Proteomics & Mass Spectrometry

The Danforth Center’s Proteomics & Mass Spectrometry Facility develops new tools and provides high quality sample analysis in proteomics, mass spectrometry and related analytical fields.

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Instrumentation and Software

Mass Spectrometers
LTQ Orbitrap Velos
6520 QTOF w/ Chip Cube (Proteomics)
6520 QTOF (Metabolomics)
QSTAR XL
4000 QTRAP - 1
4000 QTRAP - 2
GC MS

 1D/2D Gel Equipment
Protean IEF
Criterion
Protean II
Epson Expression SL
Typhoon 9410
Gel Pix
Multiprobe
Software
Same Spots
Mascot
Protein Pilot
Scaffold 3.0
Progenesis LCMS
Mass Profiler Professional

 		Separations (HPLC, CE)
Beckman Coulter HPLC
Acquity UPLC
P/ACE MDQ
Agilent 3100 OFFGEL Fractionator
Miscellaneous
Tissue Lyser II
Biacore



LTQ-Orbitrap Velos from ThermoFisher Scientific online with TriVersa from Advion or nanoLC Ultra from Eksigent    TOP



  • ESI Chip of TriVersa consists of an array of 400 nanoelectrospray emitters with different inner diameters allowing for flow rates of 20 to 300 nL/min.
  • The nozzles on the ESI Chip provide a long, stable spray, and in infusion mode, eliminate sample-to-sample carryover.
  • TriVersa can be used as Chip-based infusion or LC/MS fraction collection
  • TriVersa can be couple to any conventional HPLC system to the TriVersa NanoMate for MS analysis
  • Higher pressure capability of the NanoLC-Ultra platform to allow to use longer columns and/or columns packed with smaller particles for higher resolution separations of complex (digested) protein samples
  • Self-priming and self-purging pumps for easier changing of solvents
  • Temperature-controlled column compartment for maintaining exceptional retention time reproducibility
  • Resolution of 60,000 at m/z 400 at a scan rate of 1Hz
  • Mass accuracy of < 3 ppm with external calibration
  • Equipped with HCD cell for more efficient quantitation of isobaricallylabeled peptides
  • Equipped with Electron Transfer Dissociation (ETD) to generate complementary information for highly sensitive PTM analyses and de novo sequencing
  • Parallel MS and MSn analysis






    • 6520 Q-TOF from Agilent online with 1200 nanoLC-ChipCube from Agilent    TOP



  • High sensitivity & chromatographic performance
  • Improved MS/MS data quality
  • Easy to use, robust, plug-&-play device suitable for unattended routine identification and quantification
  • Automated Chip-system for sample enrichment and separation
  • Fast spectral acquisition
  • Sub-1-ppm MS and 2-ppm MS/MS mass accuracy
  • Up to 40,000 mass resolution






    • Ettan Dalt Unit from Amersham Biosciences    TOP



  • Second dimension gel separation unit
  • Runs 25.5cm x 20 cm gels
  • Six gels simultaneously







    • 6520 Q-TOF from Agilent online with 1200 rapid resolution HPLC from Agilent    TOP



  • Flow rate range from 0.050 to 5 mL/min
  • System delay volumes optimized for fast chromatography
  • Fast spectral acquisition
  • Sub-1-ppm MS and 2-ppm MS/MS mass accuracy
  • Up to 40,000 mass resolution




    • QSTAR XL from Applied Biosystems online with NanoLC-2D system from Eksigent    TOP



  • 2-dimensional HPLC separations
  • Pumping nanoscale HPLC system
  • Eksigent's Microfluidic Flow Control (MFC) technology
  • Nanospray source.
  • Positive and Negative ion mode.
  • CID cell (Collision induced dissociation).




    • 4000 QTRAP from Applied Biosystems online with HPLC from Shimadzu    TOP



  • CTC PAL autosampler from Leap Technologies
  • UV detector
  • Chromatography temperature control
  • Enables high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans.
  • Perform multiple reaction monitoring (MRM) for quantitation using high-sensitivity triple quadrupole.
  • Identify, characterize, and quantitate metabolites more quickly and easily.




    • 4000 QTRAP from Applied Biosystems online with Shimadzu XR UFLC    TOP



  • Flow rate range from 0.001 to 5 mL/min; Pressure up to 9500 psi
  • System delay volumes optimized for fast chromatography
  • Enables high-sensitivity full-scan MS, MS/MS, and MS3 with high-selectivity from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans.
  • Perform multiple reaction monitoring (MRM) for quantitation using high-sensitivity triple quadrupole.
  • Identify, characterize, and quantitate metabolites more quickly and easily.




