Eight steps to Rigorous and Reproducible Experiments in Biomolecular Research at UNC:
- If using a core facility, consult with the core staff in the planning stage. Consult with a statistician if you need help developing a Power Analysis to assure that your results will be adequately powered.
- Design your experiment with sufficient controls (rigor) and replicates (reproducibility).
- Assure that ALL of your reagents (antibodies, cell lines, mice) are fully validated (see below).
- Have a clear and detailed protocol (SOP) and data analysis plan. Assure that the protocol is strictly followed or that any deviation is well documented.
- Assure that the staff or students performing the experiment are well trained and understand each step and the importance of performing them precisely.
- Use only well-maintained instrumentation, preferably maintained and operated in a core facility with expert staff (see #1 above).
- Document all steps, reagents, equipment and data analysis methods used in the experiment. Assure that the both the documentation and the data itself are properly stored in a safe data management repository.
- Acknowledge the grants that support the core, the core (by name) and core staff in publications. Specifics on our Core’s Acknowledgements can be found here.
Guide to Rigor and Reproducibility for the Department of Chemistry Mass Spectrometry Core Laboratory
- Consult with the core staff in the planning stage. – Brandie M Ehrmann, PhD., Director behrmann@email.unc.edu, 919.962.6813
For more detail on how to best design your mass spectrometry experiment and ensure reproducibility, please scroll to the bottom of this page to access our sample preparation SOPs. Standards and solvents utilized in each experiment will vary based on the needs of the experimental design and we will log and furnish all relevant part numbers and/or batch numbers to ensure appropriate communication.
Instrument calibration standards:
Q Exactive HFX:
Thermo Scientific™ Pierce™ LTQ Velos ESI Positive Ion Calibration Solution Catalog number: 88323 and
Thermo Scientific™ Pierce™ Negative Ion Calibration Solution Catalog number: 88324
Exactive GC:
Perfluorotributylamine (PFTBA) Catalog number: 30482
PESciex 3000:
Sciex™ MS Chemical Kit2, Higher Conc. PPGs (polypropylene glycols) Catalog number: 4412399
LTQ:
Thermo Scientific™ Pierce™ LTQ ESI Positive Ion Calibration Solution Catalog number: 8322 and
Thermo Scientific™ Pierce™ Negative Ion Calibration Solution Catalog number: 88324
Metrohm Ion Chromatography System: TBD
For additional information on authentication of key biological or chemical standards, please visit: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-068.html
2. Sample preparation SOPs can be accessed for our main experimental workflows here. Look under the “Rigor and Reproducibility” submenu for specifics. If your samples fall outside of these outlined SOPs, please consult with Core staff.
3. All walk-up users much attend a training course with the Core Director before gaining access to the instrumentation. For information and/or training materials relevant to liquid separations, mass spectrometry analyzer, and gas chromatography, you can check the following resources:
Instrument SOPs can be accessed here for reminders on how to operate walk-up platforms.
Walk up users can access “Instrument Operation Reminders” below. We have also provided our Safety Orientation flyer for all walk-up users
Instrument Operation Reminders LC-MS
Instrument Operation Reminders GC-MS
Safety Orientation
For access to a FREE membership (academic members only) to Chromacademy click on this link: www.chromacademy.com This portal is great for providing background information and fundamental review of all things mass spectrometry related.
Each mass spectrometer vendor offers a series of training courses relevant to their platform. Check the preferred vendors webpage for more details. Often times there is a charge for these online and/or in-person courses.
4. All walk-up users must attend a 2-day training course with the Core Director for each instrument they wish to gain walk-up access to. User access to laboratories and instrument scheduling calendars is not granted without this training.
5. Our Core utilizes the following standards and solutions to perform system checks on our LC-MS and GC-MS systems.
Exactive GC: Restek™ Grob Test Mix (capillary GC) Catalog number: 35000
Q Exactive HFX with Acqity H-class:
TSQ Vantage with Classic Acquity:
LTQ with Surveyor LC system:
Our instruments maintained by experienced personel at regular intervals and the instrument manufacturer services most of our platforms under annual contracts.
Q Exactive HFX: Last PM’ed 03/2022
Exactive GC: Last PM’ed 07/2022
TSQ Vantage: Last serviced: 07/2022
LTQ: Last serviced: 07/2022
Waters Acquity H-class: 07/2022
Waters Classic Acquity: Last serviced 07/2022
Metrohm Ion Chromatography system: 08/2022
6. All data (raw and processed) obtained by our Core will be shared with the user/client. We will provide detailed sample preparation, experimental and analytical methods utilized and/or data processing parameters.
Data obtained by the Department of Chemistry Mass Spectrometry Core Laboratory is kept on file for a minimum of 2 years. However, we are not solely responsible for your data. We ask all users regularly preform backups of their data files and manage their file storage according to their laboratories preferred data storage systems.
7. For information on how to acknowledge the Mass Spectrometery Core, include our personnel on authorship, etc. please access our “Acknowlegements” page by clicking here.
Additional resources:
Learn about the NIH Initiative to Enhance Reproducibility through Rigor and Transparency. (Video)
Resource Authentication Plan: https://grants.nih.gov/reproducibility/faqs.htm#V
What Kind of Information Should I Include in My Application’s Resource Authentication Plan? Check out instructions on NIH Nexus Blog.
What are ‘Key Biological and/or Chemical Resources’ that should be addressed your application’s authentication plan? Key biological and/or chemical resources include, but are not limited to, cell lines, specialty chemicals, antibodies and other biologics. More on NIH website
FASEB report on enhancing research reproducibility identifies three main gaps to research reproducibility:
- Lack of uniform definitions to describe the problem
- Insufficient reporting of key experimental details
- Gaps in scientific training
You can find experimental rigor and reproducibility specifics on the following pages:
High Resolution/Accurate Mass