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Mass Spectrometry & Proteomics

Mass Spectrometry and Proteomics Core
The Mass Spectrometry and Proteomics Core provides high-quality mass analysis of biomolecules – proteins, glycoproteins, peptides, oligonucleotides, nucleic acids, lipids and small-molecule metabolites – for a variety of biomedical investigations. The facility offers supporting techniques as well as scientific consultation.

Notable capabilities of our facility include:

  • Purified proteins and protein complexes (isolated by affinity chromatography) can be rapidly identified by fully-automated liquid chromatography-tandem mass spectrometry (LC/MS/MS) analyses combined with our protein database search capabilities.
  • Relative protein expression levels can be determined for lysates of whole cells or subcellular organelles as well as paraffin embedded tissue sections.
  • Absolute levels of specific peptide components in complex biological samples can be determined (with appropriate stable isotope-labeled standards) via multidimensional separations and MS analysis.
  • High-resolution mass spectrometry using electrospray ionization (ESI) provides highly accurate determination of small molecule elemental composition.
  • Qualitative and quantitative analysis of small molecules by LCMS/MS including Metabolomic and Lipidomic profiling.
  • High Resolution MS and MSn
  • High-resolution mass spectrometry of small molecules and peptides, and complete sequence confirmation for synthetic peptides, can be carried out under GMP conditions. The site is FDA registered. All GMP work requires Quality and Service Agreements PRIOR to analysis. Please contact the facility manager for information regarding agreements.

Last updated: 10/23/13




  • GXP ESI MSn analysis (nanoelectrospray) for peptide sequence confirmation.*
  • ESI Mass Spectrometry (nanoelectrospray) for determination of monoisotopic mass.
  • ESI MSn analysis (nanoelectrospray) for structure confirmation.
  • LC/MS analysis
  • LC/MS/MS analysis and quantitation of small molecules, metabolites, lipids, peptides, nucleosides.
  • Multidimensional peptide and protein separations by 2D LC and off-gel electrophoresis/LC.
  • In-gel Reduction, Alkylation, and Digestion of Coomassie Blue, Silver, and Fluorescent Dye stained gels
  • Proteomic analysis of paraffin embedded tissue sections
  • Solution Phase Reduction and Alkylation
  • Solution Phase Digestion
  • Sequest, Global Proteome Machine (GPM) and Protein Lynx Global Server Database Searches for Protein Identification
  • Label free quantitation of proteins in samples and expression analysis.

*Please note:  All GMP work requires Quality and Service Agreements PRIOR to analysis.  Please contact the facility manager for more information.


  • One Waters Synapt G2 HDMS high definition mass spectrometer with ion mobility MS equipped with a Waters nanoAcquity 2D UHPLC system for high through-put proteomic, lipidomic and metabolomic analyses.
  • One Thermo Electron LTQ-FT hybrid linear ion trap - Fourier transform ion cyclotron resonance mass spectrometer equipped with an Eksigent 2D nanoflow LC system for high resolution macromolecule characterization.
  • Two Agilent 6520 Q-TOF mass spectrometers equipped with Agilent 1200 nanoflow LC system and for high through-put proteomic analyses.
  • One Agilent 6410 triple quadupole mass spectrometer equipped with an Agilent 1100 nanoflow LC system for LC/MS/MS analyses for accurate quantification. This system will be replaced in the near future with an Agilent 6490 triple quadrupole mass spectrometer with iFunnel technology equipped with a 1290 UHPLC system.
  • One Thermo Electron LCQ Deca ion-trap mass spectrometer modified for vacuum MALDI operation.
  • Sequest® and X!Tandem database search systems for Protein identification running on a 15 node computer cluster and a standalone versions of ProteinLynx Global Server.
  • Agilent 3100 OFFGEL Fractionator for protein fractionation with in-solution recovery. Uses a novel isoelectric focusing technique to achieve excellent pI-based fractionation.
  • GelFree 8100 Fractionation System for mass spectrometry sample preparation partitions complex protein mixtures into user-selectable liquid-phase molecular weight fractions. Intact protein molecular weight fractionation, isolation, and purification with liquid-phase recovery without band or spot cutting.

Using The Facility

The Mass Spectrometry and Proteomics Core is available on both a shared use (for internal users only) and full service basis. Investigators should contact the manager, Gabriel Gugiu at 626-256-HOPE (4673) ext. 63905 to discuss the experimental strategy for any sample analysis prior to sample submission.

