MALDI PROTOCOL FOR IDENTIFICATION OF MICROORGANISMS BY PROTEIN
READING CONCEPT
Introduction
The protein-reading concept using CAF-/CAF+ reagent (chemically activated fragmentation
negative/chemically activated fragmentation positive) enables fast, highly accurate, reliable and easy
to use identification of microorganisms down to the species level. It is one step derivatization
reaction easily incorporated into existing workflows commonly used by biological scientists, as
outlined in Figure 1.
SAMPLE PREPARATION (Step 1)
Isolate the proteins from your sample & perform trypsin digestion
↓
DERIVATIZATION (Step 2)
Add CAF-/CAF+ reagent to peptides
↓
SEPARATION (Step 3)
Separate tagged peptides and spot them onto MALDI plate
↓
IDENTIFICATION (Step 4)
Identify microorganism by MALDI-MS/MS & ProteinReader*
Figure 1. Workflow of MALDI-MS/MS identification of microorganisms using CAF-/CAF+ reagent.
*ProteinReader is expert software developed exclusively for species identification.
CAF-/CAF+ is a chemical reagent for the derivatization of peptide samples prior to analysis by MALDI
(Matrix Assisted Laser Desorption Ionization) Tandem Mass Spectrometry (MS/MS). Derivatization
procedure of tryptic peptides at N-terminus is illustrated by the following reaction (Figure 2.):
Figure 2. Derivatization procedure of tryptic peptide with CAF-/CAF+ reagent (5-formylbenzene-1,3disulfonic acid).
For the first time, mass spectrometry can exploit both positive and negative ion mode, either for
species or proteins identification. The CAF-/CAF+ method enables de novo sequencing of derivatized
peptides with negative and positive ion mode tandem mass spectrometry (MS/MS- and MS/MS+).
Peptide sequences are read from MS/MS spectra and matched against the NCBInr database by
developed software named ProteinReader and confirmed by the mass spectrometry data of
elucidated peptide mass sequences derived from the annotated genome.
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Benefits of using CAF-/CAF+ derivatization reagent
Accurate
CAF-/CAF+ is a mild derivatizing reagent with no side reactions resulting in peptide fingerprinting
exclusively in negative ion mode (MS-) without interferences and adducts (e.g. sodium, potassium,
ammonium) and peptide amino acid sequence analysis in positive and negative MS/MS+/-.
Fast
CAF-/CAF+ reagent significantly reduces the derivatization time to only 10 minutes.
The whole process of sample identification from sample preparation to species identification can be
finished in maximum 4 h depending on sample complexity.*
Reliable
CAF-/CAF+ reagent allows de novo sequencing from spectra of both b-ions (obtained in negative ion
mode) and y-ions (obtained in positive ion mode) making sequence reading unambiguous and easy
by using two orthogonal techniques (MS/MS negative and MS/MS positive). By reading the same
sequence twice forward and backward probability of misreading or misinterpretation of
microorganism ID is minimized.
*The protocol consists of two phases: First is sample preparation (protein extraction and digestion) and second
is sample treatment & processing (derivatization, separation and identification). Sample preparation can take
from one to two hours depending on sample complexity and digestion method used (trypsin tip or trypsin
magnetic beads). n. b. overnight in-solution tryptic digestion (9-18 h) can be applied, as well.
Materials, reagents, instruments, software
Materials
Materials enclosed in brackets are the ones used in our laboratory procedures.
