Proteomics and Metabolomics

Proteomics and Metabolomics


The Proteomics and Metabolomics Facility (PMF) at the Center for Biotechnology, Beadle Center offers a range of technical services using mass spectrometry, including identification and relative quantification of proteins and several advanced methods for profiling and quantitation of small molecules. With highly specialized technology capabilities and proficiency and expertise of personnel in the field of mass spectrometry, the facility is well-prepared and positioned to serve as a regional, national, and international resource and to foster collaboration in the fast developing field of proteomics and metabolomics.

Listed below are currently offered proteomics and metabolomics services. Please send an email if you have any questions regarding these services and/or their costs.

Proteomics services include:

  • Protein Identification from Gel Bands
  • Protein Identification from Solution or Bead Samples (from IP, Co‐IP or pull down)
  • Quantitative Proteomic Analysis using Labeling Approaches (TMT or iTRAQ) or Label-Free
  • Identification and Quantification of Post‐Translational Modifications
  • Phosphopeptide Enrichment followed by Identification and Quantification of Phosphorylation Sites (Phosphoproteomics)
  • Targeted Quantification of Peptides using Data Independent Acquisition

Metabolomics services include:

  • Free Amino Acid Analysis (A, I, L, V, F, W, Y, D, N, E, Q, M, C, S, T, R, H, K, G, P, Tau, GABA, Orn, HydroxyPro) - HPLC based
  • Hydrolyzed Amino Acid Analysis (A, I, L, V, F, Y, D, E, MetS, CyA, S, T, R, H, K, G, P) – HPLC based
  • Free Sugars Assay (Fructose, Sucrose, Glucose, Raffinose, Arabinose, Mannose, Xylose, Galactose, Lactose, Pinitol) - HPLC or GC-MS based
  • Plant Hormone Assay (ABA, SA, JA, JA‐Ile, OPDA, IAA, IAA‐Asp, Methyl-IAA, IAA-Ala, IAA-Trp, t‐Zeatin, c‐Zeatin, t‐ZRiboside) - LC-MS/MS based
  • Gibberellin Assay (GA1, GA3, GA4, GA8, GA9, GA12, GA19, GA20, GA53) - LC-MS/MS based
  • Non-Mevalonate Pathway Metabolites Assay (DXP, MEP, CDP-ME, MEcPP, DMAPP, HDMAPP, IPP) - LC-MS/MS based
  • TCA cycle and Glycolysis Metabolites Assay - LC-MS/MS based
  • Pyrimidine Pathway Metabolites Assay - LC-MS/MS based
  • Polyamines Assay (Putrescine, Spermine, Spermidine) - LC-MS/MS based
  • Targeted Quantification of Small Molecules using either HPLC separation, GC-MS or MRM-based assay
  • Untargeted Metabolomics using LC-MS/MS and/or GC-MS

The address to submit samples to can be found in the Sample Submission Form, which needs to be enclosed at submission with the samples and also sent electronically. Scientists must contact us before submitting samples to check for compatibility of sample type and format with our analytical approaches and to confirm the experimental approach and expectations for the services.

Service Fees

Please contact us if you have any questions regarding the services offered and costs.

UNL Users External Academic Users Industry Users
Full Service
HPLC targeted assay $37/sample $75/sample $110/sample
LC-MS/MS targeted assay $48/sample $110/sample $170/sample
GC-MS targeted assay $42/sample $80/sample $130/sample
Protein Identification-Low Complexity $75/sample $125/sample $180/sample
Protein Identification-High Complexity $120/sample $195/sample $270/sample
Quantitative Proteomics using labeling or label-free Contact us for quote
Phosphoenrichment and Phosphoproteomics Contact us for quote
Targeted Metabolomics Contact us for quote
Non-targeted metabolomics Contact us for quote
Instrument Time UPLC $22/hour $55/hour $100/hour
Instrument Time GC-MS $25/hour $55/hour $100/hour
Instrument Time QTRAP/QE-HF $60/hour $110/hour $150/hour
Method Development/Sample Preparation $52/hour $100/hour $150/hour
Training/Data Analysis $52/hour $100/hour $150/hour
Self Service*
Instrument Time UPLC/GC-MS $15/hour $40/hour $60/hour
Instrument Time QTRAP $20/hour $55/hour $75/hour

*Self-service rates only apply to users previously trained and checked off by facility staff.

IMPORTANT Note: Scientists must contact us before submitting samples to check for compatibility of sample type and format with our analytical approaches and to confirm the experimental approach and expectations for the services.

