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.

AccelerOme: Automated sample preparation solution to simplify mass spectrometry sample preparation

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.

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

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.

Easy-Pep Sample Prep kit selection guide

 EasyPep Mini Sample Prep KitEasyPep Maxi Sample Prep KitEasyPep 96 MS Sample Prep KitAccelerOme Sample Prep KitsAccelerOme TMT11plex KitsAccelerOme TMTpro Kits
Cat No.A40006A45734A45733A50944 and A50945A50946, A50947, A50948A50949, A50950, A50951
Multiplexing   None11plex16plex
Quantity20 reactions8 reactions96 reactions   
Sample number   16,3611,3316,32
Sample typeCells, tissue, plasma, serumCells, tissue, plasma, serumCells, tissue, plasma, serumcells, tissue, plasma, purified proteins
Capacity10–100 µg0.5–2 mg 10–100 µg10-100ug10-30ug, 30-100ug
Process combined, multiplex set of isobaric tag-labeled samplesNot recommendedYes (10–100 ug each)Not recommended Pooling and clean-up performed on AccelerOme System

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 cellsSerum, plasma, or biofluidsTissuePurified proteinIntact protein


Abundant protein depletion 

Protein enrichment

Protein interaction crosslinking

Protein quantitation assays



Gel separationOptional 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

Related products for mass spec sample prep

For Research Use Only. Not for use in diagnostic procedures.