Mass Spectrometry & Proteomics

This core provides expert mass spectrometry services and consultation for the University of Utah and Huntsman Cancer Institute (HCI) research communities, and operates as a fee-for-service resource. Off-campus samples from academic institutions or private companies are accepted, as well. While the primary emphasis of the core is geared toward supporting proteomics research, the facility continues to provide basic MS support for a broad range of research and sample types, such as polymers, natural products, small synthetic molecules, and large intact proteins and nucleic acids. Our mission is to provide the highest quality mass spectrometry analyses for protein and other biomolecule investigations.

The facility is equipped with several high-performace mass spectrometers, including a state-of-the-art FTMS instrument (LTQ-FT; ThermoElectron), with nano-LC and nano-ESI ionization.  Especially well-suited for proteomics applications, the FTMS instrument provides high sensitivity (sub-femtomole), high resolution (>500,000), and high mass accuracy (<2ppm), affording greater sequence information and high-confidence protein identifications.  The FTMS is well equipped for mapping protein modifications, with CID, IRMPD, and ECD fragmentation techniques available.  LC/MS/MS instruments in the lab are equipped with nano-LC, for ultimate sensitivity and chromatographic performance.  Our new Maldi/ToF/ToF mass spectrometer provides high sensitivity and resolution and MS/MS capability, as well as state-of-the-art tissue-imaging by mass spectrometry.

A range of proteomics services are available, for example:

  • protein ID from in-gel or solution, using LC/MS/MS, FTMS, or Maldi/ToF
  • protein ID from complex cell isolatespost-translational modifications (PTMs such as phosphorylation, GIcNAc, acetylation)
  • in-house Mascot database searching (public or custom DBs)ESI/MS for intact protein MW and identification of truncation sites
  • Tissue-Imaging, showing high resolution location and relative concentration of specific molecules within tissue sections

* This is a designated Huntsman Cancer Institute CCSG Shared Resource

To make a reservation to use our equipment or services, please go to resource.cores.utah.edu.

Proteomics mass spectrometry analysis was performed at the Mass Spectrometry and Proteomics Core Facility at the University of Utah. Mass spectrometry equipment was obtained through NCRR Shared Instrumentation Grant # 1 S10 RR020883-01 and 1 S10 RR025532-01A1

The University of Utah Mass Spectrometry and Proteomics Core Facility provides mass spectrometry services and consultation for the University of Utah and Huntsman Cancer Institute (HCI) research communities, and operates on a fee-for-service basis.

The primary focus of the Facility is support of proteomics research at the University of Utah. However, the Facility also continues to provide general mass spectrometry services for the University community, as well as biotech companies in the regional area and other academic institutions. A broad range of research applications and sample types are accepted for analysis (e.g. proteins, natural products, synthetic peptides, small molecules, polymers, PCR products, nucleic acids, and other biomolecules).

The Facility is equipped with several high-performance mass spectrometers and accessory HPLC equipment. These instruments are operated by the MS Core Facility personnel only, with the exception of the Voyager DE-STR Maldi/ToF instrument, which can be operated by trained users. Users are welcome to utilize workstation computers to review their spectra and results (in addition to the hardcopy or electronic results sent to them). If you have any questions about any of our services, we suggest that you please find your question in our FAQs tab before contacting us.

Proteomics Proficiency Testing

The Mass Spectrometry and Proteomics Facility participates occassionally in an international proteomics proficiency evaluation conducted by the Association of Biomolecular Resource Facilities (ABRF).  The results of these studies compare the competency of our proteomics facility with other leading proteomics laboratories nationwide for the structural analysis of proteins and peptides. The standings of those results will be posted on this site as they are available.

Proteomics Services

Refer to the Sample Submission tab and Guidelines & Protocols page for recommendations and information prior to preparing and submitting protein gel bands or protein samples for analysis.

