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Proteomics and Protein Markers |
1 Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital, Leipzig, Germany.
aAddress correspondence to this author at: Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Liebigstr. 27, D-04103 Leipzig, Germany. Fax 49-341-9722209; e-mail thiery{at}medizin.uni-leipzig.de.
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Abstract |
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Methods: MBs with defined surface functionalities (hydrophobic interaction, cation exchange, and metal ion affinity) were used for peptide fractionation of urine. Mass accuracy and imprecision were calculated for 9 characteristic mass signals (Mr, 1000–10 000). Exogenous variables (instrument performance, urine sampling/storage conditions, freezing conditions, and freeze-thaw cycles) and endogenous variables (pH, urine salt and protein concentrations, and blood and bacteria interferences) were investigated with urine samples from 10 male and 10 female volunteers.
Results: We detected 427 different mass signals in the urine of healthy donors. Within- and between-day imprecision in relative signal intensities ranged from 1% to 14% and from 4% to 16%, respectively. Weak cation-exchange and metal ion affinity MB preparations required adjustment of the urinary pH to 7. Storage time, storage temperature, the number of freeze-thaw cycles, and bacterial and blood contamination significantly influenced urine peptide patterns. Individual urine peptide patterns differed significantly within and between days. This imprecision was diminished by normalization to a urinary protein content of 3.5 µg.
Conclusion: This reliable pretreatment protocol allows standardization of preanalytical modalities and facilitates reproducible peptidome profiling of human urine by means of MB separation in combination with MALDI-TOF MS.
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Introduction |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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The aim of our study was to investigate instrument performance and the effect of preanalytical variables on urinary peptidome profiling with MB separation and MALDI-TOF MS and to establish a reliable pretreatment protocol for collecting and storing urine samples to permit valid and reproducible analyses of urinary peptide patterns.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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-cyano-4-hydroxycinnamic acid were purchased from Bruker Daltonics. We used 0.2-mL polypropylene tubes (8-tube strips) for manually operated MB preparations. Automated MB preparations were performed with 96-well plates and TubePlates from Biozym, low-profile polypropylene tubes from ABgene, and Modular Reservoir Quarter Modules from Beckman Coulter. For sample storage, 450-µL CryoTubesTM were purchased from Sarstedt.
urine collection and storage
First- and 2nd-morning urine samples were collected from 20 healthy volunteers (10 women and 10 men, ages 22–41 years) in 100-mL urine cups (Sarstedt). Multivariable strips (Combur10 Test®; Roche Diagnostics) were used to analyze samples for specific gravity, pH, leukocytes, nitrite, protein, glucose, ketones, urobilinogen, bilirubin, and blood, and a Hitachi 917 analyzer (Roche Diagnostics) was used for assays of electrolytes, total protein, creatinine (enzymatic test), and urea (for results, see Table 1 in the Data Supplement that accompanies the online version of this article at http://www.clinchem.org/content/vol53/issue3). Unless otherwise stated, samples were centrifuged at 10 000g for 10 min at room temperature. Aliquots of 450 µL were stored at –80 °C. Urine samples were thawed at room temperature for 30 min, adjusted to pH 7, centrifuged again, and immediately processed for peptidome separation after the sample was adjusted for total protein content. Variations in sample pretreatment are described in the experimental section. The samples from the 10 female and 10 male volunteers were pooled for precision and mass accuracy analysis.
peptidome separation
We used ClinProtTM purification reagent sets (Bruker Daltonics) for peptidome separation of samples and magnetic particles (particle size, <1 µm; mean pore size, 40 nm; specific surface area, 100 cm2/g) with defined surface functionalities [MB–hydrophobic-interaction chromatography (MB–HIC C8), MB–immobilized metal ion affinity chromatography (MB–IMAC Cu) beads, and MB–weak cation-exchange chromatography (MB–WCX)].
