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EasyPep™ Mini MS Sample Prep Kit Thermo Scientific™

The Thermo Scientific EasyPep Mini MS Sample Prep Kit provides pre-formulated reagents and a robust method for the preparation of high-quality samples for mass spectroscopy (MS) analysis in less than three hours.

Features of the EasyPep Mini MS Sample Prep Kit include:
Complete—includes pre-formulated reagents for lysis through digestion, peptide clean-up columns, and an optimized protocol for up to 20 samples
Optimized—streamlined protocol and reagents minimize the number of steps and time time needed to process samples
Flexible—reagents and protocol have been verified using cells, plasma, and tissue samples for 10 to 100 µg samples
Time-saving—sample processing time reduced from more than one day to less than three hours
Compatible—final preparation is ready for direct MS analysis and other downstream applications, including TMT labeling

The EasyPep Mini MS Sample Prep Kit enables efficient and reproducible processing of cultured mammalian cells and tissues for proteomic MS analysis. The kit contains pre-formulated buffers, MS-grade enzyme mix, peptide clean-up columns, and an optimized protocol to generate MS-compatible peptide samples in less than three hours. The kit is optimized to process protein samples from 10–100 µg with a high yield of MS-ready peptides.

The sample preparation of peptides for MS analysis is complex, with numerous steps and varied protocols, resulting in sample variability in both quality and quantity. This kit has been designed to improve reproducibility while saving hands-on and processing time. The number of steps and processing time have been reduced through the addition of Universal Nuclease to reduce viscosity from nucleic acids (replacing sonication), 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, the kit includes Peptide Clean-up columns and buffers to prepare detergent-free peptide samples for MS analysis. The optimized reagents and protocol produce high-quality peptides that are compatible with TMT labeling and other downstream applications, or are ready for MS analysis.

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Pierce™ Trypsin/Lys-C Protease Mix, MS-Grade Thermo Scientific™

Thermo Scientific Pierce Trypsin/Lys-C Protease Mix, MS-Grade, is a mass spectrometry (MS)-grade serine endoproteinase mixture of trypsin and LysC that can be used for concurrent digestion of proteins for more efficient digestion than with trypsin alone.

Features of Pierce Trypsin/Lys-C Protease Mix, MS-Grade, include:
Enhanced digestion—enzyme combination reduces tryptic missed cleavages
Convenient—trypsin and LysC proteases provided at an optimized ratio for digestion in a combined-use format
Exceptional selectivity—trypsin has >95% C-terminal lysine and arginine specificity; LysC has >90% C-terminal lysine cleavage specificity
Stable—enzyme mixture provided in a lyophilized format

Protein characterization, identification, and quantification by MS begins with efficient, reproducible protein digestion. Although trypsin is routinely used for protein digestion, this protease alone is not sufficient to fully digest proteins at the carboxyl-end of lysine and arginine residues. Therefore, Lys-C protease is commonly combined with trypsin to sequentially digest proteins with fewer missed cleavages. Pierce Trypsin/Lys-C Protease Mix is a lyophilized mixture of trypsin and LysC proteases that has been optimized to improve digestion efficiency of proteins. It is provided in flexible formats of 20 µg, 5 x 20 µg, or 100 µg, and is also included in the EasyPep Mini MS Sample Prep Kit.

The MS-grade trypsin protease in this mix is derived from porcine pancreatic extracts and has been TPCK-treated to eliminate chymotryptic activity and methylated to improve stability during digestion. The MS-grade Lys-C protease is a highly purified native enzyme from <Lysobacter enzymogenes. Unlike trypsin, Lys-C can cleave lysines followed by prolines, making it ideal for use in combination with other proteases for optimal protein digestion. When used as a mixture, digestion can be completed in as little as 1.5–3 hours or up to overnight, depending on enzyme to protein ratio. This lyophilized enzyme mixture is stable for one year when stored at -20°C.