Proteomics Platform

❖ Thermo Q-Exactive – High Field (QE-HF) coupled to Dionex U3000 nanoRSLC

  • Bottom-up proteomics for protein identification, quantification using labeling (TMT- 6 or 10 plex) or label-free approaches; PTMs characterization (phosphorylation, ubiquitination, acetylation, etc.); Intact protein characterization.
  • Targeted quantification of peptides using Parallel Reaction Monitoring (PRM) or Data Independent Acquisition (DIA).
  • High Resolution/Accurate Mass (HR/AM) instrument
  • Resolving power up to 240,000 at 200 m/z
  • Sub ppm mass accuracy
  • Scan speed of 18 Hz at 15,000 resolution
  • Flow rate of the nanopump: 20 nL/min to 1.5 µL/min
  • Pressure to 800 bar (11,600 psi)

❖ Mascot 2.5.1 (Matrix Science Ltd) for protein identification from MS/MS spectra

❖ Proteome Discoverer 2.1 Search Engine (Thermo) for metabolic, isotope labeling and label free quantitative proteomics

❖ Scaffold 4.4.7 (Proteome Software) for protein identification, reporting and label-free quantitative proteomics

❖ PEAKS 7.5 (Bioinformatics Solutions Inc) for de novo sequencing and PTM characterization

Metabolomics Platform

❖ Sciex QTRAP 6500+ mass spectrometer with SelexION+ ion mobility coupled to Shimadzu Nexera II UHPLC

  • Targeted quantification of a wide range of small molecules.
  • Up to 6 orders of detector dynamic range
  • Polarity switching speeds of 5 msec
  • Mass range 50-2000 m/z
  • Scan speeds of up to 20,000 Da/second
  • SelexION+ Differential Ion Mobility Technology for added selectivity
  • UHPLC with extended pressure range up to 19,000 psi for the smallest particle columns
  • Increased chromatographic reproducibility through use of micro-volume plungers
  • Autosampler has multiple rinsing lines enabling low sample carry over
  • High-speed injection

❖ Progenesis QI (Nonlinear Dynamics) for the qualitative and quantitative comparison of small molecules and identification using various databases including: LC-MS NIST, LipidBlast, LipidMaps, HMDB, Metlin, ChemSpider, Metascope etcplus an elemental composition calculator.

❖ Thermo Q-Exactive-HF mass spectrometer coupled to a Thermo Vanquish H UHPLC

  • Non-Targeted metabolomics for profiling and quantification of a wide range of small molecules.
  • UHPLC with extended pressure range up to 22,000 psi for the smallest particle columns
  • Flow and gradient precision
  • 2 x 3 solvent channels
  • 5 °C to 120 °C temperature range
  • Mass range of 50-6000 m/z
  • Dynamic range of >5000:1
  • Polarity switching of one full cycle in < 1sec (one full positive mode scan and one full negative mode scan at a resolution setting of 60,000)
  • Resolution up to 240,000 (FWHM) at m/z 200

❖ Agilent 1290 Infinity II UPLC

  • Separation, profiling and quantification of a wide range of small molecules: PEG, dyes, vitamins, organic acids, carbohydrates, triglycerides, phospholipids, FAME, and more….
  • Peptide and protein fractionation for proteomics applications.
  • Flow rate range: 0.05 to 5 mL/min
  • Pressure 1300 bar (18,800 psi)
  • Multicolumn thermostat and multisampler
  • DAD, ELSD and Fluorescence detector allowing detection of a wide range of compounds (absorbing, fluorescent, non-volatile, and semi-volatile compounds)

❖ Agilent GC-MS 5977A

  • Separation, profiling and quantification of volatile compounds for food regulation, environmental analysis, forensic analysis, drug detection, research.
  • Headspace sampler for analysis of volatile and semi-volatile compounds in solid, liquid and gas samples (without sample extraction)
  • NIST and Fiehn GC-MS compound libraries for identification/confirmation of unknown volatile compounds
  • Integrates with Mass Profiler Professional for qualitative and quantitative studies

Workshops & Training

The facility offers training for the walk-in equipment, including the Infinity II UPLC and QTRAP 6500+. Refer to the usage and sign-up policy documents here for more information.

Workshops and Seminars
Educational workshops and seminars are also organized by the facility throughout the year on a broad range of proteomics and metabolomics topics. See list below of previous educational workshops and seminars.

  • Women in Science, Feb 20-21, 2016
  • “Intro to Biotechnology and Other Research Core Facilities at UNL” Spring Course 2016
  • Mass Spectrometry-based Proteomics workshop, May 9-10, 2016. A total of 87 scientists attended the talks session in the morning of day 1, which included four experts in proteomics from various scientific fields: Michael Washburn (Stowers Institute), Hanno Steen (Harvard Medical School), Mary Lipton (PNNL) and Dmitri Nusinow (Danforth Center). Forty-two scientists, including faculty and undergraduate students registered and attended the two-day hands-on session.
    Meter Nusinow
    Meter Nusinow giving his talk on regulation of the circadian clock in Arabidopsis.
    Students processing data
    Students processing their data during the Workshop.
    Students submitting samples
    Attentive students submitting their samples into the mass spec instrument.
    Happy students preparing samples
    Students looking happy while preparing their samples.
  • Waters seminar : Lunch and Learn, Method Development for (U)HPLC, July 26, 2016
    Larry Meeker explaining his approach to method development for chromatography
    Larry Meeker is explaining his approach to method development for chromatography.
    Waters Seminar Agenda


Dr. Sophie Alvarez, Director
E154 Beadle Center
Email Dr. Alvarez

Dr. Mike Naldrett, Assistant Director
E154 Beadle Center
Phone: 402-472-4575
Email Mike

Contact the Director

Director: Dr. Sophie Alvarez
E154 Beadle Center

Telephone Number:


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