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Instructions for Use - Glyco Kit MB-LAC AIA - Bruker

Instructions for Use - Glyco Kit MB-LAC AIA - Bruker

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CARE products are designed <strong>for</strong> supporting our customers worldwide<br />

with high-quality consumables, accessories and dedicated kits.<br />

The CARE product range is specifically optimized and certified<br />

<strong>for</strong> all <strong>Bruker</strong> Daltonics systems.<br />

www.care-bdal.de / www.care-bdal.com<br />

<strong>Instructions</strong> <strong>for</strong> <strong>Use</strong><br />

<strong>Glyco</strong> <strong>Kit</strong> <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong><br />

As part of <strong>Bruker</strong> Daltonics’ CLINPROT system the <strong>Glyco</strong> <strong>Kit</strong>s are especially designed <strong>for</strong><br />

sophisticated glycoprotein studies and clinical proteomics research. Super-paramagnetic glycobeads<br />

are functionalized with either boronic acids (BA) or lectins like concanavalin A (Con A),<br />

wheat germ agglutinin (WGA), Lens Culinaris Agglutinin (LCA), artocarpus integrifolia (<strong>AIA</strong> or<br />

Jacalin). With a combination of different optimized beads, intelligent enrichment strategies <strong>for</strong><br />

glycosylated peptides and proteins prior to mass spectrometry enable advanced glycomic<br />

analyses. With the <strong>Bruker</strong> Daltonics’ mass spectrometry workflow, glycoproteins from complex<br />

samples like human serum can be reliably and reproducibly captured and identified within a<br />

dynamic range of eight orders of magnitudes. Besides glycoprotein identification and<br />

characterization as well as glyco-structure predictions, CLINPROT glyco-beads are suitable <strong>for</strong><br />

sample fractionation prior to profiling analyses.<br />

Sample<br />

<strong>Bruker</strong> Daltonics CLINPROT magnetic glyco-beads<br />

Separation on protein level<br />

(e.g. ConA, LCA, WGA, <strong>AIA</strong> or BA)<br />

LC-MALDI<br />

Tryptic digestion<br />

CLINPROT TM bead<br />

purification<br />

(e.g. C8, WCX, IMAC-Cu)<br />

<strong>Bruker</strong> Daltonics CLINPROT magnetic glyco-beads<br />

Separation on peptide level<br />

(ConA)<br />

PNGase F digestion<br />

LC-MALDI<br />

LC-MALDI<br />

Identification of<br />

glycoproteins<br />

Structural characterization<br />

of N-glycosylated peptides<br />

Identification of<br />

N-glycosylation sites<br />

<strong>Glyco</strong>-Profiling<br />

Fig. 1: Range of possible experimental strategies <strong>for</strong> the application of <strong>Bruker</strong> Daltonics’ CLINPROT TM<br />

magnetic glyco-beads.<br />

Page 1 of 19


Figure 1 exemplarily depictured possible experimental strategies to facilitate the identification of<br />

glyco-proteins, to enable the detection of N-glycosylation sites, to support the structural<br />

characterization of N-glycosylated peptides and to per<strong>for</strong>m glyco-profiling studies in the clinical<br />

context.<br />

General In<strong>for</strong>mation<br />

<strong>Glyco</strong>sylation is the most common post-translational modification of proteins, playing a key role in<br />

protein folding, stability, solubility, activity and molecular recognition. Altered glycosylation is known<br />

to act as an indicator or effector in pathologic mechanisms with potential impact on diagnosis and<br />

therapy of human diseases. Immunity to certain infectious diseases, prion diseases and cancer<br />

can all be associated with abnormal glycosylation patterns. As an example, increased branching<br />

and sialylation of N-linked glycans on cancer cells are potential tumor markers in molecular<br />

diagnostics.<br />

<strong>Bruker</strong> Daltonics’ CLINPROT magnetic glyco-beads, specifically functionalized with lectins or<br />

boronic acids that bind to various structural motifs, facilitate the selective isolation of different<br />

glycoproteins out of complex biological sources (Fig. 1). <strong>Bruker</strong> Daltonics has developed workflows<br />

combining the specific pre-fractionation employing glyco-specific magnetic particles, e.g. ConA,<br />

WGA, LCA or boronic acids coated beads, and LC-MALDI analysis to identify glycoproteins, to<br />

locate N-glycosylation sites and to get structural in<strong>for</strong>mation about N-glycosylated peptides.<br />