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EasyPep Mini MS Sample Prep Kit
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Chloroacetamide, No-Weigh Format

Pierce™ LC-MS/MS System Suitability Standard (7 x 5 Mix) (0.5 pmol/µL) Thermo Scientific™

The Pierce LC-MS/MS System Suitability Standard (7 x 5 mixture) contains seven HeavyPeptide AQUA Ultimate peptides provided at five dilutions distinguished by differential isotopic labeling to assess sensitivity and dynamic range of LC-MS/MS systems. The standard contains 7 of 15 Pierce Retention Time Calibration Mixture (Cat. No. 88320) peptides. Each of the seven peptides has five isotopologue versions containing no heavy, 1 heavy, 2 heavy, 3 heavy, and 4 heavy isotope-labeled amino acids. The isotopologues for each peptide are provided at a distinct concentrations to generate seven standard curves to assess system performance. The 7 x 5 mixture can be used with Skyline software (www.thermoscientific.com/pinpoint) to assess dynamic range, linearity, and lower limit of quantitation (LLOQ).

Pierce LC-MS/MS System Suitability Standard (7 x 5 mixture) features include:
High quality—contains five sets of seven HeavyPeptide AQUA Ultimate peptides, with each peptide distinguishable through unique isotopologue labeling
Optimized—enables scheduling of MS acquisition windows for improved quantification and increased multiplexing
Quantitative—enables assessment of dynamic range of instrument and instrument sensitivity
Predictive—enables assessment of chromatography and MS instrument performance

Applications:
• Standard for data-dependent acquisition (DDA)
• Standard for targeted MS (e.g., parallel-reaction monitoring (PRM))
• Optimization of LC parameters
• Identification of total peptide elution window
• Optimization of MS parameters
• Assessment dynamic range of nano or capillary flow LC-MS/MS systems

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EASY-Spray LC Analytical Column
Acclaim PepMap 100 C18 Trap Column, NanoViper
Pierce TMT11plex Yeast Digest Standard

General reference:
1. Krokhin OV, Spicer V. Peptide retention standards and hydrophobicity indexes in reversed-phase high-performance liquid chromatography of peptides. Anal Chem. 2009 81(22):9522-30.

EasyPep™ 96 MS Sample Prep Kit Thermo Scientific™

The Thermo Scientific EasyPep 96 MS Sample Prep Kit provides pre-formulated reagents and a robust method for the preparation of high-quality samples for proteomic MS analysis in a high throughput format.

Features of the EasyPep 96 MS Sample Prep Kit include:
Complete—includes pre-formulated reagents for lysis through digestion with peptide clean-up in a 96-well plate format
Optimized—streamlined protocol and reagents minimize the number of steps and time needed to process samples
Flexible—reagents and protocol have been verified using cells, plasma, and tissues for larger sample amounts ranging from 10 to 100 µg
Time-saving—sample processing time reduced from more than one day to less than four hours in a 96-well sample processing format
Compatible—final preparation is ready for direct MS analysis and other downstream applications, including TMT labeling

The EasyPep 96 MS Sample Prep Kit enables efficient and reproducible processing of cultured mammalian cells, tissues, and plasma for proteomic MS analysis. The kit contains pre-formulated buffers, MS-grade enzyme mix, peptide clean-up plate, and an optimized protocol to generate MS-compatible peptide samples in less than four hours. The kit is optimized to process protein sample sizes from 10 to 100 µg with a high yield of MS-ready peptides in a higher throughput format.

The sample preparation of peptides for MS analysis is complex, with numerous steps and varied protocols, resulting in variability in both quality and quantity of peptides. This kit has been designed to improve reproducibility while saving hands-on and processing time. MS sample preparation has been simplified and standardized through the addition of Universal Nuclease to reduce viscosity from nucleic acids (replacing sonication), 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, the kit includes a Peptide Clean-up plate and buffers to prepare detergent-free peptide samples for MS analysis. The optimized reagents and protocol produce high-quality peptides that are directly compatible with TMT labeling, phosphopeptide enrichment, fractionation, or are ready for MS analysis.

EasyPep™ Maxi Sample Prep Kit Thermo Scientific™

The Thermo Scientific EasyPep Maxi MS Sample Prep Kit provides pre-formulated reagents and a robust method for the preparation of high-quality samples for proteomic MS analysis to accommodate larger sample amounts.

