FAQs & SOPs

Frequently Asked Questions (FAQs)

Can collaborations be established with the BMS Laboratory?

The BMS Laboratory is open to research collaborations. These collaborative projects can take many forms, which may result in cost savings to the users of the Facility. The BMS Laboratory provides expertise in a variety of areas such as method development, LC-MS/MS applications, bioinformatic analysis and preparation of scientific manuscripts/reviews. Acknowdegments and publication authorship should be discussed prior to establishing the collaborative work. Contact Facility Director, Dr. Alejandro Cohen, for more information.   

Should any precautions be taken during sample preparation?

  • Wear gloves at all times, use clean reagents and glassware to avoid keratin contamination!
  • Sample prep for SDS-PAGE: Avoid boiling samples, if possible - heating at 37˚C for 15 min prior to electrophoresis is normally sufficient. If urea must be used (eg. preparation of IEF samples for 2D-PAGE analysis), never heat sample above 37˚C. Let us know if any chemical modification (eg. iodoacetamide to block sulfhydryl groups) has been used in sample preparation.
  • Protein stains: Most gel stains for proteins (eg. Coomassie Blue, GelCode, sivler staining) are compatible with MS analysis, but do not use silver stains that include covalent fixatives (ie. glutaraldehyde). If feasible, provide gel slices containing at least 1 pmol of sample (eg. 0.1 µg of 100 kDa protein), which is normally near the limit of Coomassie Blue detection. While identification is possible with lower amounts (~100 fmol), the success rate drops considerably. Do not store gels in glycerol.
  • Gel slices. This is the most critical stage to avoid contamination - use clean materials and work in a laminar flow hood wherever possible!! Using a clean scalpel, cut out each protein band. Gel slices should not be wider than a 2 or 3 millimeters. Please cut exactly around or within the stained protein to avoid excess gel. The protein should be focused on as small a piece of gel as possible. Transfer to a microfuge tube (do not mash or cut into finer pieces). Sterile 1 ml disposable pipette tips can also be used to excise 2D spots. Gel slices should be cut as soon as possible and stored in a -80˚C freezer prior to analysis.
  • Detergents: Certain detergents can give rise to a polymer-like background and cause severe signal suppression during LC-MS acquisition. Avoid detergents such as Tween-20 and Triton X-100 if possible. Due to low protein solubility the use of detergents may be unavoidable. Look for MS friendly detergents and inform us whenever nonionic detergents are used.

In what conditions should samples be shipped?

In most cases, freeze dried/lyophilized samples (eg. protein extracts) may be shipped in sterile plastic tubes (preferably 1.5 or 2 mL tubes) at room temperature. Gel bands may be dried after excision in a vacuum centrifuge.

Fresh samples can be refrigirated or frozen and shipped with ice packs or dry ice, accordingly.

ALL tubes must be labeled accordingly with the matching ID# stated in the Sample Submission Form [PDF - 49 KB].

How and when do I submit my samples?

Samples should be submitted directly to the BMS lab in person. Gel bands for protein ID are typically processed during the second and third week of each month, check the Services section for monthly submission dates. All other samples are received from Monday to Friday from 10.00-11.00 am and 2.00-3.00pm. Please contact bms@dal.ca to arrange a sample delivery date.

Samples may also be sent by courier. If shipping samples, please download the Sample Submission Form [PDF - 49KB], complete the requested information and attach it to the sample package. We recommend sending frozen/refrigerated samples early in the week (Monday-Tuesday) by express (24-48hs) delivery to avoid weekend delays. For more details, contact bms@dal.ca.

How much will my analysis cost?

The cost of analysis will depend on the type and number of analyses performed. View a detailed description of pricing or contact bms@dal.ca for specialized and custom-made analyses. Samples submitted by external Academic institutions and Industry receive an additional 25% and 50% surcharge, respectively, on their final invoice.

Are services only available to DAL researchers?

NO. Samples from external clients (Industry, Academia, Government Departments, NGOs etc) are ALSO accepted by the PCF for analysis. Please contact us at bms@dal.ca to inquire about pricing and scheduling. Samples submitted by Academic institutions and Industry receive an additional 25% and 50% surcharge, respectively, on their final invoice.

How long do the analyses take?

SDS-PAGE Gel bands or spots for protein ID should be submitted in the dates specified in Services. Reports are usually ready two or three weeks later. Gel bands received after the submission dates are stored at -20C until the next batch, the following month.

For other analyses, the duration of analysis depends on the amount of sample prepping required, the complexity of each analysis and the current workload which varies from month to month. Typically, results are reported anywhere between 1 week to 3 weeks after sample submission.

How are results reported?