    • 5975C GC-MS from Agilent    TOP



  • Inert ion source—now programmable up to 350˚C
  • Triple-Axis HED-EM Detector




    • Protean IEF Cell from BioRad and IPGphor from Amersham    TOP



  • First dimension isoelectric focusing unit
  • Take different immobilized pH gradient (IPG) strips




    • Criterion/Criterion Dodeca Cell from BioRad    TOP



  • Second dimension gel separation unit
  • Runs 13.3 cm x 8.7 cm gels
  • Twelve gels simultaneously (Dodeca Cell)




    • PROTEAN II XL Cell from BioRad    TOP



  • Second dimension gel separation unit
  • Accomodates up to 2 gels
  • Use with 17 cm IPG strips




    • Epson Expression Scanner    TOP



  • AutoFocus optics
  • 1,600 x 3,200 dpi
  • 42-bit colour and 16-bit grey
  • 12.2 x 17.2 inch scan area




    • Typhoon 9410 imager from Amersham Biosciences    TOP



  • High sensitivity and resolution
  • 5-orders of magnitude dynamic range
  • Various imaging modes:
    *PhosphorImaging
    *Blue excited fluorescence (457 nm and 488 nm)
    *Green excited fluorescence 532 nm
    *Red excite fluorescence 633 nm
    *Chemiluminescence




    • GelPix spot cutting robot from Genetix    TOP



  • 8-channel excision head, 10 spots per minute
  • Captures both visible and fluorescent images
  • Cooled CCD camera, 16-bit Tif format
  • 15 x 96 well plates, walkway automation




    • MultiProbe II protein digester from PerkinElmer    TOP



  • 4 pin head
  • Automated protein in-gel or in-solution digestion
  • 2x 96 well plate
  • Zip tipping and spotting




    • Progenesis SameSpots from NonLinear Dynamics    TOP



  • Analyze single stain and 2D DIGE experiments.
  • Optimize analysis using initial automatic image quality assessment and feedback
  • Highly advanced and automated image alignment.
  • Automatic analysis of the aligned image set and correction of dye related offsets in DIGE
  • Automatically create a ranked list of significant spots based on ANOVA p-value, fold-change and q-values for any groups you compare
  • Confirm hits using 2D and 3D montage views, expression profiles and spot data tables




    • MASCOT Search Engine v. 2.2 from Matrix Science    TOP



  • A powerful database search engine
  • Integrates all the proven methods of database searching
  • Peptide Fingerprint, Sequence Query and MS/MS Ion Search
  • Total flexibility in chemical/post-translational modifications




    • Protein Pilot 2.0 from Applied Biosystems    TOP



  • Protein identification and relative protein expression analysis for discovery research
  • Optimized support for iTRAQ reagent workflows.
  • Enable to search for hundreds of peptide modifications and non-tryptic cleavages simultaneously




    • Scaffold 3.0 from Proteome Software    TOP



  • MS/MS analysis & visualization software
  • See proteins identified across multiple samples.
  • Combine Sequest and Mascot scores for increased confidence.
  • Get more detailed and accurate information from your MS/MS experiments




    • Progenesis LCMS    TOP



  • Advanced proteomics research solution for label-free quantitative analysis.
  • Alignment automated and based on paired feature detection at the LC-MS level.
  • Detection uses isotope profiles to confidently build peptides utilizing three dimensional data.
  • Quantification of all peptides followed by independent LC-MS/MS identification.
  • Quantitative peptide ion analysis is automatically collated with protein information.




    • Mass Profiler Professional    TOP



  • Allows comparison of multiple samples and/or multiple MS analysis platforms in a single project (GC/MS, LC/MS, CE/MS and ICP-MS)
  • Designed for both scientists and statisticians, with guided and advanced workflows
  • Provides comprehensive statistical tools including ANOVA, PCA, t-tests, volcano plots, hierarchical trees, SOMs, QT clustering, and SVMs for class prediction
  • Generates inclusion list for subsequent MS/MS-based analyses to facilitate protein and metabolite identification
  • Integrated ID Browser mirrors MassHunter Qualitative Software to allow identification using LC/MS Personal Compound Databases and GC/MS libraries (NIST)
  • R Scripting compatibility within Mass Profiler Professional allows you to further extend and customize statistical analysis and visualization capabilities




    • HPLC System Gold from Beckman/Coulter    TOP



  • Autosampler
  • Diode Array Detector
  • UV/VIS Detector
  • Fluorescent Detector




    • ACQUITY UPLC System from Waters    TOP



  • Reliable, high quality chromatographic separations produced up to 10 times faster than current HPLC methods, reducing time and cost per sample.
  • Increased efficiency for sharper peaks and better resolution, resulting in better quantitative and qualitative analyses.




    • P/ACE MDQ Capillary electrophoresis system from Beckman    TOP



  • Capillary Thermoregulation with Recirculating Liquid Coolant
  • Multi-format Sample Introduction
  • High Sensitivity UV Detector
  • Multiple Separation Modes
  • Automatic Standards Co-Injection




    • Agilent 3100 OFFGEL Fractionator    TOP



  • pI-based OFFGEL fractionation with 0.1 – 0.6 pH resolution depending on consumable kit used
  • In-solution fraction recovery for easy transfer to LC/MS
  • Up to 16 samples fractionated at the same time
  • µg to mg load capacity




    • TissueLyser II    TOP





    Biacore 2000 from Biacore Inc.    TOP



  • 4 flow cells per chip allow two experiments including controls
  • Autosampler with temperature control (4-40ºC)
  • Affinity studies
  • Kinetics
  • Determination of valences





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