<strong>MB</strong>-<strong>LAC</strong><br />

Con A<br />

<strong>MB</strong>-<strong>LAC</strong><br />

LCA<br />

<strong>MB</strong>-<strong>LAC</strong><br />

WGA<br />

<strong>MB</strong>-<strong>LAC</strong><br />

<strong>AIA</strong><br />

<strong>MB</strong>-CovAC<br />

boronic<br />

High-mannose type Hybrid type Complex type<br />

<strong>Glyco</strong>rotein<br />

<strong>Glyco</strong>protein<br />

<strong>Glyco</strong>protein<br />

Man<br />

GlcNAc<br />

Gal<br />

Fuc<br />

NeuAc<br />

GalNAc<br />

<strong>Glyco</strong>protein<br />

<strong>Glyco</strong>protein<br />

<strong>Glyco</strong>protein<br />

O-linked glycans<br />

C-linked glycans<br />

N-linked glycans<br />

Fig. 2: Binding motifs of <strong>Bruker</strong> Daltonics’ CLINPROT TM magnetic glyco-beads. The different beads<br />

represent overlapping but individual binding profiles.<br />

Successful applications and reproducibility of <strong>Bruker</strong> Daltonics’ CLINPROT TM magnetic glycobeads<br />

using model systems or complex samples like serum, plasma or urine were demonstrated in<br />

various studies 1,2,3 . Further, long term stability and storage conditions were extensively<br />

investigated to assure the high quality of <strong>Bruker</strong> Daltonics’ CLINPROT TM magnetic glycobeads<br />

4 .The application of glyco-beads in the context of glyco-profiling and biomarker discovery<br />

was closely described by Drake et al. 5<br />

Page 2 of 19


Table of Contents<br />

General In<strong>for</strong>mation........................................................................................................................... 2<br />

Intended <strong>Use</strong>..................................................................................................................................... 4<br />

Product description............................................................................................................................ 4<br />

<strong>Kit</strong> Components................................................................................................................................. 5<br />

Storage and lifetime in<strong>for</strong>mation........................................................................................................ 5<br />

Risk and safety in<strong>for</strong>mation ............................................................................................................... 5<br />

General remarks <strong>for</strong> sample handling and MALDI measurements ................................................... 6<br />

Recommended sample preparation procedure ................................................................................. 7<br />

Comments ......................................................................................................................................... 9<br />

MALDI-TOF MS Target Preparation................................................................................................10<br />

Cleaning of MALDI-MS targets.................................................................................................... 10<br />

Cleaning of AnchorChip TM targets ........................................................................................... 10<br />

Cleaning of polished steel targets ........................................................................................... 11<br />

Matrix preparation on the MALDI-MS targets.............................................................................. 12<br />

Analysis of glycoproteins using 2,5-DHAP .............................................................................. 12<br />

Analysis of glycopeptides using 2,5-DHB................................................................................ 13<br />

Analysis of deglycosylated peptides using PAC targets.......................................................... 15<br />

Example .......................................................................................................................................... 16<br />

Isolation of Asialofetuin from a protein mixture ........................................................................... 16<br />

References...................................................................................................................................... 17<br />

Trouble shooting.............................................................................................................................. 18<br />

Ordering In<strong>for</strong>mation ....................................................................................................................... 19<br />

Support............................................................................................................................................ 19<br />

Page 3 of 19


Intended <strong>Use</strong><br />

The glyco kit <strong>MB</strong>-<strong>LAC</strong>-<strong>AIA</strong> (Magnetic Bead-Lectin Affinity Chromatography with Artocarpus<br />

Integrifolia Agglutinin = Jacalin) is developed <strong>for</strong> the capturing of preferentially O-glycosylated<br />

proteins derived from biological samples based on lectin affinity prior to MALDI-TOF mass<br />

spectrometry analysis by means of e.g. <strong>Bruker</strong>´s microflex ® , autoflex ® or ultraflex ® MALDI-TOF.<br />

This kit is <strong>for</strong> research use only. It is not <strong>for</strong> use in diagnostic procedures.<br />

Product description<br />

The <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> kit is designed <strong>for</strong> enrichment and purification of preferentially O-glycosylated<br />

proteins prior to MALDI-TOF MS analysis. The <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> kit is based on super-paramagnetic<br />

microparticles functionalized with Artocarpus Integrifolia Agglutinin.<br />

Artocarpus Integrifolia Agglutinin (<strong>AIA</strong>) is a lectin which specifically binds the structure galactosyl<br />

(-1-3) N-acetylgalactosamine and -D-galactose. Jacalin captures galactosyl (-1-3) N-<br />

acetylgalactosamine even in a mono- or di-sialylated <strong>for</strong>m 6 .<br />

