Proteomics

Professor in the Department of Molecular Medicine at the Faculty of Medicine of Université Laval, he leads the Proteomics Platform and the bioinformatics service at the Research Center of CHU de Québec-Université Laval. Holder of the L’Oréal Research and Innovation Chair in Digital Biology, he conducts numerous development projects on the analysis of data from omics technologies (genomics, epigenomics, proteomics, etc.) and on machine learning on biological data.

Expert in proteomics and mass spectrometry, she is responsible for developing advanced methods for the analysis of the most demanding samples. She possesses advanced knowledge of bioinformatics tools for processing proteomic data as well as their graphical representation using R software.

Expert in proteomics and mass spectrometry, Victor has a great ability to manage highly diverse projects and specializes in the analysis of atypical samples. He is also responsible for client relations for the Proteomics Platform.

Expert in proteomics and mass spectrometry, she specializes in the analysis of biofluids and clinical samples. She also develops methods for the analysis of post-translational modifications and is responsible for communication for the platform.

*Additional costs related to the purchase of specific consumables may be added.

**The rate depends on the analysis time to be determined with the platform staff according to the type of sample.

Discounts from 10% to 50% apply for 50 or more samples to be analyzed

***Includes personnel time, use of computing servers, and data storage.

Discounts from 10% to 50% apply for 50 or more samples to be analyzed

Our specialty lies in analyzing proteins through mass spectrometry. To achieve this, we extract proteins from your samples and enzymatically digest them using trypsin. The resulting peptides are then analyzed via LC-MS/MS, which involves liquid chromatography separation coupled directly with mass spectrometry detection. The acquired spectra are processed using software to identify the proteins present in the sample by comparison with public protein databases, as well as for their relative quantification. 

As a result, we can provide: 

• Identification of hundreds or thousands of proteins in each analyzed sample. 

• Relative quantification between different sample groups. 

• Identification and localization of specific post-translational modifications (phosphorylation, acetylation, methylation, O-GlcNAc, etc.). 

• Targeted analysis of up to a hundred proteins of interest (with the option for relative or absolute quantification). 

For analyses involving whole proteins (top-down proteomic analysis) or for investigating specific motifs or PTMs, please contact us to discuss the feasibility of the analysis. 

We can analyze a wide range of biological samples, including tissues (skin, muscle, brain, liver, etc.), cell pellets, biofluids (blood, urine, CSF), microbiopsies, etc. 

We can also analyze proteins from: 

• Cell culture medium 

• SDS-PAGE gel bands 

• bead-based immunoprecipitation or pull-down samples 

It’s very rare that we are unable to analyze a sample. The only constraint is that it contains proteins and that we are able to extract them. 

Feel free to contact us to confirm that we can analyze your samples.  

We can analyze all species for which a comprehensive (or nearly comprehensive) protein database is available. You can consult: https://www.uniprot.org/  

This is the case for many species, including but not limited to: human, mouse, rat, bovine, horse, E. coli, Arabidopsis, etc. 

When the database is incomplete or unavailable, we can compare the data with a database from a closely related species or use genomic data to deduce a protein database. Please consult with us to confirm the feasibility of the analysis.

Raw samples 

We can handle the entire sample preparation process, including protein extraction, protein quantification, trypsin digestion, and peptide purification. In this case, simply send your samples to us on dry ice. It may be possible to send them at ambient temperature in certain cases; please consult with us. 

Proteins in solution 

Check with us regarding the compatibility of your extraction buffer with our analyses. Buffers containing detergents such as SDS, Tween, Triton, etc., are not compatible with MS analysis. Several other compounds may also not be compatible either with trypsin digestion or with MS analysis. However, depending on the circumstances, it may be possible to dilute, precipitate, or ultrafiltrate the samples to enable their analysis. 

 Our typical extraction buffer is as follows, which is perfectly compatible with our analyses: 

 50mM Ammonium bicarbonate 

1% Sodium Deoxycholate 

Depending on the case, add: 

•  10mM DTT (1,4-DiThioThreitol) 

• Protease/phosphatase inhibitors 

Samples in solution should be sent to us on dry ice. 

Proteins in SDS-PAGE gel bands 

The gel should have been stained with Coomassie blue (e.g., Coomassie Brilliant Blue R-250 – BioRad – 1610400). Cut gel bands as small as possible while containing all proteins of interest (ideally, maximize the number of proteins in a minimum amount of gel). Place each gel band in an Eppendorf tube containing water. They can be sent to us at room temperature. 

Precipitated Proteins on Beads : 

We can analyze protein complexes from immunoprecipitations or pull-downs directly on the beads. Your beads should be washed three times with 25mM ammonium bicarbonate buffer. 

The dry beads should then be sent to us on dry ice. 

Proteins in Culture Media: 

Preferably, the culture medium should not contain bovine serum albumin (FBS, FCS), as this albumin may mask a large portion of the proteins of interest. 