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Tissue homogenizer (TissueRuptor and TissueRuptor disposable probes, Quiagen, Germany)
2.0 mL PP tubes for cell lysis (Eppendorf, Germany)
1.5 mL microcentrifuge tubes (Eppendorf, Germany)
Tube holder for 1.5 mL tubes
Tube holder cool pack for 1.5 or 2.0 mL tubes
Extraction manifold SPE system (Waters, USA)
SPE 1 mL Diol cartridge, 100 mg Sorbent per Cartridge (Sep-Pak® Diol 1 cc Vac cartridge,
Waters, USA)
Vortexer for mixing
Laboratory centrifuge with centrifugal force of at least 2,000 rcf (Centric 400, Tehtnica,
Slovenia)
Bench-top microcentrifuge with cooling system and centrifugal force of at least 4,500 rcf
(Centrifuge 5415 R, Eppendorf, Germany)
Vacuum concentrator (Concentrator 5301, Eppendorf, Germany)
Thermomixer (Thermomixer comfort, Eppendorf, Germany)
LC Column C18, 300 µm x 150 mm I.D., 3.5 μm particle size (Symmetry 300TM,Waters, USA)
Spin filters 0.22 µm, cellulose acetate membranes (Agilent)
Household microwave oven (HeatWave compact 800W, Electrolux)
Reagents used
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Ammonium bicarbonate, ≥ 99.0% (Sigma-Aldrich)
Triton X-100 (Sigma-Aldrich)
Mag-Trypsin, trypsin immobilized on magnetic beads (Clontech, USA)
Acetonitrile, gradient grade for liquid chromatography (Merck, Germany)
Ammonium formate, for HPLC, ≥ 99.0% (Sigma-Aldrich)
Trifluoracetic acid, for spectroscopy (Merck, Germany)
CAF-/CAF+ reagent (5-formylbenzene-1,3-disulfonic acid disodium salt hydrate, p.a. synthetic
product, Ruđer Bošković Institute)
Sodium cyanoborohydride, for synthesis (Merck, Germany)
Potasium dihydrogen phosphate, p.a. (Kemika, Croatia)
α-Cyano-4-hydroxycinnamic acid (Sigma-Aldrich)
Ultrapure water, TOC < 5 ppb, resistivity < 18.2 MΩ cm
Instruments
Instruments enclosed in brackets are the ones used in our laboratory procedures.
 CapLC-MALDI spotting system (Capillary LC, Waters, USA and Tempo™ LC MALDI Spotting
System, Applied Biosystems, MDS Sciex, USA)
 MALDI TOF/TOF mass spectrometer (4800 MALDI TOF/TOF™ Analyzer, Applied Biosystems,
MDS Sciex, USA)
Software
 Protein Reader (software developed by "Ruđer Bošković" Institute and Faculty of Food
Technology and Biotechnology, University of Zagreb)
Procedure
STEP 1 - SAMPLE PREPARATION
1. REMOVING CELL SUSPENSION GROWTH MEDIUM
Centrifuge suspension of cells in 50 or 15 mL culturing tubes 2,000 rcf for 15 min and aspirate the
supernatant. Resuspend the pellet in 1.5 mL of 25 mM NH4HCO3, transfer to a 2.0 mL tube and
centrifuge at 4,500 rcf for 20 min at 4°C. Aspirate the supernatant. Repeat 2-4 more times,
depending on the sample.
2. CELL LYSIS
Add 400 µL of cell lysis buffer (25 mM NH4HCO3 + 0.1% Triton-X-100) and resuspend the pellet. Keep
the tubes incubated on cool pack.
Proceed to cell rupture using TissueRuptor and disposable probe with the following settings:
Power: Position II
Grinding cycle: 45 seconds ON / 45 seconds OFF
Total grinding times: 5-6 cycles
3. BLOCKING ENDOPROTEASE ACTIVITY
Stop the TissueRuptor after 5 cycles, close the lid on 2.0 mL tube and put the sample in boiling water
for 3 minutes to inhibit endoprotease activity.
4. OBTAINING SOLUTION OF PROTEINS
Remove the sample tube from the water bath and centrifuge at 4,500 rcf for 20 min at 4°C to remove
disrupted cell material. Transfer the supernatant containing soluble proteins to a clean 1.5 mL tube.