MB purifications were performed according to the manufacturer’s protocol for serum and with the ClinProt liquid-handling robot. The protocol was adapted with regard to sample and binding-solution volumes. A 30-µL volume of the urine sample was diluted in 60 µL binding solution and added to the bead slurry (5 µL MB–HIC C8 beads, 5 µL MB–IMAC Cu beads, or 10 µL MB–WCX beads). After thorough stirring, samples were incubated for 1 min (MB–HIC C8 and MB–WCX beads) or 5 min (MB–IMAC Cu beads) at room temperature. The protein content was normalized by increasing the loaded urine sample volume in a stepwise manner. After the 1st fractionation step, residual urine was removed, and the procedure was repeated with a 2nd urine fraction (60 µL maximum). Following the stepwise application of sample and MB separation, the peptide fraction was eluted from MB–HIC C8 beads with 5 µL acetonitrile/water (1:1, volume/volume). For MB–WCX beads, we used 5 µL elution solution and 4 µL stabilization buffer, and we eluted the peptide fraction from MB–IMAC Cu beads with 10 µL of elution solution from Bruker Daltonics. To prepare the MALDI target, we spotted 1 µL of a mixture containing 10 µL 0.3 g/L -cyano-4-hydroxycinnamic acid in 2:1 ethanol/acetone (volume/volume) and 1 µL of the eluted peptide fraction onto the AnchorChipTM 600-µm target (Bruker Daltonics).
mass spectrometry
A linear MALDI-TOF mass spectrometer (Autoflex; Bruker Daltonics) was used for peptidome profiling with the following settings: linear positive mode; ion source 1, 20 kV; ion source 2, 18.50 kV; lens, 9.00 kV; pulsed ion extraction, 120 ns. For matrix suppression, we used a high gating factor with signal suppression up to an Mr of 500. Mass calibration was performed with the standard calibration mixture of peptides and proteins (Mr range, 1000–10 000). Four MALDI preparations (MALDI spots) from each sample were measured. For each MALDI spot, 450 spectra were acquired (30 laser shots at 15 different spot positions). To increase detection sensitivity, we removed excess matrix with 6 shots at a laser power of 45% before data acquisition at a power of 
25%. All signals with a signal-to-noise (S/N) ratio >3 in an Mr range of 1000–10 000 were collected with the AutoXecute tool of the flexControl acquisition software (version 2.0; Bruker Daltonics), and Bruker Daltonics flexAnalysis software was applied for data analysis. ClinProTools bioinformatics software (version 2.0 beta; Bruker Daltonics) was used for the recognition of peptide patterns.
evaluation of exogenous variables
Instrument performance.
Mass accuracy and within-day and between-day reproducibility were determined by the relative peak intensities of 9 characteristic signals of the urine sample. MB–HIC C8, MB–WCX, and MB–IMAC Cu beads were used for 10 bead preparations on 3 consecutive days.
Urine storage and freeze-thaw cycles.
The influence of storage temperature and time on the peptide profiles was investigated with the pooled urine sample after separation by MB–HIC C8. Pooled urine was divided into 2 aliquots. One milliliter of the fresh urine aliquot and 1 mL of a deep-frozen aliquot (thawed at room temperature for 30 min) were incubated in 1.5-mL vials at 4 °C, 25 °C, and 40 °C for 0, 1, 3, 6, 24, 72, and 168 h. At each defined time point, 4 30-µL aliquots were removed and prepared immediately. We also investigated the effect of up to 3 freeze-thaw cycles on the peptide pattern. A 1-mL aliquot of a pooled urine sample was frozen for 24 h and then thawed for 30 min at room temperature. Thirty microliters of urine was removed and processed immediately. The remaining sample was frozen again. The procedure was repeated twice.
evaluation of endogenous variables
Urine-collecting conditions.
We evaluated differences between urine samples collected on the 1st and 2nd mornings with urine aliquots from 5 female and 5 male volunteers. Samples were prepared with MB–HIC C8 beads according to the standard protocol. The peptide profiles were compared with respect to relative peak intensities.