Shared Use:
The facility is available to City of Hope and Beckman Research Institute users on a shared use basis. Investigators wishing to use the facility on a shared use or collaborative basis should contact Gabriel Gugiu for more information.

How to Prepare Samples:
Please see the guidelines for preparing samples in order to obtain a successful analysis. Direct any concerns to the Mass Spectrometry and Proteomics manager, Gabriel Gugiu at 626-256-HOPE (4673) x63905 prior to sample submission.

Supplies Needed:
With few exceptions (quantitation or method development standards), it is not necessary for the investigator to provide supplies for analyses and projects carried out by the Mass Spectrometry and Proteomics Core. The cost of these components is built into the fee schedule.

Turn-around Time:
The turn-around time for the mass analysis of a single sample is one to two days for nano-electrospray MS on a simple mixture and 3-4 days for more complex samples. For samples submitted for LC/MS/MS analysis with database search and/or quantitation, typical turn-around time is about two weeks (backlog dependent). For samples that require method development, investigators will be apprised of the anticipated time required to obtain results of the requested analyses on a per sample basis when experimental details are discussed with the facility manager.
All users who wish to analyze their own samples must be trained by a member of the MS facility prior to their intended use of the instrument. Please contact us to schedule a training session.
Rules for instrument use:
Users must be trained in the specific technique and instrument they wish to use. Any other use must be discussed with the manager. Any fault observed with the instruments must be communicated to the facility personnel to promptly address the problem.
Signup for instrument time

All instruments sign-up is handled through the online calendars in Microsoft Outlook which can be located in “Public Folder\All Public Folders\Mass Spectrometry core\” or through the direct links provided on this website. Note that the website links only work from Internet explorer. Please respect the signup rules below.
  • Instrument maintenance and repair takes precedence over other uses. Please discuss any concerns with us. We will attempt to accommodate you as best as we can.
  • The LTQ-FT is used for accurate mass determination for small molecule nano-electrospray peptide mass and sequence determinations and is available everyday with some exceptions noted below.
  • Thursdays after 4 PM are reserved for the LTQ-FT maintenance and calibration. No one may sign up on the LTQ-FT for more than 2 hours on Thursdays. Mondays are reserved for Synapt G2 HDMS and Agilent QQQ maintenance and calibration and Thursdays for Agilent Q-TOF maintenance and calibration.
  • LC/MS/MS time may be signed up for in 1-3-day blocks. If you need less time than that, sign up only for the number of days you need so that others can use the instrument. Exceptionally, more time can be reserved if the project requires it and if available, upon approval of the MS facility personnel.
  • For quantitation projects on any instrument it is allowed to reserve one-week block time (the time between two consecutive maintenance days).
  • No one may sign up for more than one week in any calendar month on a single instrument. For scheduling purposes, the first day of the time block determines its month.
  • No one group/laboratory may sign up for more than 6 consecutive days on one instrument in one month.
  • Please do not sign up more than 4 weeks ahead of time unless you have our permission because you need to coordinate with a collaborator who is visiting from off campus, or have lost your scheduled time due to unscheduled maintenance or repair work.
  • If any time blocks are not signed up a week in advance they can be used by anybody even if they are in violation of the above rules.

Sample submission guidelines and form

General Guidelines for All Samples:
  1. First-time users should discuss their project and the sample submission process with the manager or assistant manager before preparing their samples. We can help you design an experiment that will best take advantage of the mass spectrometers’ capabilities, but only if we can make suggestions early in the experimental process.
  2. All users should contact us before sending or bringing samples, both to check our sample backlog and to ensure that someone will be there to receive them.
  3. All samples require a guarantee of payment. On-campus users may supply a City of Hope account number. Off-campus users without an established record of timely payment must provide a purchase order or credit card number.
  4. All submitted samples must be accompanied by a filled sample submission form.  Click here to download the submission form.
Specific Guidelines for Gel Bands:
What to provide:
Each gel band that you submit should be cut out using a disposable cutting tool, placed in a clean micro-centrifuge tube, and legibly labeled with a unique name. If you give your samples descriptive names like “band 1” or “44 kDa”, please add some additional information, such as an experiment name or notebook page number, to distinguish it from similarly named samples. When submitting a large batch of gel bands, you may place them in the wells of a 96 well microtiter plate, together with a written list of which samples are in which well. In addition to your samples and the sample submission form, please include:
  1. A clearly indicated gel blank for each physical gel. The gel blank should be from a region of the gel that has no protein in it, either from between two lanes or (ideally) from a lane that was loaded only with loading buffer. Regions from any gel lane that had protein loaded in it must not be used as blanks, even if they lack any apparent stain. The gel blank will be analyzed as a control at no additional charge.
  2. A picture of the gel with the positions of each excised gel band indicated.
  3. Any other information you want us to consider when analyzing your sample, such as the organism from which the protein is purified, preparation method, identity and sequence of proteins you expect to find, etc.


