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 goal is to gain a better understanding, on a molecular level, of blood related diseases. Our service includes:

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

Lab Staff

Service Contact

• Yi Wang
  Email: YiW@psbcresearch.org
  Phone: (206) 398-5924

Instrumentation

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 instruments 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 mass spectrometer coupled
with Waters nanoAcquity UPLC System

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Waters nanoAcquity UltraPerformance LC (UPLC) system interfaced to a Thermo linear ion-trap (LTQ) MS via a nanospray ionization source. The nanoAcquity UPLC system performs high-resolution, nanobore based separations. The LTQ can perform all the functions of the LCQ-DECA while providing enhanced sensitivity and mass resolution. The optimal scanning range for this instrument is 200-2000 m/z. Generally we request 5 pmol of sample for analysis, however, if extensive method development is required we may request more. We prefer to have the sample at a concentration of 0.5-1 µM.

Both ion-trap instruments are capable of performing selected ion monitoring (SIM) or selected reaction monitoring (SRM) to increase sensitivity for known analytes in complex samples.

Data Analysis

• X!tandem search
  X! Tandem is a free open source software that can match tandem mass spectra with peptide sequences, it is developed by the GPM.
• Sequest search
  Sequest is a peptide and protein identification tool. It scans protein and DNA databases and compares them to raw mass spectra.
  
• CPAS (Labkey Server)
  CPAS stands for Computational Proteomics Analysis System. CPAS is a scientific data management system that helps researchers make sense of the vast quantities of data produced by mass spectrometers and other high-throughput technologies.