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For life science research only. Not for use in diagnostic procedures.

Trypsin, recombinant, proteomics grade

Lyophilized, recombinant porcine trypsin from Pichia pastoris

Cat. No. 03 708 985 001 4× 25 ␮g y Version 04

Cat. No. 03 708 969 001 4× 100 ␮g Content version: March 2018
Store at ⫺15 to ⫺25°C

1. Product overview Application Trypsin, recombinant, proteomics grade is specially

designed for the digestion of proteins prior to mass spec-
Formulation Lyophilizate, stabilized trometric analysis.

Origin Recombinant porcine trypsin from Pichia pastoris.
This trypsin preparation is generated from the recombi-
nant Pichia pastoris strain and is thus free of chymotryp-
sin. It also exhibits extremely high specific activity.
Molecular weight 23 475 D
Stability Stable at ⫺15 to ⫺25°C until the expiration date printed
on the label. Following reconstitution in 10 mM HCl, Tryp-
sin, recombinant, proteomics grade is stable at ⫺15 to
⫺25°C for up to one month. After first reconstitution the
product must be stored in appropriate aliquots to avoid
repeated freezing and thawing.

Activity ⱖ 150 U/mg (Chromozym TRY) Quality control Trypsin, recombinant, proteomics grade is qualified for use
with in-gel digestion and mass spectrometric analysis.
Specificity Trypsin, recombinant, proteomics grade, is a serine
protease that specifically cleaves peptide bonds at the C-
terminal side of lysine and arginine.

Purity Highly purified enzyme preparation that is free of activity

from other proteases, particularly chymotrypsin, which is
absent from the formulation.

Fig. 2: MALDI-MS spectrum of bovine Carbonic Anhydrase II (EC 4.1.1.1) digested by Trypsin,
recombinant, proteomics grade. 500 ng Carbonic Anhydrase II was separated on a SDS poly-
acrylamide gel, the coomassie stained gel band containing Carbonic Anhydrase II was excised,
Fig. 1: Purity profile of Trypsin, recombinant, proteomics grade treated according to the protocol 2.2.1. and finally digested with 50 ng Trypsin, recombinant,
(Deconvoluted spectrum, insert: raw data). proteomics grade overnight at 37 °C. The extracted peptides were analyzed in reflector mode
using a Bruker Daltonics Reflex III/TOF detector. Mass values indicate identified peptides using
Mascot Search, IS1 resp. IS2 refer to internal standards, peaks at 842.51 and 2211.26 are due
Introduction Proteome research demands the use of highly purified, to autolysis of trypsin.
specific proteases. Proteins isolated and separated from a
given sample (e.g., blood, tissue) by 2-D electrophoresis or
liquid chromatographic methods must be cleaved in the
course of sample preparation. A reproducible cleavage 2. Procedures and required materials
pattern of digested proteins is a prerequisite for the clear
identification of these proteins in mass spectrometry (1). 2.1 Before you begin
Trypsin (EC 3.4.21.4) is the most frequently used enzyme
for this purpose. Trypsin is the prototype of serine endo- Additional • 1- to 10-␮l variable pipette
peptidases from the S1 family (2). It shows primary cleav- equipment • 1- to 100-␮l variable pipette
age specificity for peptide bonds located at the C-terminal required • 100– to 1000-␮l variable pipette
side of lysine and arginine. The catalytic efficiency (Kcat/ • Pipette tips
Km) for these basic side chains is at least 105 times greater • Desalting/concentrating pipette tips (e.g., C18 resin Zip-
than for other naturally occurring amino acids. The prefer- Tipscx pipette tips Millipore).
ence for Arg over Lys is 2- to 10-fold higher (3). Trypsin • Microplate (e.g., v-shape PP-microplate, Greiner)
displays maximum activity at pH 8.0−8.5, and is stabilized • pH meter
by calcium ions in the mM concentration range. It is bio- • Measuring cylinder, 100 ml
synthesized as a proenzyme (trypsinogen) and proteolyti- • Laboratory centrifuge
cally activated by enteropeptidase. In addition, it has an • Thermo mixer
“autolysis” loop that comprises residues 143-151; it is very • Vacuum concentrator
flexible in both trypsin and trypsinogen. Cleavage of this • Scalpel
loop at Lys 145 yields ␣-trypsin, which retains some cata-
lytic activity. This and other clipped forms are present in
most trypsin preparations (4).