Avoiding contamination:
Remember that your gel is being run as a preparative technique for further analysis, not as a final analytical method. The mass spectrometers are as sensitive to contaminant proteins as to target proteins, so you must handle the gel in a way that avoids contamination. Known causes of contamination include:
  1. Contact with hair or skin. Keratin is by far the most common contaminant. Wear gloves and a lab coat whenever you work with a gel. Wear a hair net if you have long hair. Carry out as many procedures as possible in a laminar hood.
  2. Contact with latex gloves. Use nitrile gloves instead.
  3. Use of autoclaved labware. Use plastic labware straight from the manufacturer’s packaging without any additional treatment.
  4. Use of contaminated containers. Never stain a gel in a container that has been used for Western blotting. The best choice is to use disposable plastic containers.
  5. Use of old razor blades or dirty cutting surfaces when excising gel bands. Use a new razor blade, scalpel, or disposable gel cutter and either a disposable plastic surface or a freshly cleaned glass surface to cut on. A razor blade or scalpel should be cleaned between each gel band you cut out.


Specific guidelines for small molecules (metabolites, lipids, phospholipids, etc)
These will vary depending on the chemical nature of your analyte and the purpose of the analysis, and will be determined during your consultation with the manager. An internal standard will be required for quantitation. For absolute quantitation a labeled compound (stable isotope) with identical structure with your analyte must be used. Otherwise, relative quantitation can be accomplished using an internal standard with similar structure as the analyte. You must provide pure samples of all analytes for absolute or relative quantitation. Quantitation of all compounds not previously analyzed in the MS facility requires method development prior to analysis. A discussion with the manager of the facility for scientific and technical assistance it is required for all analyses of this type. Any changes in the project after the method was developed may require additional method development and associated costs. For example: you decide to add additional analytes that may require different chromatographic conditions than the analytes for which the method was initially intended.
Specific guidelines for nanospray analysis of small molecules and peptides
All nanospray samples must be pre-purified and free of buffers (such as phosphate). A negative control (blank) may also be required. Please contact the facility for sample specific information.
Specific guidelines for oligonucleotides
All oligonucleotide samples submitted must be HPLC purified and desalted using a cation exchange resin. Contact the facility for more information. Alternatively a large batch of samples can be accepted undesalted. The batch must consist of at least 20 samples. These would be analyzed by LC-nanoESi with online desalting on a PRP column using 2-10mM TEA.
Bringing or Sending Samples
If you work at or near City of Hope, feel free to bring your samples in person. Doing so will guarantee the best possible handling. Please remember to contact us before bringing the samples so we can ensure that someone is there to receive them.
If you are not able to bring your samples in person, you should send them using an overnight delivery service such as Fed Ex, UPS, etc. Please package your samples with freeze packs or dry ice to keep them cold, and be sure to label the packages “freeze on arrival” so that our receiving department keeps them cold after delivery. Avoid sending samples on Thursday or Friday to minimize the chance that the samples will remain undelivered and at room temperature over a weekend. Please email us the sample information, including tracking numbers, once you have sent it.

Recent Projects

The following recent publications illustrate the technical capabilities of the laboratory and a variety of collaborative projects.

Sharad S Singhal, James Figarola, Jyotsana Singhal, Kathryn Leake, Lokesh Nagaprashantha, Christopher Lincoln, B Gabriel Gugiu, David Horne, Richard Jove, Sanjay Awasthi, Samuel Rahbar, 1,3-Bis(3,5-dichlorophenyl) urea compound 'COH-SR4' inhibits proliferation and activates apoptosis in melanoma. Biochemical Pharmacology (2012) vol. 84 (11) pp. 1419-27.

Ashley M Crane, Hong-Uyen Hua, Andrew D Coggin, Bogdan G Gugiu, Byron L Lam, Sanjoy K Bhattacharya, Mass spectrometric analyses of phosphatidylcholines in alkali exposed corneal tissue. Invest Ophthalmol Vis Sci (2012) vol53, pp. 7122-7130.

