Overview: Proteomics encompasses large-scale detection and analysis of proteins in various biological matrices. ‘Bottom-up’ proteomics
implements tryptic digestion of intact proteins to peptides, which are then separated using nano-flow liquid chromatography and are analyzed
using a nano-ESI-MS/MS platform. The peptide fragmentation data are interpreted using algorithms employed by search engines such as
SEQUEST®, Mascot™ and Byonic™, and the peptide sequence are identified by comparing the observed fragmentation pattern with that
derived from protein sequence databases and heuristic fragmentation rules. The identity of proteins are inferred based on the peptide matches
with reference FASTA files that are species specific.
Global ProteomicsGLOBAL PROTEOME ANALYSIS
INSTRUMENTATION
• Combines quadrupole, ion trap and Orbitrap mass
analysis in a revolutionary Tribrid architecture
• Ultrahigh resolution up to 500,000 FWHM
• Sub-1-ppm mass accuracy
• Multiple dissociation techniques—CID, HCD, ETD
• ID-X capability for small molecule analysis
• Coupled to HESI and nano-ESI interfaces
• UltiMate 3000 RS UHPLC & UltiMate 3000 RSLCnano
Thermo Orbitrap Fusion™ Tribrid™ Mass Spectrometer
RESULTS
Figure 4. Venn diagram of proteins detected in yeast
cells grown in nutrient treatments (coumaric acid,
glucose, and lignin) (MUAL data).
Figure 3. Principle Component Analysis (PCA)
showing the influence of nutrient treatment in
protein yeast (MUAL data).
Protein QuantitationBottom-up ‘Shotgun’ Proteomics
Figure 2. Overview of different mass spectrometry techniques employed in proteomics.
Figure 1. General workflow of bottom-up or ‘shotgun’ proteomic analysis
highlighting the global protein coverage achieved using this technique
Figure 5. Establishment of confident peptide IDs
through complementary mass fragmentation.
111 Biosystems Research Complex (BRC)
105 Collings Street, Clemson SC 29634
Ph: (864) 656-5060
Website: https://www.clemson.edu/cafls/mual/
CONTACT USNishanth Tharayil
Facility Director
Elizabeth Leonard
Research Associate
Khang Huynh
Postdoctoral Fellow
Jisun Lee
Research Associate [email protected]
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