Features of the EasyPep Maxi MS Sample Prep Kit include:
Complete—includes pre-formulated reagents for lysis through digestion with peptide clean-up columns
Optimized—streamlined protocol and reagents minimize the number of steps and time needed to process samples
Flexible—reagents and protocol have been verified using cells and tissues for larger sample amounts ranging from 0.5 to 2 mg
Time-saving—sample processing time reduced from more than one day to less than four hours
Compatible—final preparation is ready for direct MS analysis and other downstream applications, including TMT labeling

The EasyPep Maxi MS Sample Prep Kit enables efficient and reproducible processing of cultured mammalian cells and tissues for proteomic MS analysis. The kit contains pre-formulated buffers, MS-grade enzyme mix, peptide clean-up columns, and an optimized protocol to generate MS-compatible peptide samples in less than four hours. The kit is optimized to process protein sample sizes from 0.5 to 2 mg with a high yield of MS-ready peptides ideal for phosphopeptide and other applications that require larger starting sample amounts.

The sample preparation of peptides for MS analysis is complex, with numerous steps and varied protocols, resulting in variability in both quality and quantity of peptides. This kit has been designed to improve reproducibility while saving hands-on and processing time. MS sample preparation has been simplified and standardized through the addition of Universal Nuclease to reduce viscosity from nucleic acids (replacing sonication), 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, the kit includes Peptide Clean-up columns and buffers to prepare detergent-free peptide samples for MS analysis. The optimized reagents and protocol produce high-quality peptides that are directly compatible with TMT labeling, phosphopeptide enrichment, fractionation, or are ready for MS analysis.

High Select™ HSA/Immunoglobulin Depletion Resin Thermo Scientific™

Thermo Scientific High Select HSA/Immunoglobulin Depletion Resin decreases the albumin and antibody components that are abundant in human plasma samples, helping prepare the samples for mass spectrometry or 1D or 2D electrophoresis.

Features of HSA/Immunoglobulin Depletion Resin include:
• Flexible—provided in bulk format for depletion of user-defined amount of human plasma sample
• Optimized—removes >95% of IgG and >95% of albumin
• Fast—process samples in ~10 minutes
• Economical—cost-effective bulk format

High Select HSA/Immunoglobulin Depletion Resin uses highly specific immobilized anti-HSA and anti-immunoglobulin antibodies (IgG, IgA, IgM, IgD, and IgE) to remove human serum albumin (HSA) and all major subclasses of immunoglobulins from serum or plasma. The resin is provided in an economical bulk format that may be used to fill columns or plates, depending on the sample volumes.

Analysis of human fluids is often complicated by the presence of high concentrations of albumin and IgG that can make up more than 70% of total serum protein. Removal of these proteins is often essential for the study of low-abundant proteins. High Select HSA/Immunoglobulin resin can deplete greater than 95% of HSA and 95% of IgG. Columns or plates are filled with resin based on the needs of the user, and samples are processed in approximately 10 minutes. The depletion of highly abundant proteins enables the detection of low abundant proteins in samples and subsequent identification by mass spectrometry or 1D or 2D gel electrophoresis.

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Pierce™ Reserpine Standard for LC-MS Thermo Scientific™

Thermo Scientific Pierce Reserpine Standard for LC-MS is a precise concentration of reserpine specifically designed for performance evaluation of mass spectrometers, including the Thermo Scientific ion trap and TSQ series of instruments.

Features of Reserpine Standard for LC-MS:

Convenient—provided pre-diluted and requires minimal additional dilutions to reach target concentration for injection
Safe handling—unlike glass ampules, cap can be easily removed and replaced when withdrawing solution
High-purity—mass spectrometry grade reagent in a non-leachable screw-cap vials
Stable—store at 4°C for up to one year

Pierce Reserpine Standard for LC-MS is a pre-diluted liquid formulation ideal to quickly perform installation specification tests of Thermo Scientific and other manufacturers' mass spectrometers. The standard is provided in a concentration of 100pg/µL in 50% isopropyl alcohol and requires minimal additional dilutions. The product is provided in a pack of 5 x 1 mL glass amber vials with PTFE-lined screw caps. Pierce Reserpine Standard for LC-MS is manufactured at an ISO 9001 facility and each lot is quality controlled with strict specifications.

Pierce Reserpine Standard for LC-MS can be used to assess performance of mass spectrometers, including the Thermo Scientific ion trap series and the TSQ series.

