Mass Spectrometry and Proteomics Core

Jupiter, Florida Campus

The Mass Spectrometry and Proteomics Core on the Scripps Research Florida campus has one mission: to provide a wide range of state-of-the-art mass spectrometry-based proteomics services to assist with protein characterization, identification and quantification, and apply these technologies to solve relevant biological problems. The core provides support to Scripps Florida faculty and staff who focus on such questions, as well as fee-for-service analyses for external academic and industrial researchers.

Core scientists concentrate on developing and applying the techniques of mass spectrometry for discovery and quantitative proteomic experiments. The Core's biomedical research support is focused on the search for appropriate experimental design, the constant improvement and optimization of protocols, and the actualization of equipment and expertise.


A variety of services is available on a fee-basis to internal and external scientists. We also offer help with experimental design, sample preparation, interpretation of data and unlimited consultation including support for grant writing and manuscript preparation. For pricing, please contact the Core director.

The table below lists the general services we offer.

Services Provided

Basic Protein Services


Gel Coomassie staining

Protein/Peptide Assay

Protein Precipitation

LC-MS/MS Services on Fusion Tribrid

Solution or in-gel sample digestion and high resolution LC-MS/MS using 1-4Hr gradients

LC-MS/MS Services on Q Exactive

Solution or in-gel sample digestion and high resolution LC-MS/MS using 1-4Hr gradients

LC-MS/MS Services on Fusion Tribrid

High resolution LC-MS/MS using 1-4Hr gradients (self-digested samples)

LC-MS/MS Services on Q Exactive

High resolution LC-MS/MS using 1-4Hr gradients (self-digested samples)

Other Services

Protein digest clean up

High resolution MS or LC-MS

TMT quantification

SILAC quantification

Label free quantification

HPLC peptide separation

For internal users, request for services in done using the Idea Elan Infinity lab information management system. Internal User Login URL (log in with your email credentials):

For external users, please contact the Core director for instructions how to request services. External users will need to obtain a Purchase Order (PO). At this time, credit card payments are also accepted (subject to change).

It is our policy that key collaborator(s) within the Scripps Research Florida share in co-authorship of any manuscripts that are the result of work performed at the Core. Minimally, the Proteomics Core should be acknowledged as follows in publications: This work is supported in part by Scripps Research Florida Proteomics Core. Here are the ABRF guidelines for authorship for personnel working in facilities such as Scripps Research Proteomics Core.

Stable and Potent Selenomab-Drug Conjugates
Li X, Nelson CG, Nair RR, Hazlehurst L, Moroni TMartinez-Acedo P, Nanna AR, Hymel D, Burke TR Jr, Rader C
Cell Chem Biol. 2017 Mar 9

RasGRP1 promotes amphetamine-induced motor behavior through a Rhes interaction network (“Rhesactome”) in the striatum
Shahani N, Swarnkar S, Giovinazzo V, Morgenweck J, Bohn L, Scharager-Tapia CPascal BMartinez-Acedo P, Khar K, Subramaniam S
Sci. Signal.  2016 Nov;9(454), ra111

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications
Pascal BDWest GMScharager-Tapia CFlefil RMoroni TMartínez-Acedo P, Griffin PR, Carvalloza AC
J Am Soc Mass Spectrom. 2015 Dec;26(12):2133-40

SERBP1 Is a Component of the Liver Receptor Homologue-1 Transcriptional Complex
Mari Y, West GMScharager-Tapia CPascal BD, Garcia-Ordonez RD, Griffin PR
J Proteome Res. 2015 Nov 6;14(11):4571-80

Site-Specific Proteomic Mapping Identifies Selectively Modified Regulatory Cysteine Residues in Functionally Distinct Protein Networks
Gould NS, Evans P, Martínez-Acedo P, Marino SM, Gladyshev VN, Carroll KS, Ischiropoulos H
Chem Biol. 2015 Jul 23;22(7):965-75

Mass spectrometry approach and ELISA reveal the effect of codon optimization on N-linked glycosylation of HIV-1 gp120
Honarmand Ebrahimi K, West GMFlefil R
J Proteome Res. 2014 Dec 5;13(12):5801-11

