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Liquid chromatography-mass spectrometry (LC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are key techniques in proteomic research studies. High-quality preparation of protein to peptide samples for LC-MS and LC-MS/MS is essential for high-quality results. However, protein sample preparation of peptides for mass spectrometry analysis can be 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 developed with a standardized protocol to improve reproducibility and save hands-on and processing time. Thermo Scientific AccelerOme MS Sample Preparation kits have been developed for fully automated sample preparation with the AccelerOme Automated Sample Preparation Platform.
Our LC-MS protein sample preparation kits are available in different formats to facilitate different throughput needs with manual, automation-ready, and fully automated preparation kits.
Overview demonstrates the steps of this rapid mass spectrometry sample preparation kit for protein extraction, digestion, and peptide clean-up that can be completed in 2 to 4 hours.
Watch to learn some tips for preparing high-quality peptide samples for mass spectrometry analysis.
EasyPep kits are standalone mass spec sample preparation kits that are manual or in some cases ready for automation processing in an open system format.
AccelerOme kits are fully automated and designed exclusively for use with the AccelerOme Automated Sample Preparation Platform.
Product name | EasyPep Maxi Sample Preparation Kit | EasyPep Mini Sample Preparation Kit | EasyPep 96 MS Sample Preparation Kit | EasyPep 96 Micro MS Sample Preparation Kit | EasyPep Magnetic MS Sample Preparation Kit |
---|---|---|---|---|---|
Automation compatible | No | No | Yes | Yes | Yes |
Ready-for-injection | No | No | No | No | Yes |
Capacity | 0.5–2 mg | 10–100 µg | 10–100 µg | 1–10 µg | 15–100 µg |
Format | Column | Column | Plate | Plate | Beads |
Number of reactions | 8 | 20 | 96 | 96 | 20 and 96 |
Cat. No. | A45734 | A40006 | A45733 | A57864 | A57866 and A57867 |
Peptide clean-up | Pooling of TMT-labeled peptides | Individual samples | Individual samples | Individual samples | Individual samples |
Sample type | All EasyPep kits are designed for preparation of cells, tissue, plasma, serum, and purified protein sample types. |
Product name | AccelerOme Label-Free MS Sample Prep Kit | AccelerOme TMT11plex MS Sample Preparation Kit | AccelerOme TMTpro 16plex MS Sample Preparation Kit | |||||
---|---|---|---|---|---|---|---|---|
Cat. No. | A50944 | A50945 | A50946 | A50947 | A50948 | A50949 | A50950 | A50951 |
Sample number | 16 | 36 | 33 | 11 | 33 | 32 | 16 | 32 |
Capacity | 10–100 µg | 10–30 µg | 30–100 µg | 10–30 µg | 30–100 µg | |||
Multiplexing | None | 11 plex | 16 plex | |||||
Peptide clean-up | Individual samples | Pooling of TMT-labeled peptides and clean-up performed on AccelerOme System | ||||||
Sample type | All EasyPep kits are designed for preparation of cells, tissue, plasma, serum, and purified protein sample types. |
Product name | EasyPep Maxi Sample Preparation Kit | EasyPep Mini Sample Preparation Kit | EasyPep 96 MS Sample Preparation Kit | EasyPep 96 Micro MS Sample Preparation Kit | EasyPep Magnetic MS Sample Preparation Kit |
---|---|---|---|---|---|
Automation compatible | No | No | Yes | Yes | Yes |
Ready-for-injection | No | No | No | No | Yes |
Capacity | 0.5–2 mg | 10–100 µg | 10–100 µg | 1–10 µg | 15–100 µg |
Format | Column | Column | Plate | Plate | Beads |
Number of reactions | 8 | 20 | 96 | 96 | 20 and 96 |
Cat. No. | A45734 | A40006 | A45733 | A57864 | A57866 and A57867 |
Peptide clean-up | Pooling of TMT-labeled peptides | Individual samples | Individual samples | Individual samples | Individual samples |
Sample type | All EasyPep kits are designed for preparation of cells, tissue, plasma, serum, and purified protein sample types. |
Product name | AccelerOme Label-Free MS Sample Prep Kit | AccelerOme TMT11plex MS Sample Preparation Kit | AccelerOme TMTpro 16plex MS Sample Preparation Kit | |||||
---|---|---|---|---|---|---|---|---|
Cat. No. | A50944 | A50945 | A50946 | A50947 | A50948 | A50949 | A50950 | A50951 |
Sample number | 16 | 36 | 33 | 11 | 33 | 32 | 16 | 32 |
Capacity | 10–100 µg | 10–30 µg | 30–100 µg | 10–30 µg | 30–100 µg | |||
Multiplexing | None | 11 plex | 16 plex | |||||
Peptide clean-up | Individual samples | Pooling of TMT-labeled peptides and clean-up performed on AccelerOme System | ||||||
Sample type | All EasyPep kits are designed for preparation of cells, tissue, plasma, serum, and purified protein sample types. |
Designed to simplify and standardize protein sample preparation, Thermo Scientific EasyPep Kits include unique and optimized reagents that condense the timeline to generate peptides suitable for mass spectrometry analysis.