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5. PROTEIN DIGESTION
Use one of the three trypsin digestion procedures:
a. Mag-Trypsin (trypsin immobilized on magnetic beads)
b. Trypsin tip
c. Standard in-solution tryptic digestion
STEP 2 - DERIVATIZATION
6. DERIVATIZATION PROCEDURE
Reconstitute each sample containing the evaporated tryptic peptide mixture with 60 µL of
derivatization solution. The derivatization solution contains 12.5 mM 5-formylbenzene-1,3-disulfonic
acid disodium salt hydrate (p.a. synthetic product, Ruđer Bošković Institute) and 95.5 mM of
NaBH3CN dissolved in 10 mM KH2PO4 and adjusted to pH 5. Close the tube with the sample, place it
in the holder (e.g. styrofoam) and perform the derivatization in a household microwave oven at 90W
for 10 minutes.
STEP 3 – SEPARATION
7. SOLID PHASE EXTRACTION (SPE) - OPTIONAL
Purify the peptides after trypsin digestion on Diol cartridges using vacuum manifold SPE system.
Condition the Diol cartridges in three steps: first, aspirate and dispense to waste three times 0.5 mL
of 80% acetonitrile (ACN) mixed with 20% water solution of 0.1% ammonium formate (AF) (v/v);
second, aspirate and dispense to waste three times 0.5 mL of 50% ACN mixed with 50% water
solution of 0.1% AF (v/v); and finally, aspirate and dispense to waste three times 0.5 mL of an
aqueous solution of 0.1% AF (v/v). Load the peptide sample solution onto the cartridge and wash five
times with 0.5 mL aqueous solution of 0.1% AF (v/v). Elute the peptides from the column to a clean
1.5 mL tube with 0.35 mL of 80% ACN mixed with 20% aqueous solution of 0.2% AF (v/v). Evaporate
the eluting solution to dryness in vacuum centrifuge.
8. SAMPLE FILTRATION
After derivatization, filter the sample before loading LC column by passing it through cellulose
acetate spin filter 0.22 µm using low-speed centrifugation (e.g at 4000 rpm for 30 s).
9. SEPARATION BY CAPILLARY LIQUID CHROMATOGRAPHY
The CapLC system equipped with a Photodiode Array (PDA) detector coupled to TempoTM LC MALDI
spotter is used for peptide separation and collection directly onto the MALDI plate. Perform the
chromatographic separation on a silica based LC column C18, 300 µm x 150 mm I.D., 3.5 μm particle
size at 30°C. Set the flow rate to 2 µL/min and injection volume to 8 μL. Vial temperature is
maintained at 5°C in the autosampler tray. Use following mobile phases: mobile phase A consists of
0.1% TFA aqueous solution and mobile phase B consists of 80% ACN mixed with 20% aqueous
solution of 0.1% TFA (v/v). Eluted derivatized peptides are detected by UV absorbance at 280 nm.
Program the 50 min gradient elution to increase the percentage of solvent B from 5% to 80% over 35
min and then to condition the column back to the initial conditions until completion of the run. Set
complete gradient conditions following the Table 1.
Table 1. Complete gradient conditions
Time (min)
0
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A (%)
95
95
B (%)
5
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35
40
50
20
95
95
80
5
5
Set the spotter make-up flow to 2 μL/min (5 mg CHCA matrix dissolved in 1 mL of 50% ACN aqueous
solution). Example of typical LC-MALDI chromatogram is shown on Figure 3.
Figure 3. Example of typical LC-MALDI chromatogram.
STEP 4 - IDENTIFICATION
11. MASS SPECTROMETRY
MS acquisition (CAF-/CAF+) is performed with a MALDI TOF/TOF 4800 Plus analyzer equipped with a
200 Hz, 355 nm neodymium-doped yttrium aluminum garnet Nd:YAG laser. Ions are analyzed in
reflectron negative ion mode. The instrument parameters are set using the 4,000 Series Explorer
software version (V 3.5.3, Applied Biosystems, USA). Mass spectra are obtained by averaging 1,800
laser shots covering a mass range of m/z 1,000 to 4,000.
