Bloodworks Research Institute

Mass Spectrometry Lab

Frequently Asked Questions

Is mass spectrometry right for me?

If you want information regarding protein sequence, post-translational modifications or relative quantitation of proteins in a sample then yes, mass spectrometry is right for you. For analysis of other compounds such as small molecules, lipids or nucleic acids please contact Dr. Yi Wang.

We provide the following services:

• Protein/peptide mass determination by LC-ESI-MS/MS
• Identification of post-translational modifications for gel-based or solution-based proteins (offered on a case-by-case basis)
• LC-MS/MS based de novo sequencing for both gel-separated or solution-digested samples (offered on a case-by-case basis)
• Quantitative analysis of metabolites
• Targeted metabolomics
  • Analysis of small molecular thiols and disulfides
  • Polyunsaturated fatty acids and their oxidation products
• Untargeted metabolomics analysis of biofluids
• Other specific services please contact Dr. Yi Wang

Where is the Mass Spec Lab located?

It is located in room 1123 of the Research Institute building at 1551 Eastlake Ave E, Seattle, WA 98102.

How should I prepare my samples?

Please review our protocols for sample digestion and preparation. However, if this is your first time submitting samples to us, we would like to go over these procedures with you.

My sample is not stable. What should I do?

Please contact us before submitting your sample. We will do our best to accommodate any special needs you may have.

What kind of buffer/detergents can I have in my samples?

For in-gel submissions, most of the detergents (<0.1% SDS etc) can be cleared from the system before mass spec analysis. Avoid using Triton-X100 altogether if possible. N-octyl-b-glucopyranoside is a more mass spec friendly alternative. For in-solution samples, do not use detergents like Triton-X100, SDS, Tween 20, NP40 etc. Please contact us if you have any further questions about sample prep.

Can I submit radioactive samples for analysis?

Unfortunately, the MS lab does not accept radioactive samples.

Is there a size limit for the proteins you can analyze?

That depends on whether you are planning on analyzing an intact protein or peptides from a digested protein. There is no size limit if the protein is digested. If you wish to analyze an intact protein please contact us so we can discuss your project.

Can I have my protein digested with a protease other than trypsin?

Yes, please contact us to discuss the possibility of using another enzyme for your analysis.

How do I submit a gel for in-gel tryptic digestion?

Please perform the in-gel digest and send us the digested sample. The protocol for this procedure can be found here.

What type of staining can I use for gels?

In general we encourage our clients to use a Coomassie or colloidal blue stain.

How do I avoid contamination with keratins?

Wear gloves at all times when processing the protein sample. Loose hair should be secured back. All trays and equipment can be rinsed with water before use. In general, try to be as clean as possible.

How much sample do I need to submit?

This depends on what instrument is going to be used for analysis and if we need to develop a method for your sample. Typically 10-25 pmol are required but more may be necessary for method development.

Will I get my sample back?

No.

When can I expect to receive my protein identification results?

Typical turnaround time for protein ID is variable depending on the workload in the lab. Please plan ahead for time-critical samples. If it is imperative that your sample be analyzed ASAP, please contact us to discuss what options are available.

How much will the analysis cost?

Please review the cost table for this information.

I am writing a paper that includes data acquired from the Blood Center MS lab – what should I include in my methods and how should I acknowledge Bloodworks Northwest MS lab?

Please feel free to contact us regarding experimental write-ups. Also be sure to acknowledge that the MS analysis was performed by the Mass Spectrometry Lab at Bloodworks Northwest.