 each Internal BCM $150.00 each External $240.00 each External - Special $90.00 each

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