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.

EasyPep Mini, Maxi, and 96-well plate MS Sample Prep Kits–simplified sample preparation solutions for mass spectrometry

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 improve reproducibility while also saving hands-on and processing time.


  • 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

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Figure 1. Comparison of sample preparation for MS analysis, using a traditional workflow and EasyPep MS Sample Prep Kits. Compared to a traditional workflow, the EasyPep MS Sample Prep Kit provide the same high-quality data in less time and with half the number of manipulation steps. Option for TMTpro labeling in workflows indicated.

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.

Peptide and Protein IDs comparison of samples prepared using EasyPep kits
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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 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.

Input sample types and downstream applications for EasyPep MS sample prep kits
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Figure 3. The EasyPep MS Sample Prep kits use the same chemistry and standardized method to process plasma, cells, and tissues for downstream MS-based proteomic applications. Mini, 96-well, and maxi formats can be used to generate samples for label-free quantitation, SureQuant targeted peptide assays, TMT reagent labeling, or phosphopeptide enrichment.

Easy-Pep Sample Prep kit selection guide

  EasyPep Mini Sample Prep Kit EasyPep Maxi Sample Prep Kit EasyPep 96 MS Sample Prep Kit
Cat No. A40006 A45734 A45733
Format Column Column Plate
Quantity 20 reactions 8 reactions 96 reactions
Sample type Cells, tissue, plasma, serum Cells, tissue, plasma, serum Cells, tissue, plasma, serum
Capacity 10–100 µg 0.5–2 mg  10–100 µg
Process combined, multiplex set of isobaric tag-labeled samples Not recommended Yes (10–100 ug each) Not recommended

How-to-use video for EasyPep Mini MS Sample Prep kit

Use this rapid mass spec sample prep kit for protein extraction, digestion, and peptide clean-up in 2-4 hours.

  Cultured cells Serum, plasma, or biofluids Tissue Purified protein Intact protein


Abundant protein depletion  

Protein enrichment

Protein interaction crosslinking

Protein quantitation assays



Gel separation Optional   Optional

Protein digestion

Peptide enrichment/fractionation

Peptide cleanup

Detergent removal

Peptide quantitation assays

Products for mass spec sample prep

Cell lysis is the first step when extracting proteins for mass spectrometry applications. Fractionation may be required to enrich for proteins of interest or to study protein localization

Kits for albumin, top 2, or top 12 abundant protein depletion to aid in removing the most abundant proteins so that detection of lower abundant proteins is enhanced prior to digestion

Enrichment techniques include immunoprecipitation, enrichment by PTM (such as phosphoprotein enrichment), or active site labeling and enrichment using activity-based probes

The new colorimetric and fluorescent peptide quantitation assays help to normalize the peptide concentration of samples during each processing step following protein digestion

Proteases to break the proteins of interest into smaller fragments, or peptides for mass spec analysis

Successful analysis of low-abundant proteins and identification of post-translationally modified peptides requires multiple steps: enrichment, fractionation and/or clean up

A variety of specialty devices and resins that simply and efficiently desalt, buffer exchange and remove detergents from samples

The BCA protein assay is recommended prior to protein digestion to help normalize the protein concentration of samples during each processing step

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