Registration fee: $260

Lunch will be provided

The workshop is open to all.

To register, send your name, dept., PI/lab, and Cornell account number to Tami Magnus tjm33@cornell.edu

Important: Please indicate in your registration email if you want to use your laptop during the

practice sessions about database search on day 2. Information about software requirement and

installation will be sent to you.

Space is limited to 16 seats. Register soon!

Workshop program (day 1, Oct 9th, 2024)
8:45 - 9:00 am Registration (Biotech Building, room 131)
9:00 - 9:05 am Workshop agenda overview
Sheng Zhang, Director, Proteomics & Metabolomics Facility
Biotech Bldg room 131
9:05 - 9:20 am Experiment 1: Protein denaturing, reduction and alkylation of protein extracts from liver
tissues of pigs treated with H2S for label-free quantitation (LFQ) analysis:
Attendees divided into 4 groups. Instructors:
Qin Fu (bench 1), Bob Sherwood (bench 2), Beth Anderson (bench 3), Andy Lui (bench 4)
Biotech Bldg., room 141, 147B
9:20 - 10:00 am Lecture 1: Sample Preparation & Basic liquid chromatography mass spectrometry (LC-MS)
Sheng Zhang, Biotech Bldg room 131
10:00 - 11:05 am Experiment 2: In-solution tryptic digestion by S-trap workflow for about 4+ hours
Biotech Bldg., room 141, 147B
11:15 - 12:00 pm Lecture 2: LC-MS-based proteomics analysis workflows
Sheng Zhang, Biotech Bldg room 131
12:00 – 1:00pm Lunch at Biotech Bldg room 131
1:10 - 1:50 pm Lecture 3: Mass spectrometry applications: proteomics case studies with the focus on
label-free based quantitative proteomics, protein-protein interactions analyses
Sheng Zhang, Biotech Bldg room 131
1:50 – 2: 35 pm Lecture 4: Introduction to protein database searching (Proteome Discoverer, MaxQuant)
by Qin Fu, Research Associate, Proteomics & Metabolomics Facility
2:45 to 3:30 pm Experiment 3: Collection of tryptic peptides from S-trap and drying down by speed vacuum
Biotech Bldg., room 141, 147B
3:45 - 4:30 pm Lecture 5: Statistical analysis for screening differentially abundant proteins (by Excel,
MetaboAnalyst and Perseus software tools)
by Drs. Qin Fu/Andy Lui/Sheng
4:30 to 5:30 pm Experiment 4: Reconstitute dried peptides and set up nanoLC-MS/MS analysis
Overnight run for pig liver protein digests (with 60-min gradient for each run)
8 samples on Orbitrap Eclipse, by Qin (attendees #1 - #8)
8 samples on Orbitrap Fusion, by Sheng (attendees #9 - #16)
Biotech Bldg., rooms 143, 150

Workshop program (day 2, Oct 10th, 2024)
All sessions take place in Biotech 131 unless otherwise indicated
8:30 - 9:00 am Laptop setup* (Biotech Building, room 131)
9:00 - 10:50 am Practice I: Database search practice: using PD 2.5 for BSA_E.coli, TMT-labeled pig
samples. Interested individuals can start database search for their acquired E. coli file
by Qin Fu
11:00 - 12:00 am Practice II: Database search practice using MaxQuant for E.coli_BSA files for LFQ
between samples and iBAQ within a sample for intensity-based absolute quantitation.
by Sheng Zhang
11:30 - 12:00 pm Lecture 6: Understanding PD 2.5 result reports from the Proteomics Facility: Protein IDs,
TMT, SILAC, label-free quantitation (LFQ), and PTMs reports.
by Sheng Zhang
12:00 - 1:00 pm Lunch (provided)
1:00 - 1:30 pm Lecture 7: Bioinformatics analysis for differentially abundance proteins
by Qin Fu
1:30 - 3:20 pm Practice III: Bioinformatics analysis practice: GO analysis, Pathway enrichment analysis,
Protein-protein interaction (network) analysis
by Qin Fu
3:35 - 4:30 pm Lecture 8: Useful web-based tools (Venn Diagram, Motif analysis, Clustering of multivariate
data, Volcano analysis, String network analysis) making plots for presentations and/or
publications.
by Qin Fu; and Andy Lui
4:30 – 5:00pm Practice IV: How to make publication quality of Figures for MS or MS/MS spectra of
peptide or modified peptides using Xcalibur software
*If you want to perform database search on your own laptop, you will need to install PD 2.5 demo version and
MaxQuant 2.4 software ahead of the workshop. The installation information will be sent before the workshop.