EasyPep™ Lysis Buffer Thermo Scientific™

Thermo Scientific EasyPep Lysis Buffer has been optimized for use with the EasyPep MS Sample Preparation kits to yield high quality proteomic samples for MS analysis.

Features of EasyPep Lysis Buffer include:
Optimized—efficient lysis of cells, tissues and plasma for MS proteomic sample preparation
Compatible—designed for use with EasyPep MS Sample Prep kits and MS sample preparation
Easy to use—pre-formulated reagent for efficient protein extraction

EasyPep Lysis Buffer has been formulated to efficiently extract proteins from cells, tissue, and plasma for MS sample preparation. This lysis reagent has been designed specifically for use with the EasyPep MS Sample Preparation kits and is compatible with the Pierce BCA or Rapid Gold BCA protein assays.

High Select™ Top14 Abundant Protein Depletion Mini Spin Columns Thermo Scientific™

Thermo Scientific High Select Top14 Abundant Protein Depletion Resin decreases the abundant protein and antibody components of human plasma samples, helping prepare the samples for mass spectrometry or 1D or 2D electrophoresis. The resin is provided here in a convenient single-use mini spin column format for the treatment of 10 µL samples.

Features of Top14 Abundant Protein Depletion Resin include:
• Flexible—mini spin column format is scaled and optimized for treating 10 µL human plasma samples
• Optimized—removes >95% of IgG and >95% of albumin, plus 12 other abundant proteins (Top 14)
• Fast—process samples in ~10 minutes
• Economical—cost-effective spin columns are priced for single use
• Reduce variability—one-time use prevents protein carryover and experimental variability

High Select Top14 Abundant Protein Depletion Resin uses highly specific immobilized antibodies to remove human serum albumin (HSA), albumin, IgG, IgA, IgM, IgD, IgE, kappa and lambda light chains, alpha-1-acidglycoprotein, alpha-1-antitrypsin, alpha-2-macroglobulin, apolipoprotein A1, fibrinogen, haptoglobin, and transferrin from serum and plasma.. The resin is provided in an economical and convenient spin column format specifically designed for one-step processing and single use.

Analysis of human fluids is often complicated by the presence of high concentrations of albumin and IgG that can make up more than 70% of total serum protein. Removal of these proteins is often essential for the study of low-abundant proteins. High Select Top14 Abundant Protein Depletion Resin can deplete greater than 95% of the 14 most abundant proteins in serum. Samples are loaded in a pre-filled disposable spin column and processed in approximately 10 minutes. The depletion of highly abundant proteins enables the detection of low abundant proteins in samples and subsequent identification by mass spectrometry or 1D or 2D gel electrophoresis.

Invitrosol™ LC/MS Protein Solubilizer Kit Invitrogen™

The Invitrosol™ LC/MS (Liquid Chromatorgraphy/Mass spectrometry) Protein Solubilizer Kit contains a novel, proprietary surfactant blend for simplified preparation of hydrophobic and hydrophilic proteins or peptides for ESI (Electrospray Ionization) mass spectrometry (MS) experiments.

Optimized for LC/MS analysis, Invitrosol" LC/MS Protein Solubilizer greatly improves data quality by removing detergents that are incompatible with MS ionization techniques (e.g. CHAPs, Triton-X, SDS, etc.). Invitrosol™ LC/MS Protein Solubilizer is compatible with enzymatic proteolysis and improves statistical confidence in mass spectral results for hydrophobic proteins and peptides. Additionally, Invitrosol™ LC/MS Protein Solubilizer does not interfere with your chromatography separations (Figure 1) and does not contaminate LC/MS instrumentation.

Pierce™ LysN Protease, MS Grade Thermo Scientific™

Thermo Scientific Pierce LysN Protease, MS Grade, is highly purified native Lys-N protease that has been validated for maximum activity and stability in proteomic applications.

