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Proteases for Mass Spectrometry


High-purity individual proteases for powerful analysis by mass spectrometry.

Pierce Proteases for Mass Spectrometr

These Thermo Scientific Pierce Proteases are small, convenient packages of individual, purified highly-specific proteases for use in various combinations to obtain better sequence coverage and protein identification for mass spectrometry.

Improvement in sequence coverage and overall protein characterization can result from improving peptide chromatographic or ionization properties. The masses of these larger peptides can be accurately measured at high charge states on popular high-resolution mass spectrometers, reducing the database search time and increasing the sequence coverage and confidence. Finally, larger peptides can be fragmented effectively by new fragmentation techniques like electron transfer dissociation (ETD) or electron capture dissociation (ECD) that leave post-translational modifications, like phosphorylation, intact.

Highlights:

  • Specific – proteases offer specific cleavage at multiple sites, enabling exploration of primary protein structure
  • Increased sequence coverage – Better protein characterization results from overlapping peptides with complementary chromatographic, ionization and fragmentation properties
  • Compatible – protocols are designed for MS applications
  • Robust – streamlined data processing and analysis improves interpretation and confidence

Applications:

  • In-gel digestion of cell lysates – multiple individual protease digestions improves the number and confidence of peptide and protein sequence identifications.
  • CID- and ETD-based fragmentation – powerful for indicating specific post-translational modifications, like phosphorylation and glycosylation.
  • Green stretches – quantitative and high confidence sequencing results are obtained only when multiple protease and fragmentation combinations are used.
  • Pairwise combinations – search results from two protease or fragmentation methods reveal complementary results. For example, trypsin digestion of Erk1 produces 87% coverage with CID, but when combined with LysC results, the total coverage increased to 93%.

Product Details:

Effective protein characterization and identification by mass spectrometry (MS) begins with protein digestion, thus generating peptide fragments. Trypsin is the protease of choice for accomplishing this task; however, digestion at additional sites with other proteases, such as GluC, LysC, AspN or chymotrypsin, can improve sequence coverage and generate overlapping peptides. For example, LysC cleavage after lysine residues generates larger peptides than those generated by trypsin alone, and chymotrypsin cleavage of hydrophobic regions provides complementary peptides to trypsin. These larger or more hydrophobic peptides interact more strongly with reverse-phase traps and columns and can improve detection of peptides with hydrophilic modifications like phosphorylation or glycosylation.

Table 1. Cleavage sites of various proteases.
Protease Cleavage Specificity
Trypsin Carboxyl side of arginine and lysine residues
LysN Amino side of lysine residues
LysC Carboxyl side of lysine residues
GluC Carboxyl side of glutamate
AspN Amino side of aspartate residues
Chymotrypsin Carboxyl side of tyrosine, phenylalanine, tryptophan and leucine

Table 2. Percent sequence coverage for Erk1. Results were obtained by digestion with individual proteases, MS/MS analysis with CID or ETD fragmentation methods, and pair-wise combination of search results in Proteome Discoverer MultiConsensus Reports for Erk1.
  Sequence Coverage (%)
Protease CID ETD
Trypsin 87 51
LysC 45 52
GluC 47 43
Trypsin alone + LysC alone 93 74
Trypsin alone + GluC alone 93 71

More Product Data

References:

  1. Biringer, R.G., et al.(2006). Brief Func Genom and Prot 5:144-153.
  2. Schlosser, A., et al.(2005). Anal Chem 77:5243-5250.
  3. Wu, S-L., et al.(2005). J Proteome Res 4:1155-1170.

Related Products:

Pierce Trypsin, MS Grade
Pierce Lys N Protease, MS Grade
In-Gel Tryptic Digestion Kit
In-Solution Tryptic Digestion and Guanidination Kit
Standard-grade Proteases (including Protease Agarose Resins)

Note: Trypsin (Part No. 90055) has been replaced by Pierce Trypsin, MS Grade.


Ordering Information
 
Product # Description Pkg. Size Instructions MSDS CofA Price
90051 Lys-C Protease, MS Grade
Formulation: Lyophilized enzyme powder
Sufficient For: Lot-specific activity
1 x 20µg Product Instructions for product #90051 Lys-C Protease, MS Grade MSDS for product #90051 Lys-C Protease, MS Grade Certificate of Analysis for product #90051 Lys-C Protease, MS Grade $308.00

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90053 Asp-N Protease, MS Grade
Formulation: Lyophilized enzyme powder
Sufficient For: At least 20,000 units/mg
2µg Product Instructions for product #90053 Asp-N Protease, MS Grade MSDS for product #90053 Asp-N Protease, MS Grade Certificate of Analysis for product #90053 Asp-N Protease, MS Grade $199.00

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90054 Glu-C Protease, MS Grade
Formulation: Lyophilized enzyme powder
Sufficient For: At least 500 units/mg
5 x 10µg Product Instructions for product #90054 Glu-C Protease, MS Grade MSDS for product #90054 Glu-C Protease, MS Grade Certificate of Analysis for product #90054 Glu-C Protease, MS Grade $185.00

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90056 Chymotrypsin Protease (TLCK treated), MS Grade
Formulation: Lyophilized enzyme powder
Sufficient For: At least 45 units/mg
4 x 25µg Product Instructions for product #90056 Chymotrypsin Protease (TLCK treated), MS Grade MSDS for product #90056 Chymotrypsin Protease (TLCK treated), MS Grade Certificate of Analysis for product #90056 Chymotrypsin Protease (TLCK treated), MS Grade $186.00

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Instructions | MSDS | CofA
Product Instructions | MSDS | CofA  

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