0318.04340914001 1
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Additional • Ammonium hydrogen carbonate, NH4HCO3, MW 79.06 Preparation of kit
reagents • Dithiothreitol, DTT, MW 154.3 working solutions Solu- Preparation Storage
required • Water, ultrapure tion
For in-gel digestion 8 Recon- Reconstitute the lyophilizate ⫺15 to
• Iodoacetamide, MW 185.0 stituted (one bottle) to a trypsin ⫺25°C for
• Tris-(hydroxymethyl) aminomethane, Tris, MW 121.14 Trypsin concentration of 0.1 mg/ml up to one
• Trifluoro acetic acid, TFA, MW 114.0 Solution by adding 250 ␮l Reconsti- month
• Acetone, MW 58.08 tution Solution (Solution 6)
• Acetonitrile, MW 41.05 to 25 ␮g Trypsin, recombi-
For digestion in solution nant, proteomics grade,
or
• Tris-(hydroxymethyl) aminomethane, Tris, MW 121.14
adding 1 ml Reconstitution
• Guanidine hydrochloride, MW 95.53
• Iodoacetic acid, MW 185.9 Solution (Solution 6) to
100 ␮g Trypsin, recombi-
• CaCl2 × 2 H2O, MW 147.0
nant, proteomics grade.
• Sephadex G-25 pre-packed desalting column (e.g.,
Amersham Biosciences) 9 Trypsin Dilute Reconstituted Trypsin Prepare this
Digest Solution (Solution 8) to a solution
Additional • 2 N NH4OH Solution final trypsin concentration immedi-
solutions • 1 M HCl of 0.01 mg/ml by mixing it ately before
required Note: All reagents should be of analytical grade or with a 9-fold volume of you begin
higher quality. Digestion Buffer (Solution the tryptic
7) in a separate reaction vial digest.

2.2 In-gel protein digest

General For the identification of proteins in complex mixtures, the
procedure proteins are first separated by one- or two-dimensional 2.2.1 Gel processing
electrophoresis. The proteins are typically fixed and
stained according to standard or colloidal Coomassie G Procedure Please refer to the following table.
staining protocols. Spots or bands of proteins are excised Step Action
with a scalpel, cut into pieces, then transferred to micro-
plate wells. The gel pieces are washed, and the disulfide 1 Cut the Coomassie-stained protein band out of
bonds of the proteins are reduced and alkylated. After the the gel.
final washing steps, the gel pieces are dried under a vac- 2 Cut the piece of gel into smaller pieces of
uum and rehydrated in Trypsin Digest Solution. The tryptic approx. 1 mm2 in size.
digest is performed overnight at 37°C or 15–25°C. After
desalting using, for example, Zip-Tip technology, the sam- 3 Transfer the pieces into a microplate well.
ples are ready for spotting on a MALDI target. 4 Add 100 ␮l ultrapure water to the well, then
shake for 10 min at 15 –25°C on a thermo mixer.
Preparation of Please refer to the following table.
5 Aspirate the ultrapure water with a suitable
working solutions
# Solution Composition Preparation pipette.
1 Ammo- 100 mM, pH Dissolve 790.6 mg 6 Repeat the wash steps (steps 4 and 5).
nium 8.5 NH4HCO3 in 90 ml 7 Add 100 ␮l Destaining Solution (Solution 2) to
hydrogen water, adjust the pH to the well, then shake for 15 min at 15 –25°C on a
carbonate 8.5 with 2 M NH4OH, thermo mixer.
then use water to
8 Aspirate the supernatant with a suitable pipette.
bring the final volume
to 100 ml. 9 Repeat the destaining step until the Destaining
2 Destain- 30% acetoni- Bring 30 ml acetoni- Solution remains colorless (at least four times).
ing Solu- trile in trile to a final volume 10 Add 100 ␮l ultrapure water to the well, then
tion 100 mM of 100 ml with 100 mM shake for 15 min at 15 –25°C on a thermo mixer.
NH4HCO3 NH4HCO3 (Solution 1). 11 Aspirate the water with an Eppendorf pipette.
3 Reducing 10 mM DTT in Prepare a 100 mM
12 Repeat the wash steps (steps 10 and 11).
Solution 100 mM DTT solution by dis-
NH4HCO3 solving 15.4 mg DTT/ 13 Add 100 ␮l acetonitrile, then shake for 15 min at
ml in 100 mM 15 –25°C on a thermo mixer.
NH4HCO3 (Solution 1), 14 Aspirate the acetonitrile.
then dilute 10-fold
with 100 mM 15 Dry the sample in a microplate at 10 mbar and
NH4HCO3 (Solution 1). 37°C in a vacuum concentrator for 15 min.
4 Alkylating 54 mM Iodo- Dissolve 10 mg/ml
Solution acetamide in Iodoacetamide in 100
100 mM mM NH4HCO3 (Solu-
NH4HCO3 tion1).
5 Extraction Mix 350 ␮l acetoni-
Solution trile with 650 ␮l water
and 4 ␮l TFA.
6 Reconsti- 10 mM HCl Add 100 ␮l 1 M HCl to
tution 9.90 ml water, then
Solution mix.
7 Digestion 50 mM Add 500 ␮l acetonitrile
Buffer NH4HCO3 pH to 5 ml 100 mM
8.5/5% aceto- NH4HCO3 (Solution 1),
nitrile add ultrapure water to
a final volume of 10
ml.

