FAQ

The shipping address is the same as the physical address for the core. The Targeted Metabolomics and Proteomics Laboratory (TMPL) is located at the following address:

University of Alabama at Birmingham
Bevill Biomedical Research Building- Room 709
845 19th Street South
Birmingham, AL 35205
Phone: (205) 934-3462.

For internal campus clients, Oracle account numbers are required for appropriate transfer of funds. External clients such as non-UAB academic researchers, corporations and/or charitable organizations may pay invoices by check payment, wired bank transfers and credit card payments.

Please mail your payment to:

UAB Pharmacology and Toxicology
1720 2nd Avenue South.
Volker Hall 140
Birmingham, AL 35294-0019

Phone: (205) 934-4579
Fax: (205) 934-8240.

TMPL Core personnel frequently offer aid in the construction of all figures and spectra directly extracted from the raw data. Often, the data is only accessible via proprietary software that is not readily available to clients. Any figures/tables generated by the client from raw data outside of the core is strongly encouraged to be forwarded to the pertinent analyst(s) in TMPL to verify the presentation contents as correct/acceptable for publication. Many journals have specific formats for the incorporation of spectra that can only be fabricated from the original raw data.

When citing the TMPL Core for acknowledgments, please refer to the following webpage link for grant and instrumentation information. https://sites.uab.edu/tmpl/about/grants/ Additional information for authorship should be addressed directly to the pertinent personnel involved in the drafting of the section(s) for the manuscript/abstract.

Though recognition is always welcomed, services provided by the TMPL personnel do not necessitate authorship. However, if the manuscript/abstract 1) required novel methods and/or analyses or 2) provided significant intellectual contribution in the drafting of the documents, then authorship is strongly recommended as per standard publication guidelines. At minimum, acknowledgement of the TMPL Core is required for NIH, university and other institutional recognition of provided services.

A copy of raw data for publication purposes will only be distributed to the original principal investigator(s) upon request. For most projects, Cloud Services such as BOX or OneDrive can facilitate the necessary transfer of raw data ownership. It is the responsibility of the corresponding author to upload the raw data to publication sites/institutions. TMPL personnel will provide appropriate metadata for the completion of the requirements for the raw data upload. It is strongly encouraged to consult with TMPL Core personnel before uploading and/or sharing raw data to ensure publication compliance such as file formats, sizes, etc.

NIH, UAB and other regulatory agencies require the TMPL Core to maintain all raw data and appropriate backup copies of raw data for a minimum of 7 years and recommended for 10 years. The TMPL Core aims to provide permanent raw data access when possible for clients. There are events where technology no longer exists to help facilitate transfer of legacy equipment raw data. Raw data from discontinued instrumentation will still be available though the original analysts may no longer be available to provide assistance for the legacy projects. Legacy software to analyze older data sets will also be continued when possible unless the proprietor/business no longer maintains the software suite.

TMPL Core services are open to the great UAB community including businesses and other institutions. NIH grant awardees are given priority over corporate/business sample submissions.

The TMPL Core does not offer the evaluation of any radioactive materials or depleted radioactive materials. Stable isotopic labeled compounds/materials i.e. Carbon-13, Deuterium, etc. are acceptable for sample submission.

Typically, for protein identification analyses, a Coomassie stained gel band will yield a positive result with relative ease. This translates ideally to 25-50 ng of protein in the band. For metabolomics and lipidomics samples, one million cells, 10-100mg of tissue, 50-200uL of sera/plasma and 50uL of urine are nominal amounts for samples.

Clients/Investigators are encouraged to process samples themselves with pre-approved methodology the TMPL personnel provide. Typically, samples that are processed ahead of time allow for a faster turn-around time on the instrumentation since resources and time are not needed for extractions and other processing steps.

The average return time for results for many analyses is 7-10 business days. This is particularly true for protein identification work. Targeted analyses have varying degrees of turn around because of the sample set size ranges. It is good practice to accept for every 100-150 samples, you should give one month for return.

Like most scientific experiments, the higher quality samples yield similarly higher quality results. Rigorous extraction techniques that remove salts, detergents, polymers and other offensive compounds to the mass spectrometer will yield better results. Cleaner samples also increase the longevity of the chromatographic columns. Detergents and salts are impediments to mass spectrometry detection.

New client and current client consultations are offered and encouraged for results provided by the TMPL Core. Basic result files for protein identifications, metabolomics and lipidomics are provided using in Excel worksheet and Word document formats. For many projects, basic statistical results such as MetaboAnalyst (https://www.metaboanalyst.ca/ ) are provided upon request. Protein/Gene pathways using DAVID Software also offered on request. Additional, more advanced, data processing for statistics should be provided by the client over and above the listed software suites in the core. The TMPL personnel will provide needed result data to collaborators to facilitate the use of Statisticians and Big Data Processing upon request. Coordination between collaborators and TMPL is highly encouraged.

TMPL Core uses the following software platforms in the core to generate appropriate data reports/results depending on the type of analyses: MetaboAnalyst, MS-Dial, MZMine and XCMS Online for metabolomics analyses; LipidView and PeakView for lipidomics analyses; ProteinPilot and PeakView for proteomics samples; MultiQuant, Analyst, PeakView for targeted assays. Programs such as XCMS Online and MetaboAnalyst provide statistical and pathway analyses that can be applied to all mass spectrometry data results.

There are many different modifications possible on amino acid residues. Many are possible to detect like phosphorylations, methylations, acetylations, oxidations, etc. via mass spectrometry in the TMPL Core. Some modifications however are not possible to detect based on the size, ionization and stability aspects of the addition. Additional processing steps and/or specific tailored mass spectrometers are utilized for different types of modifications.