CH 2 OH<br />

OH CH 2 OH<br />

O<br />

OH<br />

OH<br />

OH<br />

O<br />

O<br />

OH<br />

HN<br />

O<br />

Fig. 3: Structure of galactosyl-(ß-1,3)-N-acetylgalactosamine which is the main recognition motif of jacalin.<br />

Due to the binding requirements <strong>AIA</strong> preferentially binds O-glycans. This lectin has been used to<br />

exclusively purify human IgA without enriching any other human immunoglobulin class 7 .<br />

Page 4 of 19


<strong>Kit</strong> Components<br />

Materials provided in the kits Abbreviation Remarks<br />

Magnetic Beads: <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> Containing 0.02 % NaN 3<br />

<strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> Binding Buffer<br />

BB<br />

<strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> Wash Buffer 1 WB 1<br />

<strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> Wash Buffer 2 WB 2<br />

<strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> Elution Buffer<br />

EB<br />

Deionized water<br />

Storage and lifetime in<strong>for</strong>mation<br />

<strong>Kit</strong> components should be stored and handled carefully to avoid contaminations.<br />

The kit is shipped at ambient temperature. We recommend storing the kit at 2-8°C after arrival. Do<br />

not freeze!<br />

If stored unopened under above conditions, the product is stable until expiration date mentioned on<br />

the label.<br />

Please note:<br />

After the first opening, period of storage should not exceed three months. For your<br />

convenience, we provide the possibility to mark the respective expiry date on the vial’s label.<br />

After usage, keep the vials closed. A drying up of the beads will damage the product<br />

irreversible!<br />

Risk and safety in<strong>for</strong>mation<br />

The product does not have to be labeled due to the calculation procedure of the "General<br />

Classification guideline <strong>for</strong> preparations of the EU" in the latest valid version. When used and<br />

handled according to specifications, the product does not have any harmful effects according to<br />

our experience. All materials may present unknown hazards and should be used with caution.<br />

Observe the general safety regulations when handling chemicals.<br />

Beside the kit components, we recommend further chemicals within these <strong>Instructions</strong> <strong>for</strong> <strong>Use</strong>.<br />

Please read and observe the respective Material Safety Data Sheet to be provided by your<br />

supplier. Observe the general safety regulations when handling chemicals.<br />

Page 5 of 19


General remarks <strong>for</strong> sample handling and MALDI measurements<br />

MALDI-TOF mass spectrometry is a very sensitive analysis method requiring special operation<br />

procedures. There<strong>for</strong>e, we recommend considering the following aspects be<strong>for</strong>e starting an<br />

analysis:<br />

The quality of the starting material will have an enormous impact on the outcome of the<br />

experiments. Especially, collection and storage conditions have to be controlled carefully.<br />

When working with clinical samples, like serum or urine, please refer to the recent<br />

publications of Baumann et al. 8 and Fiedler et al. 9 <strong>for</strong> standardized sample handling<br />

procedures.<br />

To avoid contaminations all solvents used should be of HPLC grade or better<br />

The plastic materials used <strong>for</strong> sample purification and matrix preparation should be<br />

explicitly recommended <strong>for</strong> mass spectrometric measurements. Many common plastics<br />

may cause polymer contamination of the sample. This will interfere with the subsequent<br />

matrix preparation/crystallization and produce polymer signals during spectra acquisition.<br />

Sample purification and MALDI target preparation should be per<strong>for</strong>med under clean<br />

conditions. Dust and air pollution will decrease the spectra quality.<br />

For optimal sample/matrix crystallization on the MALDI target the following environmental<br />

conditions are recommended:<br />

Operating temperature: 5 - 40°C (41 - 104°F)<br />

Operating humidity: 25 – 65 % at 22°C<br />

Atmospheric pressure: 75 - 105 kPa<br />

For high resolution measurements and low signal to noise values a cleaning of the ion<br />

source at regular intervals is absolutely mandatory. This procedure can be per<strong>for</strong>med with<br />

the <strong>Bruker</strong> Daltonics’ source shower target (see ordering in<strong>for</strong>mation). For a complete<br />

cleaning of the ion source please ask <strong>Bruker</strong> Daltonics’ service team<br />