Influence of urea and salt.
The influence of urea and salt content on peptide profiles was examined by adding urea and sodium chloride stock solutions to the pooled urine sample to achieve final concentrations of 50, 100, 250, 500, and 1000 mmol/L. A blank sample was diluted in the same way with water and analyzed to avoid misinterpretation of spectra caused by sample dilution.
Blood and bacterial interferences.
To investigate the effect of blood contamination on peptide pattern, we added whole blood to the pooled urine samples in blood–urine ratios of 1:100, 1:500, 1:1000, 1:2500, 1:5000, 1:10 000, and 1:20 000 (vol/vol). Results were compared with uncontaminated urine samples. In addition, the influence of bacteria was determined in an ex vivo simulation. One hundred microliters of an Escherichia coli suspension (106–1010 colony-forming units/L) was added to 900 µL of pooled urine samples without significant bacteriuria. These mixtures were incubated at room temperature for 0, 30, and 60 min. Urine samples were diluted 1:1 (volume/volume) with acetonitrile containing 5 g/L trifluoroacetic acid for inactivation of bacteria. The samples were then lyophilized, resuspended with 35 µL water, and processed by MB–MALDI-TOF MS (30 µL). The results were compared with sterile urine samples.
Creatinine, protein, and pH normalization.
Urine samples collected midstream from 10 volunteers on the 1st and 2nd mornings were normalized to the creatinine concentration and to the protein content. The creatinine concentration was adjusted to the lowest measured creatinine concentration (4 mmol/L for the 1st morning’s sample and 2.5 mmol/L for the 2nd morning’s urine sample) by diluting each sample with 0.15 mol/L sodium chloride. The total protein amounts of the 1st and 2nd morning’s urine samples were adjusted to 3.5 µg by varying sample volume from 30 to 153 µL. To evaluate the optimal pH value for MB purification, we adjusted the pH of pooled urine samples to pH 6, pH 7, pH 8, and pH 9 with 1 mol/L NH4HCO3 or 1 mol/L (NH4)2SO4.
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Results |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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Urine storage and freeze-thaw cycles.
The influence of storage temperature and time on the stability of the peptide pattern was investigated by incubating fresh and once-frozen pooled urine samples. Once-frozen samples showed greater reproducibility and improved stability against increased temperatures compared with fresh urine (data not shown). We also investigated the effect of 3 freeze-thaw cycles on the peptide pattern. Generally, freezing only once decreased the relative peak intensity of some mass signals (e.g., Mrs 1936.8, 3308.0, and 3485.5), whereas other mass signals (Mrs 2051.7, 2604.0, 2700.2, and 2946.6) increased. The variation in the relative intensities of mass signals in fresh and frozen urine is shown in Fig. 1
. Compared with once-frozen samples, recurrent freeze-thaw cycles (3x) did not further affect urine peptide patterns. The peptide patterns of once-frozen urine samples were stable up to 24 h at 4 °C with no detectable degradation; however, we observed significant changes in peptide patterns at 25 °C after 6 h of storage. At 40 °C, peptide patterns showed significant decreases and increases in signal intensities for numerous signals by 3 h (Fig. 2
).
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evaluation of endogenous variables
Urine-collecting conditions.
Urine samples collected on the 1st and 2nd mornings showed significant differences in relative signal intensities. The peptide profiles of 2nd-morning urine samples obtained with MB–HIC C8 beads featured reduced intensities for several low-Mr signals (e.g., 1684.0, 1771.1, 2195.4, 2440.6, and 3015.2) and by increases in other mass signals (e.g., Mrs 1828.3, 3006.7, and 6193.5). Therefore, the peptide patterns of urine samples collected on the 1st and 2nd mornings were different (Fig. 3
). We also investigated the variation in individual urinary-peptide patterns by analyzing midstream urine samples collected on the 1st and 2nd mornings for 5 consecutive days. The variation in relative signal intensities for 9 characteristic signals ranged from 4% to 31% for samples collected on the 1st morning and from 5% to 43% for samples collected on the 2nd morning. Compared with these peptidomic data, the median between-day variations in creatinine concentration for samples collected on the 1st and 2nd mornings were 31.9% and 28.2%, respectively, and those for total protein were 41.0% and 39.5%, respectively.