New approach to capture and characterize synaptic proteome
Liu XA, Kadakkuzha B, Pascal BSteckler C, Akhmedov K, Yan L, Chalmers M, Puthanveettil SV
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16154-9

Proteomic analysis of peptides tagged with dimedone and related probes
Martínez-Acedo P, Gupta V, Carroll KS
J Mass Spectrom. 2014 Apr;49(4):257-65

Using unnatural amino acid mutagenesis to probe the regulation of PRMT1
Rust HL, Subramanian V, West GM, Young DD, Schultz PG, Thompson PR
ACS Chem Biol. 2014 Mar 21;9(3):649-55

General statistical framework for quantitative proteomics by stable isotope labeling
Navarro P, Trevisan-Herraz M, Bonzon-Kulichenko E, Núñez E, Martínez-Acedo P, Pérez-Hernández D, Jorge I, Mesa R, Calvo E, Carrascal M, Hernáez ML, García F, Bárcena JA, Ashman K, Abian J, Gil C, Redondo JM, Vázquez J
J Proteome Res. 2014 Mar 7;13(3):1234-47

Ischemic preconditioning protects cardiomyocyte mitochondria through mechanisms independent of cytosol
Ruiz-Meana M, Núñez E, Miro-Casas E, Martínez-Acedo P, Barba I, Rodriguez-Sinovas A, Inserte J, Fernandez-Sanz C, Hernando V, Vázquez J, Garcia-Dorado D
J Mol Cell Cardiol. 2014 Mar;68:79-88

Decoding split and pool combinatorial libraries with electron-transfer dissociation tandem mass spectrometry
Sarkar M, Pascal BDSteckler C, Aquino C, Micalizio GC, Kodadek T, Chalmers MJ
J Am Soc Mass Spectrom. 2013 Jul;24(7):1026-36

Direct interaction between AR and PAK6 in androgen-stimulated PAK6 activation
Liu X, Busby J, John C, Wei J, Yuan X, Lu ML
PLoS One. 2013 Oct 10;8(10):e77367

A novel strategy for global analysis of the dynamic thiol redox proteome
Martínez-Acedo P, Núñez E, Gómez FJ, Moreno M, Ramos E, Izquierdo-Álvarez A, Miró-Casas E, Mesa R, Rodriguez P, Martínez-Ruiz A, Dorado DG, Lamas S, Vázquez J
Mol Cell Proteomics. 2012 Sep;11(9):800-13

Probing adenylation: using a fluorescently labelled ATP probe to directly label and immunoprecipitate VopS substrates
Lewallen DM, Steckler CJ, Knuckley B, Chalmers MJ, Thompson PR
Mol Biosyst. 2012 Jun;8(6):1701-6

Application of iTRAQ Reagents to Relatively Quantify the Reversible Redox State of Cysteine Residues
McDonagh B, Martínez-Acedo P, Vázquez J, Padilla CA, Sheehan D, Bárcena JA
Int J Proteomics. 2012;2012:514847

Phosphorylation of Y372 is critical for Jak2 tyrosine kinase activation
Sayyah J, Gnanasambandan K, Kamarajugadda S, Tsuda S, Caldwell-Busby J, Sayeski PP
Cell Signal. 2011 Nov;23(11):1806-15

A biomimetic polyketide-inspired approach to small-molecule ligand discovery
Aquino C, Sarkar M, Chalmers MJ, Mendes K, Kodadek T, Micalizio GC
Nat Chem. 2011 Nov 20;4(2):99-104

Cell death induced by the Jak2 inhibitor, G6, correlates with cleavage of vimentin filaments
Majumder A, Kirabo A, Karrupiah K, Tsuda S, Caldwell-Busby J, Cardounel AJ, Keseru GM, Sayeski PP
Biochemistry. 2011 Sep 13;50(36):7774-86

A robust method for quantitative high-throughput analysis of proteomes by 18O labeling
Bonzon-Kulichenko E, Pérez-Hernández D, Núñez E, Martínez-Acedo P, Navarro P, Trevisan-Herraz M, Ramos Mdel C, Sierra S, Martínez-Martínez S, Ruiz-Meana M, Miró-Casas E, García-Dorado D, Redondo JM, Burgos JS, Vázquez J
Mol Cell Proteomics. 2011 Jan;10(1):M110.003335