(maldi.support@bdal.de).<br />

Page 6 of 19


Recommended sample preparation procedure<br />

Binding of samples<br />

1. Re-suspend the Magnetic Beads by shaking<br />

<strong>for</strong> at least 20 times from top to the bottom<br />

and reversed or careful vortexing (do not<br />

sonificate!) to get a homogenous suspension.<br />

Repeat shaking between pipetting steps if<br />

necessary.<br />

Re-suspend the beads<br />

2. Transfer 20 µl of resuspended Magnetic<br />

Beads to a standard thin wall PCR-tube and<br />

add 100 µl WB 1.<br />

20 µl beads<br />

100 µl WB1<br />

3. Place the tube in a Magnetic Separator and<br />

move the tubes back and <strong>for</strong>th between<br />

adjacent wells 20 times. Wait <strong>for</strong> 20 seconds<br />

to separate the beads from the supernatant.<br />

Move back and <strong>for</strong>th<br />

Collect beads<br />

4. Remove the supernatant carefully using a<br />

pipette. Avoid contact of pipette tips with the<br />

magnetic beads and take care not to remove<br />

the beads.<br />

Remove supernatant<br />

5. Resuspend the beads in 100 µl WB 1 100 µl WB1<br />

6. Repeat steps 3 and 4 to wash the beads and<br />

remove the supernatant<br />

Repeat steps 3 and 4<br />

7. Re-suspend the beads in 10 µl BB and add up<br />

to 10 µl of the sample. If you have less sample<br />

volume adjust to 10 µl by adding deionized<br />

water.<br />

For the analysis of serum, use 10 - 20 µl<br />

serum. Firstly, pipette an equal amount of BB<br />

(10 - 20 µl) to 20 µl magnetic beads and<br />

subsequently add the serum.<br />

10 µl BB<br />

10 µl sample<br />

8. Incubate the magnetic beads <strong>for</strong> 1 h at room<br />

temperature while swirling the tube from time<br />

to time to mix the beads.<br />

1 h incubation<br />

Page 7 of 19


Washing of beads<br />

9. Place the tube on the Magnetic Separator and<br />

wait <strong>for</strong> 20 seconds to separate the beads<br />

from the supernatant. (Note the movement of<br />

the magnetic beads in the tube.)<br />

Collect beads<br />

10. Remove the supernatant carefully. Avoid<br />

contact of pipette tips with the magnetic beads<br />

and take care not to remove the beads.<br />

Remove supernatant<br />

11. Add 100 µl WB 1 100 µl WB1<br />

12. Move the tubes back and <strong>for</strong>th between<br />

adjacent wells at least 20 times to wash the<br />

beads.<br />

Move back and <strong>for</strong>th<br />

13. Wait 20 seconds <strong>for</strong> collecting magnetic beads<br />

at the wall of the tubes and remove the<br />

supernatant carefully.<br />

Collect beads<br />

14. Transfer the tube from the Magnetic Separator<br />

to an alternative device. Add 100 µl WB2 and<br />

place the tube back on the Magnetic<br />

Separator. Move the tubes back and <strong>for</strong>th<br />

between adjacent wells 20 times.<br />

100 µl WB2<br />

Move back and <strong>for</strong>th<br />

15. Wait 20 seconds <strong>for</strong> collecting magnetic beads<br />

at the wall of the tubes and remove the<br />

supernatant carefully.<br />

Collect beads<br />

Remove supernatant<br />

16. Repeat steps 14 and 15 once. Repeat steps 14 and 15<br />

Elution of isolated proteins<br />

17. For the elution of captured proteins add 10 µl<br />

EB and mix thoroughly.<br />

10 µl EB<br />

18. Incubate <strong>for</strong> 25 minutes while mixing from time<br />

to time.<br />

25 min incubation<br />

Page 8 of 19


19. Place the tube on the Magnetic Separator and<br />

wait <strong>for</strong> 30 seconds <strong>for</strong> collecting the beads at<br />

the wall of the tube.<br />

Collect beads<br />

20. Finally, transfer the elution buffer containing<br />

purified glycoproteins into a fresh tube.<br />

Transfer eluate<br />

Comments<br />

Fast and successful collection of the magnetic beads is dependent on a high quality magnetic<br />

separation device. We strongly recommend the use of a <strong>Bruker</strong> Magnetic Separator (8-well,<br />

# 65554 or 96-well, # 207151).<br />

The beads can also be applied <strong>for</strong> non-MS approaches. Depending on the subsequent technique<br />

the acidic elution solution may interfere with the following protocol steps. To remove the elution<br />

solution we recommend drying the eluate in a vacuum centrifuge. Afterwards, the dried sample can<br />

be re-dissolved in an appropriate buffer or solution and processed according to the subsequent<br />

protocol. This procedure is also recommended when different glyco-capturing particles are used in<br />

succession.<br />

Different glyco-beads can also be combined in one experiment to capture glyco-proteins with<br />

different binding motifs at once. To do so, the buffer system of either a ConA or LCA kit has to be<br />

used since these buffer systems are compatible with the WGA and/or <strong>AIA</strong> beads, whereas the<br />

buffers in the WGA and <strong>AIA</strong> kits are not suitable <strong>for</strong> the ConA or LCA functionality.<br />