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2.2.2 Reduction and carboxymethylation Preparation of Please refer to the following table.
working solutions
# Solution Composition Preparation
Procedure Please refer to the following table.
Step Action 1 Denatur- Tris 100 mM, Dissolve 57.3 g guani-
ation Buf- pH 8.5, 6 M dine HCl, 1.21 g Tris,
1 Add 20 ␮l Reducing Solution (Solution 3) per fer guanidine and 30.9 mg DTT in
well, then incubate and shake at 15 to 25°C for HCl, 2 mM 60 ml water, adjust the
5 min. DTT pH to 8.5 with 2 M
2 Incubate another 30 min at 50°C. HCl, add ultrapure
water to a final volume
3 Aspirate the supernatant. of 100 ml.
4 Add 100 ␮l acetonitrile per well, then incubate Note: Guanidine HCl
for 15 min at 15 –25°C. is harmful. Handle
5 Aspirate the supernatant. with care.
6 Add 20 ␮l Alkylating Solution (Solution 4), then 2 Alkylating 200 mM iodo- Dissolve 37.2 mg in
incubate for 15 min in the dark. Solution acetic acid 1 ml water. The solu-
tion should be color-
7 Aspirate the supernatant. less.
8 Add 100 ␮l Destaining Solution (Solution 2), Note: Keep the solu-
then incubate and shake for 10 min at 15 –25°C. tion in the dark.
9 Aspirate the supernatant. 3 Reconsti- 10 mM HCl Add 100 ␮l 1 M HCl to
tution 9.90 ml water, then
10 Add 50 ␮l Destaining Solution (Solution 2), then Solution mix.
incubate and shake for 15 min at 15 –25°C
4 Dilution 100 mM Tris, Dissolve 1.21 g Tris
11 Aspirate the supernatant. Buffer pH 8.5, 1 mM and 14.7 mg CaCl2 ×
12 Dry the sample in a microplate at 10 mbar and CaCl2 2 H2O in 70 ml water,
37°C in a vacuum concentrator for 15 min. adjust the pH to 8.5
with 2 M HCl, add
ultrapure water to a
final volume of 100 ml.
2.2.3 Digestion and peptide extraction Preparation of kit Please refer to the following table.
working solutions
Procedure Please refer to the following table. # Solution Preparation Storage
Step Action 5 Reconsti- Reconstitute the lyo- ⫺15 to ⫺25°C
1 Add 20 ␮l of freshly prepared Trypsin Digest tuted Tryp- philizate (one bottle) for up to one
Solution (Solution 9), then incubate overnight at sin to a trypsin concentra- month
15 –25°C. Solution tion of 0.1 mg/ml by
adding 250 ␮l Recon-
2 Add 20 ␮l Extraction Solution (Solution 5), then stitution Solution
incubate and shake at 15 –25°C for 40 min. (Solution 3) to 25 ␮g
3 Desalt the peptide extract with Desalting/con- Trypsin, recombinant,
centrating pipette tips (e.g., C18 resin ZipTipscx proteomics grade, or
pipette tips Millipore) according to the manufac- add 1,000 ␮l Reconsti-
turer’s instructions, then elute the peptides into tution Solution (Solu-
a fresh microplate. tion 3) to 100 ␮g
Trypsin, recombinant,
4 The sample is now ready for MALDI target
proteomics grade.
preparation.
6 Trypsin Dilute reconstituted Prepare this
Digest Trypsin solution (Solu- solution
Solution tion 5) to a final tryp- immediately
sin concentration of before you
2.3 Digestion of proteins in solution 0.02 mg/ml by mixing begin the
it with a 4-fold vol- tryptic digest.
General If a complete digestion of proteins in solution is desired, ume of Dilution Buffer
procedure proteins must first be denatured under reducing condi- (Solution 4) in a sepa-
tions. This is accomplished by adding chaotropes, such as rate reaction vial.
guanidine hydrochloride or urea, or strong denaturing
detergents, such as SDS followed by a disulfide reduction
and alkylation of the SH groups.
Before adding trypsin, guanidine hydrochloride or urea
and the excess alkylating reagent must be removed via a
desalting or dialysis step. Alternatively, the reaction mix-
ture can be treated with an excess of dithiothreitol to
neutralize the alkylating reagent, then diluted to guani-
dine hydrochloride or urea concentrations that are below
0.1 M or 2 M, respectively.
Partial digestion is performed by incubating the protein
in its native state with trypsin. Trypsin can be inactivated
by lowering the pH of the reaction below pH 4 through
the addition of acid (e.g., trifluoro acetic acid, TFA) or tri-
chloro acetic acid (TCA) precipitation. The degree of pro-
teolysis can be monitored by RP-HPLC.