MS/MS acquisition is achieved by 1kV collision energy, first in negative than in positive ion mode
without usage of collision gas. The same precursor ions generated by negative ion MS were analyzed
in negative and positive MS/MS.
Precursor peak selection
LC-MALDI peak MS processing was controlled by so called job-wide peak selection method. Peak
selection was done automatically in order to analyze the MS spectra and acquire MS/MS data from
selected peaks. Parameters of MS/MS peak selection were as follows: Minimum S/N filter 15,
Minimum chromatogram peak width 3 (used to prevent redundant peak analysis in adjacent
fractions), Maximum precursors per fraction 20, Fraction-to-fraction precursor mass tolerance 200
ppm.
12. PROTEIN READER IDENTIFICATION
By depleted MS/MS spectra derived out of derivatized peptides (only b-ions in negative ion mode
and y-ions in positive ion mode are observed in MS/MS) peptide sequences can be read by specific
software named ProteinReader (Figure 4).
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Figure 4. De novo sequencing of derivatized peptide LGWYGFQNALIVR, m/z 1497.6111 obtained in
MS- and sequenced in MS/MS- and MS/MS+ by ProteinReader software.
Basic ProteinReader features are:
- Raw Data
- Database Match
- De novo Sequencing
- Report
All basic ProteinReader features are shown in Figures 5-8.
Raw Data
After the spectra data is imported into ProteinReader, a Spectrum viewer is created for
reviewing of a raw graphical spectral data. Tree view contains MS- parent directory with
MS/MS-/+ subdirectories. Raw graphical spectral data of each MS/MS spectrum allows
manual or automatic de novo sequencing from MS/MS- and MS/MS+ spectra (Figure 5).
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Figure 5. ProteinReader feature Raw Data.
Database Match
ProteinReader matches peaks from MS/MS- and MS/MS+ spectra along with MS- data against
NCBInr database to identify peptides/proteins. Processed and assembled data represents
assigned species. Identifying the same peptide from MS/MS- and MS/MS+ spectra of the
same precursor mass is referred as Sure Shot and it significantly increases reliability of
matched result. A separate Species table ranked all species by highest Sure Shot score. Based
on the number of matched peptides (primarily on quantitative number of Sure Shots),
ProteinReader is able to unambiguously determinate the species that is present in the
NCBInr database (more than 3000 species). Sure Shot does not rely on probabilistic scoring
algorithms used in similar database match search engines (e.g. MASCOT, PEAKS). It is a
simple amino acid overlap reading between MS/MS- and MS/MS+ spectra (from N-to Cterminus and back from C- to N-terminus, respectively). ProteinReader feature Database
Match is shown in figure 6.
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Figure 6. ProteinReader feature Database Match.
De novo Sequencing
Once ProteinReader Database Match identifies the species, de novo algorithm reads the
sequence from MS/MS- and MS/MS+ spectra and matches it against NCBInr database of the
selected species to perform another independent search (Figure 7). The repeated database
search does not take into consideration MS- spectra (precursor masses) and specific
algorithm for de novo reading does not match MS/MS masses against the database; it
matches final read idioms (≥ 5 amino acids in a series). Again, Sure shots of peptides read in
both forward and backward direction from MS/MS+ and MS/MS- spectra confirm veracity of
de novo read sequences. Since de novo reading algorithm does not follow database match
probabilistic logic it can be considered as independent and orthogonal peptide/protein
identifier.
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Figure 7. ProteinReader feature De novo Sequencing.
Report
Final result of analysis is reported for one species as intersection of results obtained from
Database Match and De novo Sequencing (Figure 8). Proteins found in identified species are
pull out in Report as: Sure Shots obtained in Database Match, Sure Shots obtained in De
novo reading, overlapped proteins obtained in Database Match and De novo Sequencing
with all identified peptides in both actions. Proteins that are not confirmed by Sure Shot or
Database Match and De novo Sequencing overlapping are not taken into consideration.
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Figure 8. ProteinReader feature Report.
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