Jiehui Deng, Yong Liu, Heehyoung Lee, Andreas Herrmann, Wang Zhang, Chunyan Zhang, Shudan Shen, Saul J Priceman, Maciej Kujawski, Sumanta K Pal, Andrew Raubitschek, Dave S B Hoon, Stephen Forman, Robert A Figlin, Jie Liu, Richard Jove, Hua Yu, S1PR1-STAT3 signaling is crucial for myeloid cell colonization at future metastatic sites. Cancer Cell (2012) vol. 21 (5) pp. 642-54.


Khue Truong, Terry D. Lee and Yuan Chen, Small Ubiquitin-like Modifier (SUMO) Modification of E1 Cys Domain Inhibits E1 Cys Domain Enzymatic Activity. Journal of Biological Chemistry (2012) vol. 287 (19) pp. 15154-15163.


Carissa M Thomas, Teresa Hong, Jan Peter van Pijkeren, Peera Hemarajata, Dan V Trinh, Weidong Hu, Robert A Britton, Markus Kalkum, James Versalovic, Histamine derived from probiotic Lactobacillus reuteri suppresses TNF via modulation of PKA and ERK signaling. PLoS ONE (2012) vol. 7 (2) pp. e31951.


Lei Zhang, George S Katselis, Roger E Moore, Kossi Lekpor, Ronald M Goto, Terry D Lee, Marcia M Miller, Proteomic Analysis of Surface and Endosomal Membrane Proteins from the Avian LMH Epithelial Cell Line. J Proteome Res (2011) vol. 10 (9) pp. 3973-82.


Zhanhong Wu, Ivan Todorov, Lin Li, James R Bading, Zibo Li, Indu Nair, Kohei Ishiyama, David Colcher, Peter E Conti, Scott E Fraser, John E Shively, Fouad Kandeel, In vivo imaging of transplanted islets with 64Cu-DO3A-VS-Cys40-Exendin-4 by targeting GLP-1 receptor. Bioconjug Chem (2011) vol. 22 (8) pp. 1587-94.


Diana Diaz-Arevalo, Karine Bagramyan, Teresa B Hong, James I Ito, Markus Kalkum, CD4+ T cells mediate the protective effect of the recombinant Asp f3-based anti-aspergillosis vaccine. Infect Immun (2011) vol. 79 (6) pp. 2257-66.


Kenneth J Dery, Shikha Gaur, Marieta Gencheva, Yun Yen, John E Shively, Rajesh K Gaur, Mechanistic control of carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) splice isoforms by the heterogeneous nuclear ribonuclear proteins hnRNP L, hnRNP A1, and hnRNP M. J Biol Chem (2011) vol. 286 (18) pp. 16039-51.


Lin Li, Desiree Crow, Fabio Turatti, James R Bading, Anne-Line Anderson, Erasmus Poku, Paul J Yazaki, Jenny Carmichael, David Leong, Michael P Wheatcroft, Andrew A Raubitschek, Peter J Hudson, David Colcher, John E Shively, Site-specific conjugation of monodispersed DOTA-PEGn to a thiolated diabody reveals the effect of increasing peg size on kidney clearance and tumor uptake with improved 64-copper PET imaging. Bioconjug Chem (2011) vol. 22 (4) pp. 709-16.


Daniel Tamae, Punnajit Lim, Gerald E Wuenschell, John Termini, Mutagenesis and Repair Induced by the DNA Advanced Glycation End Product N(2)-1-(Carboxyethyl)-2'-deoxyguanosine in Human Cells. Biochemistry (2011) vol.50 (12) pp. 2321-2329.


Li Zheng, Jia Jia, L David Finger, Zhigang Guo, Cindy Zer, Binghui Shen, Functional regulation of FEN1 nuclease and its link to cancer. Nucleic Acids Res (2011) vol. 39 (3) pp. 781-94.


Serina Ortiz, Wenhui Lee, David Smith, Stephen J Forman, Terry D Lee, Chih-Pin Liu, Comparative analyses of differentially induced T-cell receptor-mediated phosphorylation pathways in T lymphoma cells. Exp Biol Med (Maywood) (2010) vol. 235 (12) pp. 1450-63.