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2.3.1 Tryptic digestion 3.2 References
Procedure Please refer to the following table. 1 Mann M., Hendrickson, R.C., Pandey A. (2001) Ann. Rev. Bio-
chem. 70, 437-473.
Step Action 2 Perone J.J. et al. (1995) Biochemistry 34, 1489-1499.
1 Dissolve the target protein in Denaturation Buf- 3 Craik, C.S. et al. (1985) Science 228, 291−297.
fer (Solution 1). 4 Higaki, J.N.; Light, A. (1985) Anal. Biochem. 148, 111−120.
Caution: The Denaturation buffer contains
guanidium HCl handle with care.
2 Heat at 50°C for 60 min.
3 Add half the sample volume of Alkylating Solu- Regulatory Disclaimer
tion (Solution 2), then incubate for 20 min at 15 – For life science research only. Not for use in diagnostic
25°C in the dark. procedures.
4 Exchange buffer against Dilution Buffer (Solu-
tion 4) by gel filtration using, for example, Seph- Disclaimer of Licence
adex G-25 pre-packed desalting columns (refer
to the manufacturer’s usage instructions); the For patent license limitations for individual products
protein concentration of the eluate should be please refer to: List of biochemical reagent products
higher than 0.1 mg/ml.
5 Add the Trypsin Digest Solution (Solution 6); the Trademarks
recommended amount of enzyme is 1/100 –1/20 All third party product names and trademarks are the
of the protein by weight. property of their respective owners.
6 Incubate for 2 –18 h at temperatures not exceed-
ing 37°C. Changes to previous version
7 Halting digestion (optional for partial digestion): Editorial Changes.
Stop the reaction by
• freezing the total digestion mixture or an
aliquot thereof at ⫺20°C, OR
• lowering the pH below pH 4 by adding TFA
or TCA to a final concentration of 10%.
8 The sample is now ready for RP-HPLC/ESI MS
analysis.

3. Appendix
3.1 Troubleshooting

Problem Possible cause Recommenda-

tion
No or incom- Resistance of tar- Vary trypsin:pro-
plete in-gel get protein against tein ratio, diges-
digestion (complete) tryptic tion times, and/or
cleavage temperature.
Desalting step Optimize desalt-
failed, peptide not ing/concentra-
eluting from desalt- tion procedure
ing/concentrating according to the
pipette tips manufacturer’s
instructions.
Inactivation of tryp- After first recon-
sin in reconstituted stitution store
form due to multi- trypsin in appro-
ple freeze-thaw priate aliquots to
cycles, or use of the avoid repeated
wrong reconstitu- freeze-thaw
tion buffer cycles.
MS spectra Autolytic tryptic Can be used to
containing peptides may be calibrate MS
additional generated instrument. In
trace signals case these signals
at 841.5 appear to be too
2210.1, and strong, reduce Contact and Support
5500.8 digest time and/or
temperature. To ask questions, solve problems, suggest enhancements and report new
applications, please visit our Online Technical Support Site.
Other con- Sample contamina- Improve environ-
taminating tion during han- mental conditions, To call, write, fax, or email us, visit sigma-aldrich.com, and select your home
peptides dling by, for clean equipment, country. Country-specific contact information will be displayed.
detected example, keratin wear gloves, and
from skin or hair work in a hood.

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