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Discovery-based Quantitative MS methods

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  1. Facilities
  2. Mass Spectrometry Facility
  3. Quantitative Proteomics

Discovery-based Quantitative MS methods,(“shotgun” proteomics), aim to identify as many proteins in a sample as possible and can be completed on a wide range of samples with minimal method development.

  • DDA (data-dependent acquisition): In Data-dependent acquisition (DDA) mode a MS instrument will complete a full scan of all peptide (precursor) ions during MS1 and then select the most abundant ions for fragmentation and MS2
  • DIA (data-independent acquisition): In Data-independent acquisition (DIA) mode a MS instrument scans pre-determined, often sequential, m/z ranges and then fragments all the ions within each range for MS2 measurement

DDA vs DIA MS1 and MS2 examples

  DDA DIA
Suitable for small proteomes* Yes Yes
Suitable for large proteomes* No Yes
Dynamic range Moderate High
Complexity of spectra Low High
Search requirements Protein database Spectral library
Instrument method optimization Low Hig

Note (*) Most prokaryote proteomes can be considered a “small” proteome, vs. larger eukaryotic or mixed (e.g., infection model) proteomes

Discovery-based methods can be used to identify thousands of proteins in a single sample, and for most research questions label-free DDA is a straight-forward option that has relatively low reagents costs, and requires minimal sample preparation and instrument method optimization.  

  • Discovery-based Quantitative MS methods
  • Quantitative Proteomics to Label or not to Label
  • Targeted Quantitative Proteomics MS Methods
  • MSF LFQ Service: Requirements and Deliverables

What is the Advanced Analysis Centre?

The Advanced Analysis Centre (AAC) at the University of Guelph is a group of research laboratories housed in the University’s Summerlee Science Complex. The AAC spans an area of over 1000m2 and contains approximately $40 M of research equipment purchased with funds from the Canada Foundation for Innovation, Ontario Research Fund and Natural Sciences and Engineering Research Council of Canada.

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Quick Links

  • Genomics Facility
  • Mass Spectrometry Facility
  • Molecular and Cellular Imaging Facility
  • NMR Centre
  • Phytotron Facility

Contact Us

The Advanced Analysis Centre
Summerlee Science Complex
University of Guelph
Guelph, ON N1G 2W1

Phone: (519) 824-4120 ext. 56814
Fax: (519) 767-2044
aac@uoguelph.ca