Mass Spectrometry and Proteomics

Proteomics Core

Protein and Peptide Identification, Analyses and Quantification

The Mass Spectrometry and Proteomics Core 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 faculty and staff, 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.

NIH Awards Shared Instrumentation Grant for nano UHPLC

Dr. George Tsaprailis received a SIG from the NIH in 2024 to acquire a Thermo Vanquish Neo UHPLC, which will be used in conjunction with the Fusion Orbitrap ETD mass spectrometer. Researchers across all scientific departments, research programs, and Centers at The Wertheim UF Scripps Institute will greatly benefit from enhanced capabilities for performing liquid chromatography of complex sample digests linked to Orbitrap mass spectrometry, thanks to this new UHPLC. This instrument will be accessible to over 40 NIH-funded investigators on campus, as well as to researchers from academic institutions off-campus.

As of 11/01/2024, all users publishing Core acquired data using the Fusion Orbitrap ETD mass spectrometer coupled to the Vanquish Neo UHPLC must include the following acknowledgment:

Research reported in this publication was supported by the Office of The Director, National Institutes of Health of the National Institutes of Health under Award Number S10OD036363. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

We thank you for your cooperation!

Core RRID to be used in publications

The Mass Spectrometry and Proteomics Core has acquired a RRID.

A lab RRID (Research Resource Identifier) is a unique identifier used to reference a research lab in publications and databases. RRIDs are part of a standardized system designed to improve the reproducibility and transparency of scientific research. Lab RRIDs are assigned to specific laboratories and are used to accurately attribute research findings, materials, and resources to the originating lab, helping other researchers to track the source and context of research materials and methods.

Please add the following text to your acknowledgments in addition to acknowledging Core staff:

The analysis was performed at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Mass Spectrometry and Proteomics Core Facility (RRID:SCR_023576).

Contacts

Equipment

Orbitrap Fusion Tribrid MS

The Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer combines the best of quadrupole, Orbitrap and ion trap mass analysis in a revolutionary Tribrid architecture that delivers depth of analysis. It enables researchers analyzing challenging low-abundance, high-complexity or difficult samples to identify more compounds more quickly, quantify more accurately. Increased sensitivity, scan rate and mass resolution enhance the ability to positively identify more low-abundance proteins, such as transcription factors, in less time. The instrument combines resolution up to 450,000 to remove spectral interferences and multiple fragmentation techniques (CID/HCD/ETD) detected by the Ion Trap or Orbitrap at any level of MSn for maximum experimental flexibility, making the Fusion the instrument of choice for multiplexing quantitation approaches, allowing the identification of 4,000 proteins over an hour HPLC gradient in a single run. Ions can be created using electrospray with the HESI, Flex Source and EASY Sources, and samples can be delivered using a Syringe pump or by high pressure liquid chromatography. The Fusion is interfaced to an EASY nLC-1000 system for LC-MSn applications.

A new Thermo Vanquish Neo UHPLC has replaced the EASY nLC-1000 on the Orbitrap Fusion Tribrid mass spectrometer as of November 2024.

Q Exactive Hybrid Quadrupole-Orbitrap

The Thermo Scientific Q Exactive hybrid quadrupole-Orbitrap benchtopmass spectrometer combines high-performance quadrupole precursor selection with high-resolution (resolving power up to 140,000), accurate-mass (HR/AM) Orbitrap detection (internal: < 1 ppm and external: < 3 ppm). The Q Exactive MS/MS data provides ultimate confidence for a wide range of qualitative and quantitative applications. Its high scan speed (maximum scan speed 12 Hz) and spectral multiplexing capabilities make it fully compatible with UHPLC and fast chromatography techniques. The Q Exactive instrument can easily handle routine applications in proteomics from bottom-up protein identification to semiquantitative isotopic labeling analyses to targeted quantification experiments. The versatility of the instrument has been applied to characterization of simple and complex protein mixtures including whole cell lysates, mapping of posttranslational modifications, and quantitative proteomics analysis of metabolic labeled (SILAC) samples or identification of chemically isotope labeled proteomes using Tandem Mass Tags (TMT) for multiplexing quantitative analysis. Ions can be created using electrospray with the HESI, Flex Source and EASY Sources, and samples can be delivered using a Syringe pump or by high pressure liquid chromatography. The Q Exactive is interfaced to an EASY nLC-1000 system for LC-MS and LC-MS/MS applications.

Tims-TOF Pro2

The Bruker Tims-TOF Pro2 is an advanced analytical instrument that combines two powerful technologies: trapped ion mobility spectrometry (TIMS) and time-of-flight mass spectrometry (TOF-MS). This instrument is primarily used in the field of proteomics and metabolomics for high-resolution analysis of complex biological samples.

Here’s what the Bruker Tims-TOF Pro2 can do:

1. Ion Mobility Separation: The instrument utilizes trapped ion mobility spectrometry (TIMS), which separates ions based on their size, shape, and charge. This separation step provides an additional dimension of separation, enhancing the resolving power of the mass spectrometer.

2. Accurate Mass Analysis: The instrument employs time-of-flight mass spectrometry (TOF-MS) to measure the mass-to-charge ratio (m/z) of ions with high precision and accuracy. This allows for the identification and quantification of individual ions in a sample.