Highlights:
The number of steps and time have been reduced through multiple optimizations. First, Thermo Scientific Pierce Universal Nuclease replaces sonication to reduce viscosity from nucleic acids. Second, a collapsed and rapid incubation for cysteine modification has been employed with a “one pot” reduction/alkylation solution. Third, protein digestion has improved efficiency through the development of an optimized trypsin/Lys-C protease mixture to sample ratio. Finally, the kits include peptide cleanup columns (or plates) and buffers to prepare detergent-free peptide samples ready for mass spectrometry analysis in less than 4 hours.
Figure 1. Comparison of sample preparation for mass spectrometry analysis, using a traditional protein sample preparation workflow and EasyPep MS Sample Prep kits. Compared to a traditional workflow, the EasyPep MS Sample Prep kits provide the same high-quality data in less time and with half the number of manipulation steps. The optional step for TMTpro peptide labeling is indicated in both workflows.
Compared to other methods and commercial kits, the EasyPep MS sample prep kits produce peptides consistent with mass spectrometry analysis, having 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.
Figure 2. HeLa cell lysates prepared using the EasyPep Mini MS Sample Prep Kit compared to other commercially available kits. The EasyPep Mini MS Sample Prep Kit provides similar reduction and alkylation efficiencies with more protein identifications and better digestion efficiency (higher percentage of zero missed cleavages) than other methods per microgram of sample analyzed. Thermo Scientific Pierce HeLa Protein Digest Standard (Cat. No. 88328) was used as a control sample.
The EasyPep MS sample prep kits are available in five formats to support a wide range of sample numbers and input amounts.
The EasyPep Maxi MS Sample Prep Kit is optimized to process eight 0.5–2 mg protein samples excellent 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.
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 mass spectrometry-ready peptides.
The EasyPep 96 Micro MS Sample Prep Kit can process 96 protein samples of 1–10 µg in parallel for increased throughput. Included in the kit is a peptide clean-up plate and solutions to prepare detergent-free peptide samples for 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.
EasyPep Magnetic MS Sample Prep kits are developed for sample preparation processing using magnetic beads to bind and isolate proteins either on manual stands or on automated sample preparation platforms, including the KingFisher Instrument Platform.
Figure 3. The EasyPep MS sample prep kits use the same chemistry and standardized method to process purified proteins, cells, plasma, serum and tissues for downstream mass spectrometry-based proteomic applications. All formats can be used to generate samples for label-free quantitation, SureQuant targeted peptide assays, TMT reagent labeling, or phosphopeptide enrichment.
EasyPep Magnetic MS Sample Preparation kits are a mass spectrometry compatible magnetic bead sample preparation method. Our magnetic beads were specifically developed for mass spectrometry to be compatible with the harsh conditions of broad pH ranges and organic solvents. Other commercially available beads result in clumping and adherence to plastics used in the processing. Sample processing is the same as EasyPep column-based kits including lysis, nuclease, reduction, alkylation, digestion, binding and clean-up, but utilizing a magnetic bead procedure. A standard protocol, quality reagents, and specific beads designed for mass spectrometry protein sample preparation result in high reproducibility.
Magnetic bead sample preparation offers throughput options from manual processing to automation-friendly workflows including KingFisher instruments with protocols created for each instrument.
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.
Figure 5. Supporting kits and workflow of AccelerOme automated sample preparation system.
Product Name | Size | Cat. No. |
---|---|---|
EasyPep Lysis Buffer | 100 mL | A45735 |
Peptide Clean-up Plate | 96 reactions | A57865 |
Pierce Proteomic Magnetic Clean-up Beads | 5 mL | A57868 |
Pierce BCA Protein Assay | 500 mL | 23227 |
Pierce Dilution-Free Rapid Gold BCA Protein Assay | 250 mL | A55861 |
Pierce Quantitative Colorimetric Peptide Assay Kit | 500 assays | 23275 |
Pierce Quantitative Fluorometric Peptide Assay | 500 assays | 23290 |
Pierce Trypsin/Lys-C Protease Mix, MS Grade | 20 µg | A40007 |
For Research Use Only. Not for use in diagnostic procedures.