Depending on the amount of protein in the medium, 0.5 to 10mL may be necessary for the analysis. 

Send us your frozen media on dry ice.

Proteins Already Digested with Trypsin: 

We recommend that tryptic digestion and peptide purification be performed in our facility. However, if you still wish to send digested proteins, please note that the obtained peptides must be purified on C18 resin (SPE, stage tips, etc.) before analysis. If this is not done, we will perform the purification in our laboratory. 

Other Types of Samples: 

Please consult us. We can adapt our methods according to the constraints of your project. 

We can receive your samples on any weekday. They will be registered in our sample management system and stored appropriately until analysis. 

However, please make sure to follow these instructions carefully: 

Before Sending Your Samples: 

1. Complete the analysis request form available for download here and send it to this address: proteomique@crchudequebec.ulaval.ca. 
2. Always notify us when sending your samples and provide the shipment tracking number. 
3. Label each sample clearly, matching the information on the analysis request form. The container must always indicate your name and the name of the principal investigator (PI). 

For Samples on Dry Ice: 

Ensure there is enough dry ice for the duration of the transport (1 day for Quebec City, 2-3 days for the rest of the province, 4-5 days minimum for the rest of Canada and international shipments). 

For Samples Sent at Room Temperature: 

Protect the samples from crushing by using bubble wrap if sending in an envelope. 

If You Are Sending from Quebec City: 

You can use the MedExpress service for delivery within 1 to 4 hours. 

Use the following address: 

Plateforme Protéomique
Centre de Recherche du CHU de Québec
CHUL TR-072
2705 boulevard Laurier
Québec, QC, G1V 4G2 

You can also drop off your samples at the CHUL reception at the Research Center, T Section Block during the following hours: 8 am to 12 pm / 1 pm to 4 pm. 

We can also receive your samples outside these hours: call us at 418-654-2261 (or 42261 internally). 

If You Are Sending from the Province of Quebec or the Rest of Canada: 

Samples on dry ice can be sent via a rapid carrier such as Purolator, FedEx, or UPS. 

Prefer sending on Monday or Tuesday to avoid the package sitting in a warehouse over the weekend. 

Use the following address: 

Plateforme Protéomique
Centre de Recherche du CHU de Québec
CHUL R-2710
2705 boulevard Laurier
Québec, QC, G1V 4G2  
Tél : +1 418 654-2261 

If You Are Sending from International Locations : 

Contact us before sending so we can provide you with a customs form to be attached to the outside of the package and email us a copy. 

Notify us immediately after sending the package and provide the tracking number. 

This procedure will allow us to organize the customs clearance of your package before it arrives in Canada, avoiding any delays. 

Samples can be sent via a rapid carrier such as FedEx or UPS. 

For dry ice samples, prefer sending on Monday. 

For highly valuable samples, you may use a specialized carrier like World Courier, which will monitor the temperature of the package throughout the journey and add dry ice if needed. 

Use the following address: 

Plateforme Protéomique
Centre de Recherche du CHU de Québec
CHUL R-2710
2705 boulevard Laurier
Québec, QC, G1V 4G2
Tél : +1 418 654 2261 

We generally need very little amount protein to perform the analysis. 

We typically recommend providing enough biological material to obtain 5 to 10 µg of protein after extraction. However, the analysis may still be possible with less material. 

For tissues, this usually represents a very small volume (5-10 mm in diameter). In some cases, we can also work with micro-biopsies of 1 mm or less. 

For cells, we can achieve a high-quality analysis with 5000 cells. However, we are currently developing protocols that allow us to analyze down to the single-cell level! 

For culture media, depending on the amount of secreted proteins, we can analyze 0.5 to 10 mL of the medium. 

For plasma or blood serum: 2 µL is sufficient if we do not perform albumin depletion. 

For urine: Ideally, please provide 0.5 mL. 

Feel free to contact us for more information. 

Identification Analysis: 

If you only wish to know the list of proteins contained in your samples, we will provide you with a .sf3 file that you can open after downloading the Scaffold software. Read the instructions in the section « How to install Scaffold for visualization of identification results? ». 

With Scaffold, you will be able to visualize the list of proteins obtained for each sample as well as the number of peptides identified for each protein. A semi-quantitative spectral count value is also available. 

The protein list can also be exported in Excel format. 

Identification and Quantification Analysis: 

We provide 2 files: 

• A complete table in Excel format containing the list of identified proteins and their quantification in each sample. The table also contains, for each protein, the ratios and statistical values (p-value/q-value) for comparison between the different groups. 

• A comprehensive report of the experiment along with graphs to understand the results: PCA, heatmap, Volcano plots, etc. 

An example report is available here (Excel format) and here (html format). 

Please note that for quantification analyses, we require a minimum of 3 biological replicates for each group/condition to allow us to perform statistical tests and identify regulated proteins between different groups. 

Depending on the variability between your samples, it may be necessary to analyze more replicates: please consult us. 

