FAQ for New Users

Q: What should I do first?

A: If you’ve never used our facility before, please contact us and request a consultation before you begin preparing samples for submission. Proper experimental design and sample preparation are critical to the success of any proteomics analysis. We’ve made every effort to provide as much useful information as possible on our website, but no two experiments are exactly alike. A brief discussion can often result in an experimental design better suited to your research goals.

 

Q: How should my proteomics experiment be designed?

A: The specific research goals are often critical in optimizing experimental design. For example, the abundance of a protein of interest within the cell may dictate the choice of experimental platform or the amount of instrument time used to acquire data. The number of biological replicates included for each experimental condition is also very important. A minimum of three replicates is essential for quantitative analysis, with five or more recommended in many cases.

 

Q: Should I use TMT or DIA?

A: The selection of TMT (tandem mass tag) or DIA (data independent acquisition) analysis depends on how many samples you have and how many proteins you want to identify. TMT analysis is best suited for maximizing proteomic depth or for phospho-proteomic analysis, but is not practical with more than about 20 samples. DIA analysis is optimal for larger experiments with dozens or hundreds of samples.

 

Q: What types of sample can you analyze?

A: We can process and analyze cultured cells, tissue lysates, serum/plasma, IP/affinity pulldowns, gel bands, and many other sample types.

 

Q: How should I prepare my samples for analysis?

A: The compatibility of sample preparation protocols with our instrument systems is critical to obtaining high-quality data from any proteomics analysis. For example, even small amounts of non-ionic detergents can interfere with chromatography. If you have not submitted samples to our facility before, or you are submitting a new type of sample, please contact us before preparing your samples.

 

Q: How much protein do I need to submit?

A: Depending on the type of analysis, the ideal minimum sample requirement is between 50 and 200 micrograms total protein per sample.

 

Q: What if I don’t have enough protein or enough replicates?

A: We can often generate a good preliminary data set or a semi-quantitative comparison with limited sample numbers or protein amounts. Please contact us to discuss your options.

 

Q: How do I ship my samples?

A: All samples should be shipped on dry ice by Fedex Priority Overnight shipping. Sample tubes should be clearly labeled and packed securely in cryo/freezer boxes. We recommend using enough dry ice to keep samples frozen for up to 48 hours. Please notify us in advance and send a tracking number to ensure proper delivery.

 

Q: How long will it take to analyze my samples?

A: Our typical turnaround time for most sample sets is 4 to 6 weeks. This includes sample processing, data acquisition, and data analysis.

 

Q: How many proteins will you be able to identify from my samples?

A: Depending on sample type, sample quality, and the amount of instrument time allocated to data acquisition, we expect to identify and quantify from 2,500 to 10,000 proteins in cell or tissue samples, or from 500 to 1,500 proteins in serum or plasma samples.

 

Q: How much data analysis will you do?

A: Our standard services include database search, normalization, and differential expression analysis. We provide comprehensive reports including spreadsheets and interactive figures.

 

Q: How much will it cost to analyze my samples?

A: The exact cost depends on the experimental design and the number of samples. A 10-sample TMT analysis or 20-sample DIA analysis, for example, would cost about $2000 including sample processing, data acquisition, and data analysis. Please contact us for a quote for any specific experiment.

 

Q: Will you analyze my samples for free?

A: Our facility offers vouchers for free analysis (up to $2000) to researchers funded by NIGMS, funded through the NIGMS-IDeA Program, and early-stage/new investigators working within the mission of NIGMS. Please contact us for more information about eligibility and how to apply.

 

Q: Who do I contact for more information?

Samuel G. Mackintosh, Ph.D.
Associate Professor of Biochemistry and Molecular Biology
Managing Director, IDeA National Resource for Quantitative Proteomics
University of Arkansas for Medical Sciences

sgmackintosh@uams.edu

IDeAproteomics@uams.edu