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Stanford University Mass Spectrometry Vincent Coates Foundation
Vincent Coates Foundation

FAQ

PUBLICATION QUESTIONS:

I am writing a paper that includes data acquired at SUMS - what should I put in the experimental?

Please feel free to contact us regarding experimental write-ups. We will be glad to help you with the content and/or review the text.

Why is acknowledging grants and resources important?

Authorship/acknowledgement of the core lab is crucial in supporting ongoing core operations and development, as well as in acquiring future instrumentation and capabilities. Publication lists are essential to demonstrate impact, support grant proposals, and comply with federal reporting requirements.

I am writing a paper that includes data acquired at SUMS - how should the lab be acknowledged?

Stanford Policy: As with all Stanford core labs, if work done with SUMS produces data in a publication, the lab must be acknowledged in the publication, e.g. "This work was supported by the Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University Mass Spectrometry (RRID:SCR_017801) utilizing the [insert instrument & RRID]." Further, if SUMS staff provide significant experimental design, data interpretation, or other intellectual contribution (as evaluated by the PI), then it is expected that these individuals will be coauthors on the publication.

RRIDs for non-NIH funded instruments (see next question for NIH-funded instrument identifiers):

  • Agilent 6495C Triple Quadrupole LC/MS (RRID:SCR_023937)
  • Sciex 7500+ Triple Quadrupole LC/MS (RRID:SCR_026608)
  • Bruker timsTOF Ultra nanoLC/MS system (RRID:SCR_025639)
  • Bruker timsTOF HT nanoLC/MS (RRID:SCR_029018)
  • Thermo Exploris 240 LC/MS (RRID:SCR_022986)
  • Thermo Eclipse nanoLC/MS (RRID:SCR_022212)
  • Waters SELECT SERIES Xevo MRT (RRID: SCR_029019)
  • Waters SQD2 LC/MS system (RRID:SCR_022217)

 

I am writing a paper that includes data acquired at SUMS - what grant numbers should I acknowledge?

As a Stanford Cancer Institute Shared Resource, our lab receives grant support from the National Cancer Institute, which should be acknowledged in all publications containing data collected at SUMS. The following statement is suggested: “This work was supported in part by NIH P30 CA124435 utilizing the Stanford Cancer Institute Proteomics/Mass Spectrometry Shared Resource.”

The NIH requires that all publications containing data collected on our Shared Instrumentation Grant (SIG) or High End Instrumentation (HEI) Program funded instruments acknowledge NIH grant support. 

Orbi Elite: "This work utilized the Thermo LTQ-Orbitrap mass spectrometer system (RRID:SCR_018694) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant S10RR027425."

Xevo TQ-XS: "This work utilized the Waters Xevo TQ-XS mass spectrometer system (RRID:SCR_018510) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant S10OD026962."

Orbi Eclipse: "This work utilized the Thermo Orbitrap Eclipse nanoLC/MS system (RRID:SCR_022212) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant 1S10OD030473."

6495 Triple Quad: "This work utilized the Agilent 6495 Triple Quadrupole LC/MS system (RRID:SCR_023937) that was purchased with funding from National Institutes of Health Shared Instrumentation Grant 1S10OD034374."

 

I just published a paper including data acquired at SUMS - what should I do to let SUMS know?

We ask that our collaborators provide citations for all publications containing data generated at SUMS; this information is essential to support the continued existence of the core and bring in new instrumentation. Enter your publication info at https://tinyurl.com/SUMSpubs

 

Proteomics

Proteomics General Questions

  1. What are your current rates?

Our rates can be found in: Rates | Stanford University Mass Spectrometry, but they vary depending on several factors like number of samples, if the client is internal or external, whether the client is for-profit, etc.

2. Are there any opportunities to reduce costs or adjust pricing? 

Running samples in bulk (4 or more samples) may help reduce the total cost, as you will be charged per hour instead of per sample. Additionally, we offer several training opportunities in sample preparation, instrumentation, and data analysis to reduce costs in future projects. 

3. How do I submit samples to SUMS? 

We utilize iLab to streamline the entire sample submission process. Make sure you use the ‘Proteomics’ form. To learn more, please visit iLab | Stanford University Mass Spectrometry

4. How long does it typically take to receive my data? 

Our timeline is usually 2-3 weeks, but it may change depending on instrument availability. Additionally, we have a rush rate in case you need your results as soon as possible. 

Sample formats

5. Are there any specific considerations I should keep in mind when submitting my samples in gel form? 

For Coomassie- and Sypro Ruby-stained gels, destain the gels as much as possible. Soak gels for at least 2 hours in 10% acetic acid, 50% methanol, and 40% water. The maximum size of a gel band should be 1.5 cm. If gels are larger than this, please cut them into small pieces and place them in a clean Eppendorf vial with a 1% acetic acid solution. Store the gels at 4 °C before submission. For metal-stained gels (silver and zinc), please provide aliquots of the destaining solutions and deliver them to SUMS along with the samples. 

6. Are there any specific considerations I should keep in mind when submitting my samples in bead form?

Do multiple PBS washes (5-10) before submitting samples. Please DO NOT freeze beads. Avoid detergents like Triton and NP40. If you have to use them, let us know. Beads are processed the same day. Please contact us to arrange your sample drop-off. We do not accept beads on Fridays. 

7. Can I get my samples back after SUMS has finished analyzing them? 

Yes, you can email us and schedule a sample pickup no later than 30 days after getting your results. 

Data Analysis/ Results

8. How many biological replicates should I include in my project? 

In general, including at least 3 biological replicates helps ensure more robust results, but the ideal number varies by field of study and your study goals. 

9. Can SUMS do biological inferences or data interpretation of my project? 

We can’t do any biological interpretations; we only deliver mass spectrometry data.