Proteomics Service Itemized Fees
Protein ID from SDS Gel
Identification of proteins from 1D gel bands or 2D gelspots
$165 per excised gel band or gel spot
$15 for samples requiring ZiptipTM purification
Protein ID from Solution
Identification of proteins from affinity purifications, HPLC, or other purified protein solution
$165 per sample
$15 for samples requiring Ziptip purification**Added costs apply for digests with certain enzymes (e.g. Asp-N)
* Added costs apply for digests requiring denaturants, such as ProteaseMaxTM
Protein ID from Complex Isolates in Solution and IP Pull-down Experiments
Identification of proteins from affinity purifications, cell extracts, tissues, and other complex mixtures in solution
$55 per digest*
$55 for SCX fractionation
$110 per LC/MS/MS run for each SCX fraction
$15 for samples requiring Ziptip purification
* Added costs apply for digests with certain enzymes (e.g. Asp-N)
* Added costs apply for digests requiring denaturants, such as ProteaseMaxTM
Identification of Protein Modifications Target Peptides or Amino Acids $55 per digest*
$110 per LC/MS/MS run
$20 setup charge for special exclusion and/or inclusion lists for targeted peptides
$15 for samples requiring ZiptipTM purification
$55 for IMAC purification of phosphopeptides
* Added costs apply for digests with certain enzymes (e.g. Asp-N)
Intact Protein MW Analysis $45 per sample with deconvolution
$15 for samples requiring ZiptipTM purification
$20 for sequence elucidation; searches to assign observed truncation, cut sites, or protein degradation products
Peptide Sequencing with MS/MS (FTMS) and accurate mass denovo sequencing and Sequence-Tag Searches $50 per sample or peptide
$20 for each additional peptide analyzed in the same sample
$20 for each denovo sequence prediction using MascotTM or PEAKSTM software
Inquire for sequence-tag searches PEAKSTM software
Disulfide Linkage Characterization
Determine protein disulfide linkages
Inquire
Identification of Sulfur-containing peptides
i.e. cysteine or methionine
“Top-Down” Proteomics
FTMS with ECD fragmentation an sequencing intact proteins and peptides
Protein Expression/Quantitation Analysis
Custom Database Searching
Service Itemized Fees
Create a custom MascotTM database
For specific protein sequences not in the MSDB or NCBI databases
$22 per protein sequence created for the custom database
Create a custom modification for MascotTM searches
For searching custom or non-standard modifications or derivatives
$22 per custom modification created for searches
Special request/additional modification searches with MascotTM or additional database searches $22 per search
Sequence-Tag Searches Inquire for cost
FTMS Services
Service Itemized Fees
Accurate Mass Measurement – External Calibration
(Positive-ion)
$50 per sample
$20 for generating elemental composition list
Accurate mass measurement – internal calibration(Positive-ion) $80.00 per sample
$20.00 for generating elemental composition list
Accurate mass measurement – (Negative-ion) Inquire
Peptide Sequencing with MS/MS and accurate mass Denovo Sequencing

$50.00 per sample or peptide$20.00 for each additional peptide analyzed by MS/MS in the same sample