Features of LysN Protease, MS Grade:

Thermostable – provides better digestion at higher temperatures (e.g., 50°C) in less time
Complementary to tryptic digests cleaves the opposite side of lysine from trypsin
High purity – no additional (off-target) protease activity detected
N-terminal lysine cleavage specificity – at least 90% for a complex protein sample
Versatile – enzyme is effective at many temperatures and in denaturing conditions
Stable – provided in a lyophilized format

Thermo Scientific Pierce LysN is a mass spectrometry (MS)-grade zinc metalloprotease derived from Grifola frondosa. The native Pierce LysN Protease has been highly purified to improve stability, specific activity, and cleavage selectivity. Unlike trypsin, LysN protease cleaves at the amino-terminus of lysine residues. As a result, the peptides generated by LysN are longer than those generated by trypsin and have more prevalent charged amino terminal peptide fragments. Additionally, LysN protease is more promising for epigenetic MS applications than LysC or trypsin because it is capable of cleaving methylated lysines [1]. The thermostability and chemical compatibility with denaturants make LysN protease ideal for digestion of complex protein samples for “shotgun” proteomics.

Applications:
• Improved sequence coverage of protein digests
• De novo sequencing with collision induced dissociation (CID)
• Epigenetic studies
• In-solution digestion of proteins

LysN protease is active over a wide range of temperatures and denaturing conditions. Efficient protein digestion can be completed in 2 hours at 50°C or 4 hours at 37°C, however, digestion is possible at both lower and higher temperatures. LysN also remains active under moderate denaturing conditions including 0.1% SDS, 6M urea or heating to 70°C. Maximal LysN activity occurs at pH 7 to 9. The lyophilized enzyme is stable for 2 years when stored at -20°C, and reconstituted stock solutions of LysN are stable at -80°C for 2 years or -20°C for one year without significant loss in activity.

High Select™ HSA/Immunoglobulin Depletion Mini Spin Columns Thermo Scientific™

Thermo Scientific High Select HSA/Immunoglobulin Depletion Resin decreases the albumin and antibody components that are abundant in human plasma samples, helping prepare those samples for mass spectrometry or 1D or 2D electrophoresis. The resin is provided here in a convenient single-use mini spin column format for the treatment of 10 µL samples.

Features of HSA/IgG Depletion Resin include:
• Flexible—mini column format is scaled and optimized for treating 10 µL human plasma samples
• Optimized—removes >95% of IgG and >95% of albumin
• Fast—process samples in ~10 minutes
• Economical—cost-effective spin columns are priced for single use
• Reduce variability—one-time use prevents protein carryover and experimental variability

High Select HSA/Immunoglobulin Depletion Resin uses highly specific immobilized anti-HSA and anti-Immuoglobulin antibodies (IgG, IgA, IgM, IgD, and IgE) to remove human serum albumin (HSA) and all major subclasses of immunoglobulins from serum and plasma. The resin is provided in an economical and convenient spin column format specifically designed for one-step processing and single use.

Analysis of human fluids is often complicated by the presence of high concentrations of albumin and IgG that can make up more than 70% of total serum protein. Removal of these proteins is often essential for the study of low-abundant proteins. High Select HSA/Immunoglobulin Depletion Resin can deplete greater than 95% of HSA and 95% of IgG. Samples are loaded in a pre-filled disposable spin column and processed in approximately 10 minutes. The depletion of highly abundant proteins helps enable the detection of low abundant proteins in samples and subsequent identification by mass spectrometry or 1D or 2D gel electrophoresis.

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Pierce™ HeLa Protein Digest Standard Thermo Scientific™

The Thermo Scientific Pierce HeLa Protein Digest Standard is a highly validated mammalian protein digest that may be used as a quality control sample for mass spectrometry (MS) analysis of complex proteomic samples.

Features of HeLa Protein Digest Standard:

Positive control sample—complex mammalian proteome sample protein digest (>15,000 proteins) from the HeLa S3 cell line
Thorough tryptic digestion—prepared using both LysC and trypsin to ensure less than 10% tryptic missed cleavages
Validated peptide quality—less than 10% methionine oxidation and less than 10% lysine carbamylation
Rigorously tested—high-quality, consistent protein digest guaranteed and documented via lot-specific certificates of analysis
Stable—provided in a stable lyophilized format

The protein digest standard is derived from a well-established adenocarcinoma reference HeLa S3 cell line. HeLa S3 cells express over 15,000 proteins with relevant post-translational modifications, making this cell line an ideal standard for complex proteome mass spectrometry applications. The cell lysate has been digested with both LysC and trypsin to minimize tryptic missed cleavages and improve protein sequence coverage. Moreover, unlike other commercially available protein digests for MS, the Pierce HeLa Protein Digest Standard meets stringent quality testing specifications, including peptide quality, digestion efficiency, and lot-to-lot digest uniformity.