Targeted Proteomics Analysis: 

We can track and quantify up to a hundred proteins of interest in a single analysis. 

You will receive an Excel table presenting the quantification value of each protein in each sample as well as the ratios and statistical values (p-value/q-value) for comparison between different groups. 

Post-Translational Modification (PTM) Analysis: 

For each type of analysis (identification, quantification, or targeted), it is possible to search for certain post-translational modifications. 

In this case, we will provide, in addition to the usual results, the list of peptides carrying a modification and their quantification in the case of quantitative or targeted analyses. 

Other Bioinformatics Analyses: 

For global proteomics analyses (identification or quantification), it is possible to perform more advanced bioinformatics analyses on the obtained results: functional analyses (Gene Ontology), multi-omics analysis, signature/classification search using artificial intelligence. 

For these analyses, we closely collaborate with the bioinformatics platform of the Centre de Génomique de Québec. 

Please consult us for more details. 

Quality Controls: 

We use several quality standards to ensure that your samples are analyzed under the best conditions by our mass spectrometers. 

Moreover, except in a few specific cases, we ensure to analyze at most half of the available sample to allow for re-injection in case of a technical issue. 

Raw Files: 

Upon request, we can provide you with a copy of the raw files (.raw) produced by the mass spectrometer (can only be read with the manufacturer’s software) as well as the output files from the software. 

We can also assist you in submitting your files to the public data repository ProteomeXchange to make them available to the community (required by some scientific journals). 

IMPORTANT: Please note that we guarantee the retention of your files on our servers for a duration of 3 years after analysis. 

Our usual turnaround times are: 

• 2 to 3 weeks for an identification analysis 

• 4 to 6 weeks for a quantification analysis or a targeted analysis 

Additional time may be required for analyses involving: gel bands, purifications of peptides carrying PTMs, a large number of samples (>100), complex bioinformatics analyses. 

It is important to note that these turnaround times are provided as estimates. A high volume of analysis requests or technical issues with an instrument could result in additional delays. We will keep you informed in such cases. 

Please refer to the « Pricing » section

We invoice our services as follows: 

• Sample preparation: each step (extraction, quantification, digestion, etc.) is individually invoiced per sample. This rate includes labor and consumable costs (except for specific steps). 
• LC-MS analysis: it is invoiced per sample based on instrument occupancy time (longer runs = more protein identifications) and the type of analysis (standard, performance, sensitive) adapted to the sample complexity. Decreasing rates are applied depending on the number of samples to be analyzed.
  This rate includes labor, mass spectrometry consumable costs, and instrument maintenance costs.
  Quality control injections are included free of charge. 
  
• Bioinformatics analysis: identification analysis is included free of charge, while quantitative and statistical analysis is invoiced per sample (decreasing rate).  
  This rate includes labor as well as the cost of server usage and file storage. 

Free test analyses: 

To allow you to validate that quantitative proteomic analysis of your samples will identify a sufficient number of proteins, we offer the free analysis of 1 sample. 

This offer is valid only for quantitative or targeted analysis projects. The free analysis includes only sample preparation and protein identification analysis. 

The analysis is free only if you proceed with the quantitative/targeted analysis at a later time. Otherwise, the test analysis will be invoiced. 

Please contact us for more details. 

Our state-of-the-art instruments enable us to handle projects ranging from less than ten samples to hundreds or even thousands of samples! 

In consultation with you, we will adapt the analysis method based on the number of samples and the desired proteome coverage depth. 

Please note that our rates decrease based on the number of samples. 

Contact us for more details. 

Installation of Scaffold 

1. 1. Open the Proteome Software website at http://www.proteomesoftware.com/.  
   2. Click on “Download Scaffold” on the left side of the screen. 
   3. Select Scaffold for Mac or PC. 
   4. Save the installation file to your computer’s desktop. 
   5. Run (double-click) this file and follow the installation steps. 

Visualization of results: 

This is a quick summary; more details can be found in the software’s “Help” menu. 

1. Open a result file with the .sf3 extension. 
2. On the left side of the screen, click on “SAMPLES” to access the list of proteins detailing their accession numbers, molecular weights, and numbers of uniquely identified peptides. 
3. Generally, the minimum probability percentage should be adjusted to 50% for both proteins and peptides (see menu at the top of the page). 
4. The display option (see menu at the top of the page) should be set to “unique peptides.” 
5. If you select a specific protein and click on the “PROTEINS” icon on the left, the sequence of identified peptides will appear on the right side of the screen. If you select any of these peptides, the MS/MS spectrum, protein sequence, or other information depending on the selected tabs will appear at the bottom of the screen. 
6. You can return to the list of identified proteins by clicking on the “SAMPLES” icon. 
7. In addition to the list of proteins, this page provides links (to NCBI, among others) to obtain additional information about the identified proteins. 
8. It is possible to export the results to an Excel file. Simply go to the “EXPORT” menu and select one of the available options. 

Contact us:  proteomique@crchudequebec.ulaval.ca