Sample Preparation for Mass Spectrometry

Sample preparation remains one of the largest bottlenecks associated with mass spectrometry (MS) analysis, and consistent and reproducible sample preparation can make the difference between a successful analysis and a failed outcome. Thermo Scientific reagents and kits are optimized for sample preparation for every step of the process, from depletion strategies to reduce complexity, to protein extraction, enrichment, and clean-up for the isolation of low-abundance proteins. Post digestion, peptide enrichment, fractionation, and clean-up steps are often critical for proper analysis. The colorimetric and fluorometric Quantitative Peptide Assays enable sample normalization following digestion.

Break free from the long reaction times, high costs, and method complexity of manual proteomic sample preparation with the Thermo Scientific AccelerOme automated sample preparation platform. With factory-supplied reagents and kits and step-by-step onscreen instructions, high reproducibility and confident results are delivered for both label-free and tandem mass tag (TMT) multiplexing strategies with minimal effort providing several reagents to perform Label-free, TMT 11-plex, and TMT pro16-plex workflows at different sample scales. The AccelerOme platform is optimized to fit into the Thermo Scientific Orbitrap mass spectrometer ecosystem, streamlining the entire workflow from sample preparation to data processing.

Designed to simplify and standardize mass spectrometry sample preparation, whether you're working with 1 μg or up to 10 μg samples, the Thermo Scientific EasyPep Kit offers a comprehensive and user-friendly solution for mass spec sample prep on a large scale. With the Peptide Clean-up Plate, streamline peptide clean-up, embrace an efficient way of preparing your samples for downstream analysis.

• Efficient and reproducible processing of cultured mammalian cells and tissues for proteomic mass spectrometry (MS) analysis
• Optimized to process protein samples from 1–10 μg with a high yield of MS-ready peptides
• Kit includes a peptide clean-up plate and solutions to prepare detergent-free peptide samples for direct LC-MS analysis or further sample processing such as isobaric tag (e.g., TMT reagent) labeling, and high pH reversed-phase fractionation with TMT/TMTpro pooled samples

• Efficient contaminant removal from 10 μg to 100 μg peptide samples following enzymatic digestion
• Resin contained in each well provides excellent binding and recovery characteristics of peptide samples in preparation for mass spectrometry and other methods
• Plate format allows the processing of multiple samples (1–96) in parallel in less than 30 minutes

Order now

Sample preparation of peptides for MS analysis is complex, with numerous steps and non-standard protocols, resulting in variable sample quality and poor reproducibility. To address these issues, the Thermo Scientific EasyPep MS Sample Prep kits have been designed using a standardized workflow to help improve reproducibility while also saving hands-on and processing time.

Highlights

• Complete—includes pre-formulated reagents for lysis through digestion, peptide cleanup columns, and an optimized protocol for processing up to 20 samples (mini-column), 8 samples (maxi-column), or one 96-well plate
• Optimized—streamlined protocol and reagents minimize the number of steps and time it takes to process samples
• Flexible—reagents and protocol have been verified using cells, plasma, and tissue samples for 10 µg to 2 mg samples
• Time-saving—sample processing has been reduced from more than 1 day to less than 4 hours

Order now

The number of steps and time have been reduced through the addition of Thermo Scientific Pierce Universal Nuclease as a replacement for sonication to reduce viscosity from nucleic acids, a rapid “one pot” reduction/alkylation solution for cysteine modification (carbamidomethylation, +57.02), and a trypsin/Lys-C protease mix for more complete digestion. In addition, these kits include peptide cleanup columns (or plates) and buffers to prepare detergent-free peptide samples for MS analysis in less than 3 hours.

Compared to other methods and commercial kits, the EasyPep MS Mini Sample Prep kit produces MS ready peptides with higher protein yields and more unique protein group identifications. This is due to the high quality of the samples which have fewer contaminants and higher digestion efficiency compared to traditional overnight digestion with trypsin alone.

The EasyPep MS Sample Prep kits are available in three formats to support a wide range of sample numbers and input amounts. The EasyPep Mini and 96 MS Sample Prep kits are optimized to efficiently process protein samples of 10–100 µg with a high yield of MS-ready peptides. The EasyPep Maxi MS Sample Prep kit is optimized to process eight 0.5–2 mg protein samples ideal for phosphopeptide enrichment and other applications that require larger starting sample amounts. Alternatively, each Peptide Clean-Up Maxi Column can be used to process a combined set of isobaric tag-labeled samples (10–100 ug each, ≤2 mg total) for multiplex proteomic quantitation.