Protein identification from Proteome Discoverer Software is typically reported in user friendly Excel files. The filenames are structured as:

YYMMDD_AAAA_BBB_S##

Where:

YYMMDD corresponds to the date of MS aquisition
AAAA: Request/Invoice number
BBB: Researcher's ID number
S##: Sample ID number as entered in the Request Form.

The Excel files (.xlsx) contain all the information generated by ProteomeDiscoverer software. The information is nested into Protein Groups, Proteins and Peptides tables. Each one of these tables can be exposed by clicking on the '+' signs found on the left hand side of the spreadsheets (Columns 1, 2 and 3). The identifications scores, peptide sequences, PTM modifications and complementary data are found in columns within each nested table.

Important reminder: Bottom-up proteomics relies on the digestion of proteins into peptides, usually done with trypsin. When the digests are analyzed by LC-MS/MS, the data collected is used to identify the peptides using data base search algorithms. Based on these peptide hits, Protein identifications are inferred. Proteins are grouped together (Protein Groups) when there is insufficient evidence to claim the presence of any single proteoform, and is quite common with proteins that share many digested (tryptic or other enzyme) peptide sequences.
The proteins within a group are ranked according to the number of peptide sequences, the number of PSMs, their protein scores, and the sequence coverage. The top-ranking protein of a group is labeled as the 'master protein', and appears as the Protein Group 'representative'.

The reports can also be explored using Proteome Discoverer software in the PCF lab with support from our staff. Contact us at proteomics@dal.ca to arrange an appointment.

Alternatively, .raw, .msf (Thermo’s Mass Spec Format files), .wiff (ABSciex files), .mgf, .mzML and .mzXML can be provided upon request via Dalhousie's File Exchange server.

Standard Operating Procedures (SOPs)

Silver Stain

After electrophoresis:

1.      Fix the gel slab in 50% methanol, 5% acetic acid in water for 20 min.

2.      Wash for 10 min with 50% methanol in water and additionally for 10 min with water to remove the remaining acid.

3.      Sensitize gel by a 1 min incubation in 0.02% sodium thiosulfate, and then rinse with two changes of distilled water for 1 min each.

4.      Stain: submerge gel in chilled 0.1% silver nitrate solution and incubated for 20 min at 4 °C. After incubation, discard the silver nitrate, and rinse twice the gel slab with water for 1 min

5.      Develop the gel in 0.04% formalin [35% formaldehyde in water] in 2% sodium carbonate with intensive shaking. After the developer turned yellow, discard and replace with a fresh solution. It is essential that the developing is carried out in an absolutely transparent solution. After the desired intensity of staining is achieved, the development is terminated by discarding the reagent, followed by washing of the gel slab with 5% acetic acid.

Silver-stained gels were stored in a solution of 1% acetic acid at 4 °C until analyzed.

* Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels

Andrej Shevchenko, Matthias Wilm, Ole Vorm, and Matthias Mann
Anal. Chem. 1996, 68, 850-858

Protein Precipitation Techniques

Note: All steps should be carried out in glassware or solvent-compatible plasticware.  

Acetone Precipitation Protocol


1. Cool the required volume of acetone to -20°C.
2. Add four times the sample volume of cold (-20°C) acetone to the tube.
3. Vortex tube and incubate for 60 minutes at -20°C.
4. Centrifuge 10 minutes at 13,000-15,000 x g.
5. Decant and properly dispose of the supernatant, being careful to not dislodge the protein pellet.
Optional: If additional cycles of precipitation are necessary to completely remove the interfering
substance, then repeat steps 2-5 before proceeding to step 6.
6. Allow the acetone to evaporate from the uncapped tube at room temperature for 30 minutes. Do not over-dry pellet, or it may not dissolve properly.
7. Resuspend in appropriate buffer.

 

TCA Precipitation Protocol

1. Add an equal volume of 20% TCA (trichloroacetic acid) to protein sample.
2. Incubate 30 min on ice.
3. Spin in microfuge at 4 deg. For 15 min.
4. Carefully remove all supernatant.
5. Add ~300 ul cold acetone and spin 5 min at 4 degrees.
6. Remove supernatant and dry pellet.
7. Resuspend samples in desired buffer.
Warning: TCA is a strong acid and should be handled with care

 

Chloroform/Methanol Precipitation

1. To sample of starting volume 100 ul
2. Add 400 ul methanol
3. Vortex well
4. Add 100 ul chloroform
5. Vortex
6. Add 300 ul H2O
7. Vortex
8. Spin 1 minute @ 14,0000 g
9. Remove top aqueous layer (protein is between layers)
10. Add 400 ul methanol
11. Vortex
12. Spin 2 minutes @ 14,000 g
13. Remove as much MeOH as possible without disturbing pellet
14. Speed-Vac to dryness


Reference: Wessel, D. and Flugge, U. I. Anal. Biochem. (1984) 138, 141-143