$20.00 for each denovo sequence prediction using MascotTM or PEAKSTM software

LC/MS and LC/MS/MS on the FTMS instrument $110.00 per LC/MS run
$15.00 per sample for ZiptipTM purification as requiredDiscount rates apply for high number of samples. Depending on gradient or isocratic LC run, price may be lower or higher (e.g. for long LC gradients)
“Top-Down” Proteomics Inquire
Identification of Sulfur-containing peptides
Intact Protein MW Analysis $55.00 per sample
$15.00 for samples requiring ZiptipTM purification
$20.00 for sequence elucidation; searches to assign observed truncation, cut sites, or protein degradation products
Other Special Requests for FTMS Investigations Inquire
General MS Services
Service Itemized Fees
ESI/MS $40.00 per sample or acquisition
$15.00 per sample for ZiptipTM purification as required
ESI/MS/MS
(Electrospray Ionization/ Mass Spectrometry/ Mass Spectrometry)
$50 per sample
$20 for each additional parent ion analyzed by MS/MS in the same sample
$15 per sample for ZiptipTM purification as required
Ion-trap, Triple quad, or Q-ToF instruments
For structure elucidation, confirmation of structure, and determining fragmentation pathways
Nucleic Acids
DNA oligomers, RNA oligomers, PCR products, other nucleic acids
$40 per sample or acquisition
$35 per sample requiring precipitation purification prior to analysis
LC/MS and LC/MS/MS
(Liquid Chromatography/ Mass Spectrometry)
$110 per LC/MS run
$15 per sample for ZiptipTM purification as required
Discount rates apply for high number of samples and depending on gradient or isocratic LC runs
MALDI/ ToF (UltrafleXtreme)
(Matrix-assisted Laser Desorption Ionization/ Time of Flight)
$25 per sample or acquisition
$45 per accurate-mass measurement (i.e. high-resolution measurement with internal standard)
$15 per sample for ZiptipTM purification as required
$8 per sample or acquisition if the user provides the samples pre-spotted on their own plate
$50 Denovo peptide sequencing with LID fragmentation
MALDI/ToF (Voyager DE-STR)
User Hands-on training and use available
Sign up or call to schedule time on the instrument or schedule training
Users must provide their own Maldi target plates
$50 per hour of instrument time
$25 minimum (less than 30 min use)
Tissue-Imaging MS Services
Service Itemized Cost
Cryostat Tissue Sectioning and Maldi Plate Setup
Tissue sectioning and placement on target plate by Core personnel
$30 per experiment or slide
Includes special glass slide
Tissue Section Preparation and Setup
Tissue slice washes, matrix application, and data acquisition setup
$30 per experiment or slide
Maldi/ToF Imaging of Tissue Sections
Positive-ion Maldi or negative-ion Maldi
$60 per hour of instrument analysis time
Software Data Processing and Image Generation
Generate images from data acquisitions by Core Personnel.
Bruker FlexImaging software is used
$30 per hour
Software Data Processing and Image Generation – by User
Generate images from data acquisitions by User
No Charge – Users are welcome to use the available Bruker tissue-imaging workstation and software to process their data files

The MS and Proteomics Core Facility is equipped with several high-performance mass spectrometers, including a state-of-the-art FTMS (LTQ-FT, ThermoElectron) and a new Maldi/ToF/ToF (UltrafleXtreme, Bruker Daltonics). These instruments are operated by the MS Core Facility personnel only. Users are welcome to utilize workstation computers to review their data, in addition to hardcopies of their data.
instrumentation
Users can sign up for training and hands-on use of the Voyager DE-STR Maldi/ToF mass spectrometer to run their own samples (users must have their own Maldi target plates).

LTQ-FT (ThermoElectron)

The LTQ-FT instrument is a linear ion-trap/FTMS hybrid mass spectrometer. Recently installed at the MS Core Facility in Feb 2006, it is an extremely powerful instrument that is one of the highest-performance mass spectrometers in the world for proteomics research.

The combination of very fast MS/MS scanning in the linear ion-trap, high resolution and high mass accuracy measurements in the FTMS, and very high sensitivity, make this instrument ideal for analysis of complex protein digests for protein ID and characterization of post-translational modifications. This instrument provides ultimate sensitivity and confidence in protein ID, in which proteins can be identified from a Mascot database search with as few as one or two peptides identified from attomole-level of digest injected on column.

For applications of the instrument, see available Services.

Performance and Capabilities

  • Nano-LC/MS/MS —
    • splitless gradients as low as 20 nl/min; 75um ID C18 column; typical run at 400nL/min; peak widths 3sec wide at half height
    • AP Maldi/MS/MS (femtomole sensitivity for peptides; < 4000 MW limitation due to linear ion-trap)
  • > 500,000 resolution at m/z 400
  • < 2ppm mass error with FTMS (external standard calibration)
  • < 1ppm mass error with FTMS (internal standard calibration)
  • Attomole-range sensitivity for protein ID (e.g. 500 attomoles BSA digest injected on column yields 10 peptides identified with less than 2 ppm mass error) (e.g. 200 attomoles BSA digest injected on column yields 8 peptides identified with less than 2ppm mass error)
  • MS/MS fragmentation techniques for peptide sequencing and structure elucidation:

Electron-capture dissociation (ECD) in the FTMS

Infrared multiphoton dissociation (IRMPD) in the FTMS

Collision-induced dissociation (CID) in the linear ion-trap

  • ECD for identification of labile protein modifications (e.g. phosphorylation, GlcNAc)
  • ECD for “Top-down” analysis of intact proteins (generally < 30k Da MW)
  • Very fast MS/MS scanning for complex protein digests (e.g. “mudpit”)
  • Resolution of 13C and 34S isotopes in peptides

Demonstrate if unknown peptides contain cysteine or methionine (peptides <1000 MW)

  • Accurate MW measurement of intact proteins and other biomolecules

(e.g. <0.2 Da mass error for small proteins isotope-resolved; <3 Da for large proteins)

  • Accurate mass measurements for structure elucidation (<1ppm with internal std.)