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Influence of urea and salt.
Increasing urea and sodium chloride concentrations did not disturb sample preparation or MS analyses up to a concentration of 1000 mmol/L.
Blood and bacterial interferences.
Blood contamination influenced the peptide patterns of urine samples. New mass signals were detected up to a urine–blood ratio of 2500:1 (see Fig. 1 in the online Data Supplement). For samples with a urine–blood ratio of 100:1, we detected both completely new signals and ion-suppression effects on previously detected signals.
We evaluated the effect of bacterial interference on peptide profiles with an ex vivo simulation. Comparison of the 4 sample groups (control urine and urine incubated at room temperature for 0, 30, and 60 min with 106–1010 colony-forming E. coli units/L) showed decreases in intensity for several signals in all urine samples incubated with a bacterial suspension for 
30 min. The most significant differences were observed for mass signals of Mrs 2794.5 and 4756.7 (Fig. 4
). This effect was not observed immediately after the addition of the bacteria.
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pH, creatinine, and protein normalization.
Urine pH influenced protein separation with the MB–WCX and MB–IMAC Cu beads. The best signal yield and highest signal intensities were obtained at pH 7 with MB–WCX beads (217 signals with an S/N ratio >3) and MB–IMAC Cu beads (197 signals with an S/N ratio >3). The numbers and intensities of signals with Mrs >3500 were decreased above pH 7. We observed no pH-dependent differences in peptide patterns with MB–HIC C8 beads.
We normalized creatinine concentrations by diluting urine samples to a particular creatinine concentration. Creatinine concentrations varied from 4.0 to 29.2 mmol/L for 1st-morning samples and from 2.5 to 15.9 mmol/L for 2nd-morning samples. We adjusted creatinine concentrations to 4 mmol/L (1st-morning samples) and 2.5 mmol/L (2nd-morning samples). A comparison of the spectra for normalized and nonnormalized urine samples after MB purification showed a decline in signals with an S/N ratio >10 of up to 15% in diluted samples, compared with undiluted samples. Signal losses of up to 35% were detected after normalizing the creatinine concentrations of 2nd-morning samples. Generally, adjustments in creatinine concentration via dilution did not decrease the variation in individual signals but produced a loss of mass signals.
Concentrations of total protein for the 20 analyzed urine samples ranged from 29.0 to 141.7 mg/L for 1st-morning samples and from 8.2 to 110.1 mg/L for 2nd-morning samples. Sample dilution to the lowest protein concentration produced a loss of mass signals similar to that observed for creatinine. Therefore, we varied the urine sample volume from 30 to 60 µL to obtain a maximal loading of the MBs. The capacity of the pipetting robot limited the maximum sample volume to 60 µL. Therefore, we normalized the total protein content of urine samples to 3.5 µg for the 1st- and 2nd-morning samples. With MB–HIC C8 purification, the number of mass signals in the urine with an S/N ratio >10 increased from 60 before protein normalization to 90 after normalization. In addition, interindividual variation in the urine peptide patterns of the 20 healthy volunteers was minimized (Fig. 5
).