In principle, the amount of beads can be scaled up and down according to the experimental<br />

requirements. When doing this, it is important to keep the ratio of sample volume and <strong>AIA</strong>-BB<br />

volume constant.<br />

The provided buffer system has not been tested <strong>for</strong> the capturing of glycopeptides. Respective<br />

buffers will have to be optimized by the customer himself.<br />

Please note:<br />

After elution using the provided EB, glyco-proteins are denatured. This will have an impact on<br />

folding and functional activity.<br />

Page 9 of 19


MALDI-TOF MS Target Preparation<br />

MALDI-TOF MS target preparation is one of the most critical steps <strong>for</strong> high quality and reproducible<br />

results. Depending on the application, different target types and MALDI matrix preparations are<br />

favored. For all applications it is mandatory to use a thoroughly cleaned target plate. In<br />

dependence on the type of target <strong>Bruker</strong> Daltonic recommends different cleaning procedures.<br />

Cleaning of MALDI-MS targets<br />

Cleaning of AnchorChip TM targets<br />

This is an advanced cleaning protocol differing from the standard cleaning procedure<br />

recommended in the product description.<br />

1. Rinse the target intensively under<br />

flowing hot tap water<br />

Hot tap water<br />

2. Wipe the target intensively with acetone<br />

using a kimwipe kimwipe.<br />

: Acetone is highly flammable and<br />

irritant (R: 11-36-66-67; S: (2)-9-16-26)<br />

Acetone<br />

3. Rinse the target with distilled water<br />

(Milli-Q).<br />

Distilled water<br />

4. Rinse the target with methanol and let it<br />

dry.<br />

: Methanol is highly flammable and<br />

toxic (R: 11-23/24/25-39/23/24/25; S:<br />

(1/2)-7-16-36/37-45)<br />

Methanol<br />

Page 10 of 19


Cleaning of polished steel targets<br />

This is an advanced cleaning protocol differing from the standard cleaning procedure<br />

recommended in the respective target’s product description.<br />

1. Rinse the target intensively under<br />

flowing hot tap water.<br />

Hot tap water<br />

2. Wipe the target intensively with acetone<br />

using a kimwipe.<br />

: Acetone is highly flammable and<br />

irritant (R: 11-36-66-67; S: (2)-9-16-26)<br />

Acetone<br />

3. Rinse the target intensively under<br />

flowing hot tap water.<br />

Hot tap water<br />

4. Wipe the target intensively with 80%<br />

TFA using a kimwipe.<br />

: 80% TFA is corrosive (R: 20-35-<br />

52/53; S: (1/2)-9-26-27-28-45-61)<br />

80 % TFA<br />

5. Rinse the target intensively under<br />

flowing hot tap water.<br />

Hot tap water<br />

6. Rinse the target with distilled water<br />

(Milli-Q).<br />

Distilled water<br />

7. Rinse the target with methanol and let it<br />

dry.<br />

: Methanol is highly flammable and<br />

toxic (R: 11-23/24/25-39/23/24/25; S:<br />

(1/2)-7-16-36/37-45)<br />

Methanol<br />

Page 11 of 19


Matrix preparation on the MALDI-MS targets<br />

Analysis of glycoproteins using 2,5-DHAP<br />

For preparation of glycoproteins within the mass range of 6 – 100 kDa on AnchorChip TM 600<br />

targets (#209513) we recommend the use of 2,5-dihydroxyacetophenone (2,5-DHAP, #231829 or<br />