How the LTQ-FT is Equipped

  • Nanospray, static nanospray, or microspray ESI
  • AP Maldi; Nd:YAG laser (MassTech)
  • NanoLC 2D system (Eksigent Technologies) – splitless gradients as low as 20 nl/min; 75um ID C18 column; protein digests typically analyzed at a flow rate of 400nl/min
  • MS/MS fragmentation techniques for peptide sequencing:

Electron-capture dissociation (ECD) in the FTMS

Infrared multiphoton dissociation (IRMPD) in the FTMS

Collision-induced dissociation (CID) in the linear ion-trap

  • Software for the LTQ-FT from ThermoElectron:

Excalibur 1.4 SRI, Bioworks 3.2, ProMass 2.5, Salsa, Xtract , Sequest.

UltrafleXtreme (Bruker Daltonics)

In early 2011, a new Maldi/ToF/ToF mass spectrometer (UltrafleXtreme, Bruker Daltonics) was installed at the MS and Proteomics Core. The instrument has MS and MS/MS capability with high resolution and high mass accuracy. The instrument has laser-induced dissociation (LID) fragmentation for denovo peptide sequencing, top-down protein sequencing, and other applications, as well as high-energy CID fragmentation. This instrument is equipped with state-of-the-art tissue-imaging capability. The UltrafleXtreme is a high-performance instrument well suited for a wide range of applications, including polymers, proteins, peptides, carbohydrates, and other biomolecules.

Tissue-Imaging with the UltrafleXtreme

The UltrafleXtreme provides state-of-the-art tissue-imaging capability and software. Tissue-imaging by mass spectrometry is the only imaging technique that provides information about tissue specifically at a molecular level.  Tissue slices can be analyzed directly for a wide range of biomolecules, such as: proteins, peptides, lipids, polymers, and introduced drugs.  Tissue imaging provides a high resolution color 2-D image showing the spatial location and relative concentration of specific target molecules within the tissue.

Tissue imaging by mass spec is a complementary technique to traditional histology methods.  In fact, many researchers are utilizing both techniques in parallel, in which one tissue section is stained and another corresponding section is analyzed directly by mass spectrometry.  Stained areas of interest can then be compared side-by-side with information obtained on a molecular level by mass spectrometry.  Bruker software available at the MS Core permits mapping and overlaying images from both techniques. Users are able to process their scan images and create their own 2D color images at a workstation in the MS Core. Information from tissue imaging can also be utilized in coordination with tissue sampling and proteomics by LC/MS/MS, now done routinely at the MS and Proteomics Core.

For applications of the UltrafleXtreme instrument, see available Services.

UltrafleXtreme Maldi/ToF/ToF – Performance and Capabilities

  • Maldi/MS (positive or negative ion mode; linear or reflectron mode)
  • Maldi/MS/MS (positive or negative; reflector mode)
  • Low-energy LID fragmentation (in source laser fragmentation)
  • High-energy CID fragmentation
  • Parent-ion mass isolation window about 1 to 3 Da, depending on mass
  • SmartLaser; 1000 Hz shot frequency; fast for tissue-imaging acquisitions
  • High resolution (10,000 to 30,000 resolution, depending on mass)
  • Accurate mass measurements less than 5 ppm with internal standard calibration
  • Accurate mass measurements generally less than 20 ppm with external calibration
  • Femtomole-range sensitivity (e.g. peptides)
  • Tissue-imaging capability and FlexImaging software
  • ProteinScape software for proteomics applications
  • Denovo peptide sequencing
  • Top-Down protein sequencing (with LID fragmentation)
LCQ-Deca (ThermoElectron)

The LCQ-Deca is an ion-trap mass spectrometer with electrospray (ESI) ionization and MS/MS or MSnth capabilities. This instrument is primarily dedicated for protein ID, analysis of peptides, and other proteomics work, but is also utilized for LC/MS/MS of small-molecule samples that require LC introduction. It is equipped with a nanoLC system (Eksigent) and is routinely used for protein ID from in-gel digests and protein ID from solution.