3. High Sensitivity: The Tims-TOF Pro2 offers exceptional sensitivity, enabling the detection of low-abundance molecules in complex mixtures. This is crucial for comprehensive analysis of proteomes and metabolomes.

4. Data Acquisition Speed: With its high-speed data acquisition capabilities, the Tims-TOF Pro2 can rapidly analyze samples, allowing for efficient processing of large datasets. This is especially important in high-throughput studies where numerous samples need to be analyzed.

5. Structural Characterization: The instrument supports structural characterization of molecules through its ability to perform tandem mass spectrometry (MS/MS) experiments. This involves fragmenting ions of interest and analyzing the resulting fragmentation patterns, providing valuable information about the structure and composition of molecules.

6. Comprehensive Analysis: The Tims-TOF Pro2 enables comprehensive profiling of complex samples, such as biological fluids, tissues, and cell extracts. It can identify and quantify a wide range of compounds, including proteins, peptides, metabolites, lipids, and small molecules.

7. Quantitative Analysis: The instrument supports both targeted and untargeted quantitative analysis. It allows for the quantification of specific molecules of interest, as well as the discovery of new biomarkers or metabolites without prior knowledge.

8. Software Capabilities: The Tims-TOF Pro2 is equipped with sophisticated software for data processing, analysis, and visualization. It offers tools for peak detection, deconvolution, identification, statistical analysis, and integration with various databases for annotation and interpretation of results.

Overall, the Bruker Tims-TOF Pro2 is a cutting-edge instrument that combines high-resolution ion mobility separation with accurate mass analysis, allowing for comprehensive and in-depth characterization of complex biological samples in the fields of proteomics and metabolomics.

Non-MS Instruments

The Agilent Technologies 1100 HPLC is a well-established and robust instrument used for peptides or small proteins purification using reverse phase separation. The system includes an autosampler, column heater compartment, UV detector, and fraction collector. Our current system is dedicated to a novel basic reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling based on the methods of Wang T et al. Proteomics. 2011 May;11(10):2019-26.

Services

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 director.

The table below lists the general services we offer.

• Mini SDS-PAGE

• Gel Coomassie staining

• Protein/Peptide Assay

• Protein Precipitation

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

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

• High resolution MS and MS/MS via direct infusion

• Protein digest clean up

• TMT quantification

• SILAC quantification

• Label free quantification – DIA-NN using Bruker Tims TOF Pro2

• HPLC peptide separation

FAQs

How do I submit a sample?

In-house samples can be dropped off in B139 and placed in the small -20C white freezer. Sample drop off should happen only after a sample request form has been made.

For all user, requests for service are now made via iLab. For assistance, please contact Core Staff

External samples should be sent by courier to the following address on ice or on dry ice. Please email the tracking number to the staff when samples are being shipped. Preferably ship during the beginning of the week and do not ship on a Friday.

Proteomics Core
c/o The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology
130 Scripps Way, 1B2
Jupiter, FL 33458

How much protein do I need to submit for protein identification?

Our most sensitive mass spectrometers can detect 20 fmol; for a 50K D protein that corresponds to 1 ng.

How pure does the sample have to be?

For identification of a single protein, the sample should be as pure as possible. Purity may be judged by the presence of a single Silver or Sypro stained gel band on a gel. We have often seen many proteins identified from a darkly stained Coomassie band.

What buffer should my sample be in for MS-only measurements?

For MS-only measurements using infusion of whole proteins or small molecules, the sample should be in ideally water, or a volatile solution that can be removed by evaporation. Solvents such as acetonitrile or methanol are fine too. Salts, detergents, chaotropes, glycerol, DMSO and DMF can interfere with MS analysis. Many clean up procedures are available and can be suggested by a staff member. Salty samples for MS-only will require the use of an LC with a trap and an analytical column. We have C4, C8 and C18 reversed phase separation system in line with MS detection. For optimal results, please discuss your project with a staff member prior to generating the samples.

What buffer should my protein sample be in for MS/MS measurements?

Protein solutions should be in a buffer compatible with digestion. For optimal results, please discuss your project with a staff member prior to generating the samples.

What is the best protein assay to use?

The answer to this question really depends on your expected protein concentration, and most importantly, the buffer the sample is in. Many common buffer ingredients interfere with colorimetric assays. We recommend also using your sample buffer for making the standard curve and as the blank. For a good overview on assays, visit the ThermoFisher Scientific website. Please consult a  staff member to discuss your particular sample.

Data Retention

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 Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology 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 UF Scripps Dropbox Business site at the time of acquisition for long-term storage.

Publications/Citations

It is our policy that key collaborator(s) within The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology community 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 The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Mass Spectrometry and Proteomics Core. Here are the ABRF guidelines for authorship for personnel working in facilities such as the Mass Spectrometry and Proteomics Core of this Institute.

To view publications co-authored by Mass Spectrometry and Proteomics Core staff or those that resulted from the use of Core data, click here. Publications by Proteomics Core Staff: Co-authorship earned by the staff of the UF Scripps Mass Spectrometry and Proteomics Core. » Publications by Proteomics Core Staff » Scripps Biomedical Research » University of Florida (ufl.edu)