#231830) as matrix solution.<br />

2,5-DHAP preparation on AnchorChip600 targets<br />

1. Dissolve 7.6 mg DHAP in 375 µl<br />

ethanol.<br />

: DHAP is irritant (R: 36/37/38; S:<br />

26-28-36/37-60), ethanol is highly<br />

flammable (R: 11; S: (2)-7-16)<br />

7.6 mg DHAP<br />

375 µl ethanol<br />

2. Add 125 µl (18 mg/ml in Milli-Q water)<br />

of a di-ammonium hydrogencitrate<br />

solution (= 10 µmol).<br />

: Diammonium hydrogencitrate is<br />

irritant (R: 36/37; S: 26)<br />

125 µl Diammonium<br />

Hydrogen Citrate<br />

3. Vortex <strong>for</strong> 1 min at RT. Vortex<br />

4. Sonicate <strong>for</strong> 15 min. Sonificate<br />

5. Vortex <strong>for</strong> 1 min at RT. The matrix<br />

solution is stable <strong>for</strong> at least one week<br />

when kept in the dark<br />

Vortex<br />

6. Mix 2 µl of the sample with 2 µl 2 %<br />

TFA and subsequently add 2 µl matrix<br />

solution.<br />

: 2% TFA is irritant (R: 36/38; S: 26-<br />

28-37-60)<br />

2 µl Sample<br />

2 µl 2% TFA<br />

2 µl DHAP Matrix Solution<br />

7. The mixture of sample, TFA and DHAP<br />

has to be vigorously mixed by pipetting<br />

up and down. It is important that the<br />

solution becomes turbid be<strong>for</strong>e spotting<br />

Vigorously mixing<br />

Page 12 of 19


8. 1 µl of the turbid suspension has to be<br />

spotted on an AnchorChip TM 600 target<br />

without generating air bubbles.<br />

Spot 1 µl<br />

9. After drying of the spots the target can<br />

be transferred to the MALDI-TOF MS<br />

<strong>for</strong> measurements.<br />

Dry the spot<br />

Analysis of glycopeptides using 2,5-DHB<br />

For preparation of glycopeptides (e.g. after proteolytic digest of the glycoprotein) within the mass<br />

range of 1 – 10 kDa we recommend the use of AnchorChip 600 targets (#209513) or polished<br />

steel targets (#209520) and 2,5-Dihydroxybenzoic acid (DHB, #201346 or #203074) as matrix.<br />

2,5-DHB preparation on AnchorChip600 targets<br />

1. Dissolve 5 mg DHB in 300 µl<br />

acetonitrile<br />

: DHB is harmful (R: 22-36/37/38;<br />

S: 26-28-36/37-60), acetonitrile is<br />

highly flammable and harmful (R: 11-<br />

20/21/22-36; S: (1/2)-16-36/37)<br />

5 mg DHB<br />

300 µl acetonitrile<br />

2. Add 700 µl TFA (0.1 %) 700 µl 0.1 %TFA<br />

3. Vortex <strong>for</strong> 1 min at RT Vortex<br />

4. Sonificate <strong>for</strong> 15 min Sonificate<br />

5. 1 µl of the freshly prepared matrix has to<br />

be spotted onto an AnchorChip 600<br />

target<br />

Spot 1 µl matrix<br />

6. After drying spot 1 µl of sample onto the<br />

matrix<br />

Spot 1 µl sample<br />

Page 13 of 19


7. After drying of the spots the target can<br />

be transferred to the MALDI-TOF MS <strong>for</strong><br />

measurements.<br />

Dry the spot<br />

2,5-DHB preparation on polished steel targets<br />

1. Dissolve 10 mg DHB in 300 µl<br />

acetonitrile<br />

: DHB is harmful (R: 22-36/37/38; S:<br />

26-28-36/37-60), acetonitrile is highly<br />

flammable and harmful (R: 11-20/21/22-<br />

36; S: (1/2)-16-36/37)<br />

5 mg DHB<br />

300 µl acetonitrile<br />

2. Add 700 µl TFA (0.1 %) 700 µl 0.1 %TFA<br />

3. Vortex <strong>for</strong> 1 min at RT Vortex<br />

4. Sonificate <strong>for</strong> 15 min Sonificate<br />

5. 1 µl of the freshly prepared matrix has to<br />

be spotted onto an AnchorChip TM 600<br />

target<br />

Spot 1 µl matrix<br />

6. After drying spot 1 µl of sample onto the<br />

matrix<br />

Spot 1 µl sample<br />

7. After drying of the spots the target can be<br />

transferred to the MALDI-TOF MS <strong>for</strong><br />

measurements.<br />

Dry the spot<br />

Page 14 of 19


Analysis of deglycosylated peptides using PAC targets<br />

For the analysis of deglycosylated peptides (e.g. after PNGase F treatment) the use of PAC (Prespotted<br />