Abstract for Grants

The Mass Spectrometry and Proteomics Core facility has the following major equipment available:
The shared mass spectrometry facility includes one Thermo Finnigan LTQ-FT linear ion trap/ion cyclotron resonance mass spectrometer, two Agilent 6520 electrospray Quadrupole Time of Flight mass spectrometers for high throughput proteomic analyses and an Agilent 6410 Triple Quadrupole mass spectrometer for accurate quantitation, to be replaced in the near future with an Agilent 6490 Triple Quadrupole with iFunnel technology and UHPLC. The core has recently added a Waters Synapt G2 HDMS high definition mass spectrometer with ion mobility MS and nanoacquity UHPLC for high through-put proteomic, lipidomic and metabolomic analyses. Available to the core facility are a Thermo Finnigan LCQ-Deca mass spectrometer equipped with a vacuum MALDI source and a Thermo Finnigan LCQ classic equipped with a nanoelectrospray source. In summary, the Mass Spectrometry and Proteomics Core can now provide protein identification by top-down and bottom-up (utilizes enzymatic digestion to reduce whole proteins into peptides) methods. Additionally, oligonucleotide, oligosaccharide, and intact glycoprotein characterization can be carried out using either nanospray or LCMS using the LTQ-FT. Relative quantitation of proteins in mixtures and cross sample comparison can be achieved easily on the Waters Synapt G2 HDMS. Qualitative and quantitative analysis of small molecules can be carried out, including metabolites, lipids, peptides, and nucleosides. Protein identifications from MS data is accomplished using Sequest or X!Tandem search engines running on a 15-node computer cluster, or with standalone Spectrum Mill or Protein Lynx Global Server. Metabolomics data is analyzed with XCMS or MarkerLynx and Mass Profiler Pro is to be acquired shortly. All data is backed up on two duplicate hard drives over the network in addition to the automatic 7x24 campus network backup routine to prevent any data loss.

Resources & Links

  • American Society for Mass Spectrometry (ASMS)

  • Association of Biomolecular Resource Facilities (ABRF)
  • FASEB-Federation of American Societies for Experimental Biology  - The largest coalition of life sciences societies in the United States, and represents over 42,000 biomedical and biological scientists.

  • National Center for Biotechnology Information (NCBI) - The NCBI is responsible for building, maintaining, and distributing GenBank, the NIH genetic sequence database that collects all known DNA sequences from scientists worldwide. The NCBI is a division of the National Library ofMedicine (NLM) and is located on the campus of the National Institutes of Health (NIH) in Bethesda, Maryland.

  • National Science Foundation World Wide Web Server - All NSF program announcements, publications, and program deadlines are available here. An NSF award database is also available.

  • Protein Data Bank (PDB) -  An archival computer database of three-dimensional structures of biological macromolecules. The database contains atomic coordinates, bibliographic citations, primary sequence and secondary structure information, as well as crystallographic structure factors and 2D-NMR experimental data. Information is available on protein, DNA, RNA, virus and carbohydrate structures.

  • The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
  • ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions.
  • Proteome Software – Download Scaffold
  • XCMS Online is a cloud-based metabolomic data processing platform that provides high-quality metabolomic analysis in a user-friendly, web-based format.
  • The LIPID MAPS infrastructure is a unique resource for the biomedical community. In addition to providing the largest database of lipid molecular structures, the lipid maps resource contains information on the lipid proteome, quantitative estimates of lipids in the human plasma, the first complete map of the macrophage lipidome, and a host of tools for lipid biology including mass spectrometry tools, structure tools and pathway tools.
  • The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education.
  • The software package OMA & OPA was created to support the interpretation of oligonucleotide mass spectra. It can rapidly calculate all theoretically possible fragment ions for a given input sequence and annotate them to an experimental spectrum, thus, saving a large amount of manual processing time.
  • Ariadne - a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data


Prices and availability vary. Please Contact Us for current information.

If you are a City of Hope employee, please click here for pricing.



Contact Us

Email us for more information about Mass Spectrometry or to schedule an appointment for services or equipment. Please see the Fee Schedule for pricing for various analyses or shared instrument usage. A completed submission form must accompany all samples submitted for analysis.

City of Hope and Beckman Research Institute
1500 East Duarte Road
Hilton Building
Room H134
Duarte, CA  91010-3000

Phone:  626-256-HOPE (4673), Ext. 62601
Fax:  626-301-8186
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City of Hope embodies the spirit of scientific collaboration by sharing services and core facilities with colleagues here and around the world.

Recognized nationwide for its innovative biomedical research, City of Hope's Beckman Research Institute is home to some of the most tenacious and creative minds in science.
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