Academic Director: Anna Malovannaya, Ph.D.
Core Directors: Sung Jung, Ph.D. and Hon-Chiu Eastwood Leung, Ph.D.
Email: msproteomicscore@bcm.edu

Overview

The Mass Spectrometry (MS) Proteomics Core at Baylor College of Medicine offers three specialized and comprehensive project packages: (1) “365” Profiling – a proteome-wide label free quantitative proteomic profiling of cells and tissues; (2) IP/MS Analysis – isolation and identification of endogenous or tagged protein complexes via immunoprecipitation followed by mass spectrometry; (3) PTM Analysis – a post-translational modification analysis on purified proteins; (4) “Per-Band” Sequencing – routine protein identification from single samples prepared by the users (e.g. verification of protein identity). 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.

Services

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

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 label-free 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 Fusion Tribrid or Thermo Scientific Q–Exactive 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.

Protein Complex Identification by IP/MS

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 Scientific Elite 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.

Post-Translational Modification (PTM) Analysis

Our Core provides PTM (post-translational modifications) 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. 

"Per-Band" Sequencing

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 2.0 software (Thermo Scientific) with the Mascot search engine (Mascot 2.5, Matrix Science). The assigned peptide spectra and peptide peak quantification is then processed through a custom protein inference algorithm that accounts for distribution of shared peptide quantities. 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 solution for users who are accustomed to proteomics data analysis. Quality control, normalization, and primary analysis of differential expression and interactions are included as a package with the MS technology platforms. 

Secondary analyses are referred to the Bioinformatics Group.  Examples of secondary data analysis include: 

  • Pathway mapping using commercial proteomics software (e.g. Ingenuity, GSA)
  • Annotation enrichment analyses (e.g. GO term enrichment)Integration with orthogonal omics data (such as RPPA, transcriptomics, or metabolomics)
  • Integration with orthogonal omics data (such as RPPA, transcriptomics, or metabolomics)

Equipment

MS Proteomics core features several state-of-the-art ultra high resolution and high mass accuracy mass spectrometers. Thermo Scientific Orbitrap Velos Pro, Orbitrap Elite, Orbitrap Fusion Tribrid and AB Sciex Triple TOF 5600. Additional sequencing time is available on shared Orbitrap Fusion Tribrid, Q-Exactive Plus and, coming later in 2016, Orbitrap Fusion Lumos instruments. All instruments are equipped with ultra high performance liquid chromatography (UHPLC) platforms, including Thermo EASY-nLC1000 and Dionex Ultimate 3000 RSLCnano systems.

Recent Publications Supported by the Core

(1) Fleet T, Zhang B, Lin F, Zhu B, Dasgupta S, Stashi E, Tackett B, Thevananther S, Rajapakshe KI, Gonzales N, Dean A, Mao J, Timchenko N, Malovannaya A, Qin J, Coarfa C, DeMayo F, Dacso CC, Foulds CE, O'Malley BW, York B. SRC-2 orchestrates polygenic inputs for fine-tuning glucose homeostasis. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E6068-77. doi: 10.1073/pnas.1519073112. Epub 2015 Oct 20. PMID: 26487680.

(2) Han,S.J., Jung,S.Y., Wu,S.P., Hawkins,S.M., Park,M.J., Kyo,S., Qin,J., Lydon,J.P., Tsai,S.Y., Tsai,M.J., DeMayo,F.J., and O'Malley,B.W. (2015). Estrogen Receptor beta Modulates Apoptosis Complexes and the Inflammasome to Drive the Pathogenesis of Endometriosis. Cell 163, 960-974. PMID: 26544941.

(3) Bissig-Choisat B, Wang L, Legras X, Saha PK, Chen L, Bell P, Pankowicz FP, Hill MC, Barzi M, Leyton CK, Leung HC, Kruse RL, Himes RW, Goss JA, Wilson JM, Chan L, Lagor WR, Bissig KD. Development and rescue of human familial hypercholesterolaemia in a xenograft mouse model. Nat Commun. 2015 Jun 17;6:7339. doi: 10.1038/ncomms8339. PubMed PMID: 26081744; PubMed Central PMCID: PMC4557302.

(4) Hsu,T.Y., Simon,L.M., Neill,N.J., Marcotte,R., Sayad,A., Bland,C.S., Echeverria,G.V., Sun,T., Kurley,S.J., Tyagi,S., Karlin,K.L., Dominguez-Vidana,R., Hartman,J.D., Renwick,A., Scorsone,K., Bernardi,R.J., Skinner,S.O., Jain,A., Orellana,M., Lagisetti,C., Golding,I., Jung,S.Y., Neilson,J.R., Zhang,X.H., Cooper,T.A., Webb,T.R., Neel,B.G., Shaw,C.A., and Westbrook,T.F. (2015). The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature525, 384-388. PMID: 26331541.

(5) Kang, Y. K., Jung, S. Y., Qin, J., Li, C., Tsai, S. Y., Tsai, M. J., and O'Malley, B. W. (2014) E2/Estrogen receptor/sjogren syndrome-associated autoantigen relieves coactivator activator-induced G1/S arrest to promote breast tumorigenicity. Mol. Cell Biol. 34, 1670-1681. PMID: 24567374.

(6) Karlin,K.L., Mondal,G., Hartman,J.K., Tyagi,S., Kurley,S.J., Bland,C.S., Hsu,T.Y., Renwick,A., Fang,J.E., Migliaccio,I., Callaway,C., Nair,A., Dominguez-Vidana,R., Nguyen,D.X., Osborne,C.K., Schiff,R., Yu-Lee,L.Y., Jung,S.Y., Edwards,D.P., Hilsenbeck,S.G., Rosen,J.M., Zhang,X.H., Shaw,C.A., Couch,F.J., and Westbrook,T.F. (2014). The oncogenic STP axis promotes triple-negative breast cancer via degradation of the REST tumor suppressor. Cell Rep. 9, 1318-1332. PMID: 25453754.

(7) Foulds CE, Feng Q, Ding C, Bailey S, Hunsaker TL, Malovannaya A, Hamilton RA, Gates LA, Zhang Z, Li C, Chan D, Bajaj A, Callaway CG, Edwards DP, Lonard DM, Tsai SY, Tsai MJ, Qin J, O'Malley BW. Proteomic analysis of coregulators bound to ERα on DNA and nucleosomes reveals coregulator dynamics. Mol Cell. 2013;51(2):185-99. PMID: 23850489.

(8) Han K, Holder JL Jr, Schaaf CP, Lu H, Chen H, Kang H, Tang J, Wu Z, Hao S, Cheung SW, Yu P, Sun H, Breman AM, Patel A, Lu HC, Zoghbi HY. SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties. Nature. 2013, 503(7474):72-7. PMID: 24153177.

(9) Liu J, Wang Y, Li L, Zhou L, Wei H, Zhou Q, Liu J, Wang W, Ji L, Shan P, Wang Y, Yang Y, Jung SY, Zhang P, Wang C, Long W, Zhang B, Li X. Site-specific acetylation of the proteasome activator REGγ directs its heptameric structure and functions. J Biol Chem 2013, 288(23):16567-78. PMID: 23612972.