Cyclosporine A-induced nitration of tyrosine 34 MnSOD in endothelial cells: role of mitochondrial superoxide
Redondo-Horcajo M, Romero N, Martínez-Acedo P, Martínez-Ruiz A, Quijano C, Lourenço CF, Movilla N, Enríquez JA, Rodríguez-Pascual F, Rial E, Radi R, Vázquez J, Lamas S
Cardiovasc Res. 2010 Jul 15;87(2):356-65

Sperm proteomics reveals intensified selection on mouse sperm membrane and acrosome genes
Dorus S, Wasbrough ER, Busby J, Wilkin EC, Karr TL
Mol Biol Evol. 2010 Jun;27(6):1235-46

A novel cross-talk in diacylglycerol signaling: the Rac-GAP beta2-chimaerin is negatively regulated by protein kinase Cdelta-mediated phosphorylation
Griner EM, Caino MC, Sosa MS, Colón-González F, Chalmers MJ, Mischak H, Kazanietz MG
J Biol Chem. 2010 May 28;285(22):16931-41

Activation domain-dependent degradation of somatic Wee1 kinase
Owens L, Simanski S, Squire C, Smith A, Cartzendafner J, Cavett VCaldwell Busby J, Sato T, Ayad NG
J Biol Chem. 2010 Feb 26;285(9):6761-9

Mapping the phosphorylation sites of Ulk1
Dorsey FC, Rose KL, Coenen S, Prater SM, Cavett V, Cleveland JL, Caldwell-Busby J
J Proteome Res. 2009 Nov;8(11):5253-63

Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: application to the study of vascular endothelial growth factor-induced angiogenesis in endothelial cells
Jorge I*, Navarro P*, Martínez-Acedo P*, Núñez E, Serrano H, Alfranca A, Redondo JM, Vázquez J Mol Cell Proteomics. 2009 May;8(5):1130-49 (*These authors contributed equally to this work.)

Strategies to recover proteins from ocular tissues for proteomics
Patel N, Solanki E, Picciani R, Cavett VCaldwell-Busby JA, Bhattacharya SK
Proteomics. 2008 Mar;8(5):1055-70

A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway
Amelio AL, Miraglia LJ, Conkright JJ, Mercer BA, Batalov S, Cavett V, Orth AP, Busby J, Hogenesch JB, Conkright MD
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20314-9

High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: application to biological studies
Jorge I, Casas E, Villar M, Ortega-Pérez I, López-Ferrer D, Martínez-Ruiz A, Carrera M, Marina A, Martínez P, Serrano H, Cañas B, Were F, Gallardo JM, Lamas S, Redondo JM, García-Dorado D, Vázquez J
J Mass Spectrom. 2007 Nov;42(11):1391-403

The N-terminal SH2 domain of the tyrosine phosphatase, SHP-2, is essential for Jak2-dependent signaling via the angiotensin II type AT1 receptor
Godeny MD, Sayyah J, VonDerLinden D, Johns M, Ostrov DA, Caldwell-Busby J, Sayeski PP
Cell Signal. 2007 Mar;19(3):600-9

Proteomic analyses of zebra finch optic tectum and comparative histochemistry
Sloley S, Smith S, Gandhi S, Busby JA, London S, Luksch H, Clayton DF, Bhattacharya SK
J Proteome Res. 2007 Jun;6(6):2341-50

Proteomic analyses of songbird (Zebra finch; Taeniopygia guttata) retina
Sloley S, Smith S, Algeciras M, Cavett VBusby JA, London S, Clayton DF, Bhattacharya SK
J Proteome Res. 2007 Mar;6(3):1093-100

Trizol-based method for sample preparation and isoelectric focusing of halophilic proteins
Kirkland PA, Busby J, Stevens S Jr, Maupin-Furlow JA
Analytical Biochem. 2006 Apr 15;351(2):254-9

Both short-term and long-term archival of the acquired raw data files is ultimately the sole responsibility of the users of the Core. The Scripps Research Mass Spectrometry and Proteomics Core in Jupiter will strive to maintain (but not guarantee) copies of acquired raw data files for up to one year of the acquisition date on local computers as space permits. All data is archived, however, to the Scripps Dropbox Business site at the time of acquisition for long-term storage.