Mass Spectrometry Lab

Our Mission at the Mass Spectrometry Laboratory at Puget Sound Blood Center is to aid researchers in their studies using mass spectrometry and proteomics. With our state-of-the-art facility we are now able to provide analysis, training, and consultation to investigators within the Blood Center and external collaborators. Our service includes:

  • Identification of proteins and peptides
  • Detection of metabolites
  • Characterization of post-translational modifications
  • Protein profiling
  • Relative quantitation of differential protein expression


Thermo-Finnigan LCQ Deca XP Plus mass spectrometer
coupled with Agilent 1100 HPLC System

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Agilent 1100 HPLC system interfaced to a Thermo-finnigan LCQ Deca XP Plus MS detector via an electrospray ionization source. The HPLC system is equipped with a narrow bore reverse phase C18 column for routine analysis of peptides, small proteins and metabolites mixtures. The instrument's scanning range is 200-2000 m/z. Generally we request ~25 pmol of sample for analysis. However, if method development for your sample is necessary, we will need more depending on your project. We prefer to have the sample (peptides or proteins) at a concentration of 1-5 µM.

Thermo-Finnigan LTQ Orbitrap Velos hybrid FT mass spectrometer
coupled with Waters nanoAcquity UPLC System

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Thermo linear ion-trap (LTQ) Orbitrap Velos Mass spectrometer provides ultra-high resolution and accurate mass for confident structural identification as well as molecular weight determination for intact proteins. This instrument is equipped with multiple fragmentation techniques including collision-induced dissociation (CID), Higher-Energy Collisional Dissociation (HCD), and Electron Transfer Dissociation (ETD) for Tandem Mass Spectrometry (MS/MS) analysis. Importantly CID and ETD generate complementary MS/MS spectra for confident identification of both post-translational modifications and peptide sequence. Samples can be introduced directly into the Electrospray ionization (ESI) or nanoESI source or coupled with Waters nanoAcquity ultra performance liquid chromatography (UPLC) system to perform nanoLC-MS/MS analyses for digestion mixture or complex samples. Generally we request 5 pmol of protein of interest or at least 20 μg total proteins of cell lysate or biological samples for analysis. However, if extensive method development is required we may request more.

Data Analysis
We use Thermo Scientific* Proteome Discoverer software with SEQUEST search algorithm to perform proteomic data analysis. The ability to combine results from multiple dissociation techniques (CID, ETD, and HCD) allows for confident identification and robust quantitation of peptides and PTMs from the same analytical run. It also enables isobaric mass tagging (TMT, iTRAQ), and HeavyPeptide techniques for relative or absolute quantification.

Read more about the Mass Spectrometry Laboratory (PDF)

Xiaoyun Fu, PhD
Associate Member
Director of Mass Spectrometry Laboratory

Research Associate
Professor of Medicine
Division of Hematology
University of Washington School of Medicine

Puget Sound Blood Center
Research Institute
1551 Eastlake Avenue E.
Seattle, WA 98102

Phone: (206) 568-2250
Fax: (206) 587-6056

Service Contact
Yi Wang, Ph.D
Phone: (206) 568-2243
Fax: (206) 587-6056