For applications of the instrument, see available Services.

LCQ-Deca Performance and Capabilities

  • Nano-LC/MS/MS
  • < 0.5 Da mass error (full scan); <0.05 Da mass error (zoom scan)
  • Femtomole-range sensitivity (e.g. <10 femtomoles BSA digest injected on column)
  • MS/MS with CID fragmentation (peptide sequencing or structure elucidation)

How the LCQ-Deca is Equipped

  • Nanospray or microspray ESI
  • NanoLC 1D system (Eksigent Technologies) –

splitless gradients as low as 20 nl/min; 75um ID C18 column;

protein digests typically analyzed at a flow rate of 400nl/min

  • Collision-induced dissociation (CID) for MS/MS or MSnth
Voyager DE-STR (PerSeptive Biosystems/ ABI)

The DE-STR instrument is a time-of-flight (ToF) reflectron mass spectrometer with Maldi ionization. This instrument is primarily utilized for analysis of peptides, small molecules, polymers, and other general applications. With internal standards, this high-resolution instrument provides accurate mass measurements with less than 10 ppm mass error.

For applications of the instrument, see available Services.

DE-STR Maldi/ToF Performance and Capabilities

  • Maldi/MS (positive or negative ion mode; linear or reflectron mode)
  • Nitrogen UV (337nm) laser
  • High resolution (i.e. 10,000 resolution at m/z 500)
  • Accurate mass measurements less than 10 ppm with internal standard calibration
  • Accurate mass measurements generally less than 50 ppm with external calibration
  • Femtomole-range sensitivity (e.g. peptides)
Quattro-II (Micromass/ Waters)

The Quattro-II is a triple-quadrupole mass spectrometer with electrospray (ESI) ionization and MS/MS capabilities. This instrument is primarily used for analysis of large biomolecules, such as intact proteins, nucleic acids (e.g. RNA, tRNA, DNA oligos, or PCR products) with sample introduction by infusion, but can also be used occasionally for LC/MS or LC/MS/MS of small-molecule samples that require LC introduction.

Intact protein molecules (potentially up to 150k Da or 200 kDa MW) can be accurately measured if the sample is prepared in high purity. Multiply-charged molecular ions are deconvoluted with MaxEntTM software (Micromass) and the resultant neutral Molecular-mass spectrum typically has mass errors less than 0.005% with a quality spectrum (e.g. less than 2 to 3 Da at 50,000 MW).

For applications of the instrument, see available Services.

Quattro-II Performance and Capabilities

  • ESI/MS and ESI/MS/MS (sample introduction by infusion)
  • LC/MS or LC/MS/MS (microbore column at 3 to 10 ul/min flow rate)
  • 0.1 Da mass error (small molecules)
  • Intact protein or nucleic acid analysis (e.g. typical mass error <3 Da at 50,000 MW)
  • Femtomole to picomole-range sensitivity (large intact proteins usually require picomole amounts and must be highly purified)
  • MS/MS with low-energy CID fragmentation for structure elucidation

MS/MS scan functions:
Daughter-ion (product-ion)
Parent-ion (precursor-ion)
Neutral-loss

How the Quattro-II is Equipped

  • Microspray ESI/MS or ESI/MS/MS (infusion of samples)
  • LC/MS or LC/MS/MS (Shimadzu 10AD HPLC system; microbore LC, 1mm C18; 10 uL/min flow rates)
  • MS/MS with collision-induced dissociation (CID)
Q-ToF-II (Micromass/ Waters)

The Q-ToF-II is a quadrupole/Time-of-Flight hybrid mass spectrometer with electrospray (ESI) ionization and MS/MS capabilities. This instrument is primarily used for analysis of small biomolecules, peptides, and synthetic molecules, but can also be utilized for intact proteins or nucleic acids (e.g. RNA, tRNA, DNA oligos, or PCR products). Sample introduction is normally done by infusion with a nanoflow autosampler with microchip nano-ESI (Advion, NanoMate), but can also be utilized with LC/MS or LC/MS/MS for small-molecule samples.