Applications:
• Qualitative LC assessment
• LC/MS standardization
• LC/MS method development
• TMT™ Reagent method development

The Pierce HeLa Protein Digest Standard is a lyophilized tryptic peptide mixture that can be used as a quality control standard for liquid chromatography (LC) separation, MS method development and MS performance benchmarking. The digest is specifically formulated for LC/MS experiments and does not contain salts or detergents. Using the digest standard routinely before analysis of complex samples makes it possible to monitor and normalize LC/MS performance between samples and over time.

Pierce™ Quantitative Fluorometric Peptide Assay Thermo Scientific™

The Thermo Scientific™ Pierce™ Quantitative Fluorescent Peptide Assay is a sensitive, mix-and-read fluorescent microplate assay for the quantitative measurement of peptides and peptide mixtures.

Sensitive—accurately detect as little as 5.0 µg/mL of single peptides or peptide mixtures
Robust— assay performance rigorously tested using both peptides and peptide digest mixtures
Robust peptide digest standard—kit includes a validated peptide digest standard for improved reproducibility of quantitation
Compatible—works with many reagents, including those used in mass spectrometry sample preparation
Convenient—easy mix-and-read format and stable fluorescent signal that may be read in as little as 5 minutes up to several hours

The Pierce Quantitative Fluorescent Peptide Assay reagents include peptide assay buffer, fluorescent peptide labeling reagent, and a peptide digest assay standard for the quantitative measurement of peptide concentrations. In this assay, peptides are specifically labeled at the amino-terminus using an amine-reactive fluorescent reagent, and the fluorescently labeled peptides are detected using ex390/em475.

Because of the labeling mechanism of the fluorescent assay reagent, this assay is suitable for the quantitative measurement of synthetic peptides as well as peptide digest mixtures. A high quality peptide digest reference standard is included for use in generating linear standard curves and as a calibration control for improved accuracy and reproducibility. This sensitive assay requires only 10 µL of sample, produces a linear response with increasing peptide concentrations (5–1000 μg/mL), and results in a stable final fluorescence that can be detected in as little as five minutes.

Applications:
• Recommended for use with peptide mixtures and synthetic peptides with an unblocked amino-terminus (amino-terminus-labeled peptides, such as TMT-labeled peptides, are not compatible with this assay)
• Normalizing sample concentrations for quantitative downstream applications
• Normalizing sample loading volumes for LC, MS, and LC/MS applications
• Measuring recovery after peptide clean-up procedures.

Pierce™ Graphite Spin Columns Thermo Scientific™

Thermo Scientific Pierce Graphite Spin Columns improve phosphopeptide analysis by efficiently binding hydrophilic peptides and efficiently removing urea, salts and other contaminants before mass spectrometry analysis.

Features of Graphite Spin Columns:

• Convenient spin format for parallel processing of multiple samples
• High-binding capacity with excellent recovery of up to 100 µg of hydrophilic peptides per column
• Porous graphite resin for cleaning up phosphopeptide samples before MS analysis

Pierce Graphite Spin Columns enable fast and efficient capture, concentration, desalting and elution of hydrophilic peptides in less than 10 minutes. These columns are ideal for improving mass spectrometric (MS) analyses of samples from protein digests), strong-cation exchange fractions, and enriched phosphopeptides eluted from titanium dioxide and immobilized metal affinity chromatography (IMAC) columns and tips.

The Pierce Graphite Spin Columns improve phosphopeptide analysis by efficiently binding hydrophilic peptides and efficiently removing urea, salts and other contaminants before MS analysis. The C18 resins and C18 tips that are commonly used to desalt peptides are excellent for use with hydrophobic peptides but do not efficiently capture hydrophilic peptides, like phosphopeptides, resulting in enrichment of only hydrophobic fragments. The Pierce Graphite Spin Columns address this issue and are ideal for matrix-assisted laser desorption ionization (MALDI) or nanoelectrospray ionization techniques.
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