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

ntharay@clemson.edu

Elizabeth Leonard

Research Associate

eleona2@clemson.edu

Khang Huynh

Postdoctoral Fellow

khuyhn@clemson.edu

Jisun Lee

Research Associate jisunl@clemson.edu