MSF LFQ Service: Requirements and Deliverables

Project Requirements of Clients:

MSF clients must provide replicate samples of digested protein (i.e., peptides). Minimum four replicates per sample group is recommended, and a starting concentration of 25 micrograms per sample for complex proteomes. All peptides must be de-salted prior to injection using C18 spin columns, ZipTipTM, or similar. Recommended protocol.

Alternately, undigested protein samples can be submitted and associated fees will be applied for all additional processing completed by MSF staff (e.g., pre-digestion quantitation, in-solution digestion, desalting, etc.). Please refer to the MS Fees page for additional details.

Project Deliverables from MSF:

Upon completion, quantitative proteomics projects will include a set of raw data files and initial quantitative analysis with PEAKS Q software (Bioinformatics Solutions Inc., Waterloo, Ontario). Q exports include a volcano plot of significantly different proteins, protein profile heatmap, protein identifications and sample (or group) ratios, and a list of supporting peptides. Completed PEAKS projects can be viewed with a free downloadable viewer.

Add ons: Sample processing, peptide labelling, PEAKS software training, use and/or training with alternate analysis tools (e.g., MaxQuant and Perseus, Skyline).

Requirements and Deliverables may vary for other (i.e. non-LFQ) services. Please contact the MSF for more information.

Workflow for protein identification.Proteins are extracted and can be fractionaled,enriched or separated on a gel followed by digestion with protease into small peptides between 8 and 30 aminoacids. These peptides can first be enriched or fractionaled followed by a clean-up and then separated using chromatography and detected by mass spectrometry and fragmented. The data is then analyzed using Peaks 10.0 software and compared to protein databases which leads to protein identification.


Discovery-based Quantitative MS methods

Quantitative Proteomics to Label or not to Label

Targeted Quantitative Proteomics MS Methods

MSF LFQ Service: Requirements and Deliverables