AnchorChip) targets prespotted with α-Cyano-4-hydroxycinnamic acid (HCCA) is<br />

recommended (#231968 or #227463).<br />

Sample preparation onto pre-spotted disposable AnchorChip targets<br />

1. Deposit 0.3 – 3 µl sample soluton onto<br />

the matrix spot. The acetonitrile<br />

concentration of the sample must not<br />

exceed 40 %<br />

Spot 0.3 – 3 µl sample<br />

2. Incubate the sample <strong>for</strong> 3 min onto the<br />

spot, but do not let the droplets dry<br />

3 min incubation<br />

3. Remove the residual solvent Remove droplet<br />

4. Add 7 – 10 µl of washing buffer (10mM<br />

Ammonium phosphate, monobasic, in<br />

0.1 % TFA)<br />

Wash with 7 – 10 µl<br />

5. Incubate <strong>for</strong> a few second and<br />

subsequently remove the wash buffer<br />

Remove wash buffer<br />

after a few seconds<br />

Page 15 of 19


Example<br />

Isolation of Asialofetuin from a protein mixture<br />

Sample:<br />

Protein mixture consisting of Protein Standard II (1 µl, #207234) and<br />

Asioalofetuin (AF, 1 µg)<br />

Beads:<br />

<strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong><br />

Target: MTP AnchorChip 600/384<br />

Matrix:<br />

2,5-DHAP<br />

MALDI mode: Linear<br />

Asiaolofetuin (43.2 kDa) was successfully isolated by <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> beads from a protein mixture<br />

consisting of BSA (66.4 kDa), Protein A (44.5 kDa) Trypsinogen (23.9 kDa) and Asialofetuin (43.2<br />

kDa). Only Asialofetuin was detected in the eluate and no residual Asiaolfetuin was detected in the<br />

supernatant.<br />

Page 16 of 19


References<br />

1 Sparbier K, Koch S, Kessler I, Wenzel T, and Kostrzewa M.(2005). Selective Isolation of<br />

<strong>Glyco</strong>proteins and <strong>Glyco</strong>peptides <strong>for</strong> MALDITOFMS Detection Supported by Magnetic Particles. J<br />

Biomol Tech, 16: 407 – 413.<br />

2 Sparbier K, Wenzel T, Kostrzewa M. (2006). Exploring the binding profiles of ConA, boronic acid<br />

and WGA by MALDI-TOF/TOF MS and magnetic particles. J ChromB, 840: 29–36.<br />

3 Sparbier K, Asperger A, Resemann A, Kessler I, Koch S, Wenzel T, Stein G, Vorwerg L, Suckau<br />

D, Kostrzewa M. (2007). Analysis of <strong>Glyco</strong>proteins in Human Serum by Means of <strong>Glyco</strong>-specific<br />

Magnetic Bead Separation and LC-MALDI-TOF/TOF Analysis with Automated <strong>Glyco</strong>peptide<br />

Detection. J Biomol Tech, Sept., accepted <strong>for</strong> publication.<br />

4 Sparbier K; Kessler I, Koch S, Mix G, Kostrzewa M. (2007). CLINPROT <strong>Glyco</strong>-beads: Verification<br />

of Long-Term Stability and Batch-to-Batch Reproducibility. Technote <strong>Bruker</strong> Daltonic (tn-20).<br />

5 Drake RR, Schwegler EE, Malik G, Diaz J, Block T, Mehta A, and Semmes OJ. (2006). Lectin<br />

Capture Strategies Combined with Mass Spectrometry <strong>for</strong> the Discovery of Serum <strong>Glyco</strong>protein<br />

Biomarkers. Mol&CellProt, 5.10:1957 – 1967.<br />

6 Jeyaprakash AA, Katiyar S,. Swaminathan CP, Sekar K, Surolia A, Vijayan M. (2003) Structural<br />

Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study. J Mol Biol.<br />

332(1):217-28<br />

7 . Hihmstra PS. Gorter A. Stuurman ME. Van Es LA, Daha MR. (1987). The IgA-Binding Lectin<br />

Jacalin Induces Complement Activation by Inhibition of Cl -Inactivator Function. Scand. J.<br />

Immunol. 26: 111 - 117.<br />

8 Baumann S, Ceglarek U, Fiedler GM, Lembcke J, Leichtle A, Thiery J. (2005): Standardized<br />

approach to proteome profiling of human serum based on magnetic bead separation and matrixassisted<br />

laser desorption/ionization time-of-flight mass spectrometry. Clin Chem., 51, 973-80.<br />

9 Fiedler GM, Baumann S, Leichtle A, Oltmann A, Kase J, Thiery J, Ceglarek U. (2007):<br />

Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted<br />

laser desorption/ionization time-of-flight mass spectrometry. Clin Chem. 53, 421-8.<br />