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Discussion |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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MB–MALDI-TOF MS seems to be more sensitive than SELDI-TOF MS. With 3 different MB preparations (MB–HIC C8, MB–WCX, and MB–IMAC Cu beads), we detected 427 mass peaks with an S/N ratio >3 (Mr range, 1000–10 000). Previous investigations of urine with SELDI-TOF MS yielded fewer mass peaks. The WCX2 ProteinChipTM detected 180 peaks in 138 samples (7), the CM10 (cationic) and the IMAC30 (anionic) ProteinChips detected 133 peaks in the Mr range of 2000–20 000 (26), and use of the NP20 ProteinChip demonstrated only 25 peaks/spectrum (21). One reason for the improved sensitivity might be the higher adsorption capability of the beads’ porous surface structure compared with on-layer chips (3). Analysis of urine with MB–HIC C8 beads produced fewer mass peaks with an S/N ratio >3 than serum analysis (serum, 250 peaks; urine, 200 peaks) (29), but the 20% higher proportion of signals with an S/N ratio >10 in urine samples might improve data analysis. We also determined the reproducibility and mass accuracy of the MB–MALDI-TOF MS method. The within-day and between-day imprecision of urine peptidome profiling was <16%. SELDI-TOF MS produced imprecision values of up to 30% (21). One reason for the improved precision of MB–MALDI-TOF MS might be the application of 4-fold spotting of the MALDI target for each urine sample. The determination of the mass accuracy (Mr range, 1000–10 000) produced absolute differences in Mr of 0.35–3.5, which are comparable to our data for serum and in accordance with the known mass accuracy of MALDI-TOF MS (29)(31).
Differences in collection, sample storage, blood and bacterial interferences, and modes of normalization (creatinine, protein, and pH) of urine samples had significant effects on the variation in the peptide patterns. The time of urine collection (1st or 2nd morning) significantly influenced the peptide pattern because of the varying concentrations of urine components; therefore, it is important that collection times be defined exactly for all samples according to the requirements of the clinical study. Compared with our peptide analysis of serum, the urine peptide pattern is much more stable at room temperature (29); however, a storage time >6 h induced significant changes in peptide patterns and therefore should be avoided. In contrast to the results of Schaub et al. (21), we found differences between fresh and once-frozen samples. The peptide profiles of once-frozen urine samples showed better reproducibility. Therefore, we recommend that urine samples be frozen at –80 °C before processing.
We demonstrated that bacterial (E. coli) contamination affected the time-dependent alteration of several urine peptide mass signals (Mr range, 1000–10 000). Contamination with blood also interfered with the peptide pattern down to a urine–blood ratio of 2500:1, a contamination level that produces no change in urine color. It is important, therefore, that each urine sample be checked with a urine test strip for the presence of leukocytes, nitrite, and blood.
The use of MB–WCX and MB–IMAC Cu beads requires adjusting the urine pH to pH 7. In contrast, no pH adjustment is necessary for MB–HIC C8 separation because of the strongly acidic fractionation conditions and the hydrophobic interactions between analytes and the beads’ porous surface structure.
A sensitive point in urine proteome profiling is the dependence of the urinary protein concentration on the fluid intake and whether urine samples should be normalized to the protein content. We showed that adjusting the protein concentration by varying the volume of the applied sample minimized the influence of variation in urine protein concentration. Sample preparation for the MBs enables stepwise sample loading on the bead surfaces up to 5 µg total protein (the maximum loading capacity).
In conclusion, we showed that MB separation in combination with MALDI-TOF MS is a sensitive and reproducible analytic platform for peptidome profiling of human urine. The influence of various preanalytical variables must be taken into account, however. The reliable pretreatment protocol we have presented (Fig. 6
) allows standardization of the critical preanalytical phase and facilitates the reproducible peptidome profiling of human urine.
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Acknowledgments |
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Footnotes |
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1 Nonstandard abbreviations: SELDI-TOF, surface-enhanced laser desorption/ionization time-of-flight; MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight; MS, mass spectrometry; MB, magnetic bead; MB-HIC C8, magnetic bead–hydrophobic-interaction chromatography; MB-IMAC Cu, magnetic bead–immobilized metal ion affinity chromatography; MB–WCX, magnetic bead–weak cation-exchange chromatography; S/N, signal-to-noise.
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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