The Q-ToF-II has high resolution and high mass accuracy capability with the ToF analyzer.

Intact protein molecules (potentially up to 150k Da or 200 kDa MW) can be accurately measured if the sample is prepared in high purity. Multiply-charged molecular ions are deconvoluted with MaxEntTM software (Micromass) and the resultant neutral Molecular-mass spectrum typically has mass errors less than 0.005% with a quality spectrum (e.g. less than 2 to 3 Da at 50,000 MW).

For applications of the instrument, see available Services.

Q-ToF-II Performance and Capabilities

  • ESI/MS and ESI/MS/MS (sample introduction by infusion)
  • LC/MS or LC/MS/MS (microbore column at 3 to 10 ul/min flow rate)
  • 0.01 Da to 0.1 Da mass error (small molecules)
  • Intact protein or nucleic acid analysis (e.g. typical mass error <3 Da at 50,000 MW)
  • Femtomole to picomole-range sensitivity (large intact proteins usually require picomole amounts and must be highly purified)
  • MS/MS with low-energy CID fragmentation for structure elucidation
  • MS/MS scan functions:
    Daughter-ion (product-ion)

How the Q-ToF-II is Equipped

  • Microspray ESI/MS or ESI/MS/MS (infusion of samples)
  • Nanospray ESI/MS (infusion of samples with Advion NanoMate system)
  • LC/MS or LC/MS/MS (Shimadzu 10AD HPLC system; microbore LC, 1mm C18; 10 uL/min flow rates)
  • MS/MS with collision-induced dissociation (CID)
Other Equipment and Software
  •  Mascot software and license:
    Mascot protein database searching software and peptide denovo sequencing
    2-processor Mascot license for in-house computer searches
  • PEAKS (BSI) software and license:
    Peptide denovo sequencing and protein database searching software
    PEAKS license for in-house computer searches
    Sequence Tag searches
  • ProteoIQ (NuSep) software and license:
    Protein quantitation software (SILAC, ICAT, ITRAQ, Label-free)
  •  ProteinScape (Bruker Daltonics)
    Bruker Maldi/ToF data processing software
    Protein data processing for other instrument manufacturers
    Tissue-imaging software
    Quantitation and protein processing
    Polymer software
  • Sequest software and license:
    Sequest protein database searching software for in-house searches
    (The Mascot search engine is preferred for accuracy compared to Sequest)
  • ThermoElectron software and licenses on the LTQ-FT:
    Excalibur 1.4 SRI, Bioworks 3.2, ProMass 2.5, Salsa, Xtract , Sequest.
  •  Waters/Micromass software:
    Masslynx, Biolynx, MaxEnt software for analyzing protein data on the Quattro-II
    MaxEntTM deconvolution software processes multiply-charged ESI data into neutral molecular mass spectra
  • Workstation computers for users to review data if desired
  •  Advion NanoMate nanoESI autosampler for nano-ESI infusion or nanoLC
  •  HPLC systems:Two Eksigent 1D nanoLC systems
    One Eksigent 2D-Ultra system (interfaced on Q-ToF-II or LTQ-FT instruments)
    splitless nanoLC, gradients as low as 20 nl/min
    75um ID, 3um C18 packed-tip columns
    typical flow rate 350 nl/min for analysis of protein digests
    peptide peak widths 3 to 4 seconds wide at half-heightTwo HP1100 systems (not equipped with on-line UV detectors)

Two Shimadzu LC-10AD systems
Can be interfaced with Quattro-II mass spectrometer for microspray applications
(i.e. 3 to 10 ul/min flow rates)
Not equipped with an on-line UV detector

Hours of Operation

Monday-Friday 9am-5pm

Location

Mass Spectrometry and Proteomics Core

15 N Medical Drive East, Room A306

University of Utah

Salt Lake City, Utah 84112-5650

Staff

James Cox, Ph.D. , Director
jcox@cores.utah.edu
Phone: 801-587-7779
Fax: 801-585-6362

Krishna Parsawar, Ph.D., Co-Director
krishna@genetics.utah.edu
MS Lab: 801-581-5018