Page 17 of 19


Trouble shooting<br />

Problem Reason What to do<br />

Sample does not crystallize,<br />

crystallization looks<br />

strange<br />

Plastics (tips, tubes, flasks)<br />

are not MS-compatible<br />

Solvents are not of HPLC<br />

grade or better<br />

Environmental conditions<br />

are not compatible with MS<br />

preparations<br />

Change plastics (referr to<br />

the ording in<strong>for</strong>mation <strong>for</strong><br />

MS compatible plastics<br />

Exchange the solvents and<br />

use higher quality solvents<br />

Prepare under a clean<br />

bench, check humidity,<br />

maybe humidify the room,<br />

switch off the air condition<br />

Polymer contaminations<br />

Plastics (tips, tubes, flasks)<br />

are not MS-compatible<br />

Solvents are not of HPLC<br />

grade or better<br />

Change plastics (refer to<br />

the ordering in<strong>for</strong>mation <strong>for</strong><br />

MS compatible plastics)<br />

Exchange the solvents and<br />

use higher quality solvents<br />

Low signal/noise values Environmental conditions<br />

are not compatible with MS<br />

preparations<br />

Air pollution and subsequent<br />

contamination with<br />

sodium or potassium<br />

Prepare under a clean<br />

bench, check humidity,<br />

maybe humidify the room,<br />

switch off the air condition<br />

See above<br />

Quality of the starting<br />

material<br />

No detection of glycoproteins/-peptides<br />

<strong>Glyco</strong>-proteins/-peptides do<br />

not represent the required<br />

binding motifs<br />

Try other glyco-beads<br />

functionalized with another<br />

lectins or boronic acids<br />

beads<br />

Page 18 of 19


Ordering In<strong>for</strong>mation<br />

Product<br />

Size (purifications or<br />

applications per kit)<br />

Part No.<br />

<strong>Glyco</strong> <strong>Kit</strong> 20 <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> 20 250359<br />

<strong>Glyco</strong> <strong>Kit</strong> 100 <strong>MB</strong>-<strong>LAC</strong> <strong>AIA</strong> 100 249174<br />

<strong>Glyco</strong> <strong>Kit</strong> 20 <strong>MB</strong>-CovAC boronic 20 241104<br />

<strong>Glyco</strong> <strong>Kit</strong> 20 <strong>MB</strong>-<strong>LAC</strong> Con A 20 252665<br />

<strong>Glyco</strong> <strong>Kit</strong> 20 <strong>MB</strong>-<strong>LAC</strong> LCA 20 246534<br />

<strong>Glyco</strong> <strong>Kit</strong> 20 <strong>MB</strong>-<strong>LAC</strong> WGA 20 244669<br />

<strong>Glyco</strong> <strong>Kit</strong> 100 <strong>MB</strong>-CovAC boronic 100 236594<br />

<strong>Glyco</strong> <strong>Kit</strong> 100 <strong>MB</strong>-<strong>LAC</strong> Con A 100 252664<br />

<strong>Glyco</strong> <strong>Kit</strong> 100 <strong>MB</strong>-<strong>LAC</strong> LCA 100 246533<br />

<strong>Glyco</strong> <strong>Kit</strong> 100 <strong>MB</strong>-<strong>LAC</strong> WGA 100 244668<br />

Magnetseparator 016 8-well 65554<br />

Magnetseparator 104 II 96-well 207151<br />

2,5-Dihydroxyacetophenone, 1g 231829<br />

2,5-Dihydroxyacetophenone, 5g 231830<br />

2,5-Dihydroxybenzoic acid, 1 g 201346<br />

2,5-Dihydroxybenzoic acid, 5 g 203074<br />

α-Cyano-4-hydroxycinnamic acid, 1g 201344<br />

α-Cyano-4-hydroxycinnamic acid, 5g 203072<br />

MTP AnchorChip 600/384 T F 209513<br />

PAC96 Set <strong>for</strong> Proteomics 231968<br />

PAC384 Set <strong>for</strong> Proteomics 227463<br />

MTP PAC Frame 221598<br />

MTP 384 target plate polished steel T F 209520<br />

MTP Ion Source Shower Target 226054<br />

8-Well Strips 60550<br />

CapStrips 60551<br />

96-Well TubePlates 61565<br />

<strong>Bruker</strong> Daltonics’ Recommendations<br />

Pipette tips<br />

Vials<br />

Bottles<br />

Eppendorf standard tips<br />

Eppendorf safe-lock<br />

Nalgene PP<br />

Support<br />

Email: care@bdal.de<br />

Phone: +49 (421) 2205-0<br />

Web: www.care-bdal.de<br />

For research use only. Not <strong>for</strong> use in diagnostic procedures.<br />

Revision 1, January 2012<br />

Copyright 2012 <strong>Bruker</strong> Daltonik GmbH<br />

Descriptions and specifications supersede all previous in<strong>for</strong>mation and are subject to change without notice.<br />

Page 19 of 19

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