Comprehensive human urine standards for comparability and standardization in clinical proteome analysis

Authors


Abstract

Purpose: Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized “real life” sample that can be used as reference standard in urine clinical proteomics studies.

Experimental design: We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds.

Results: The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in “inter-laboratory” and “inter-platform” data comparison is also demonstrated.

Conclusions and clinical relevance: These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.

1 Introduction

The usefulness of urine analysis in clinical proteomics has been advocated in several initial studies 1–3 and was demonstrated in several recent studies (reviewed in 4, 5). Urine has become a main target in clinical proteome analysis and is already applied in clinical settings 6.

The multi-parametric analysis enabling identification of valid biomarkers mandates the availability of data sets from several hundred to thousands of patients and controls, as observed in genomics 7. Generally, the large data sets cannot be produced by a single laboratory. Hence, inter-laboratory comparison becomes essential, and the comparability of data sets will be the key success factor in clinical proteomics.

However, the current situation is far away from this need: comparability between laboratories and analytical platforms generally does not exist. The validation of platforms, if done at all, usually relies on the use of only a few highly purified proteins and synthetic peptides, providing a limited assessment of the technical variability of a platform. Importantly, such standards do not reflect the variability introduced during pre-analytical sample handling, associated with suppression effects, endogenous enzyme activity, adsorption, etc. These factors are regularly encountered during analysis of complex samples.

Furthermore, the exact composition of the urinary proteome remains largely unknown. While extensive lists of proteins based on the detection of tryptic peptides have been presented 8, 9, these usually lack measurements of abundance and precise information on the native peptides or proteins identified. For example, among several different fragments of collagen α-1(I) present in urine, some are disease-specific biomarkers, while others are not. However, most reports list the database hit, i.e. collagen α-1(I) chain precursor (a ∼110 kDa pre-protein) that is in fact unlikely to be present as a full length protein in urine.

Thus, an essential step forward is the introduction of a well-characterized urine sample that could be used as “standard”. This sample should (i) be representative of the currently identifiable normal urine proteome; (ii) be characterized in depth by different methods and platforms; (iii) enable to assess platform capability including pre-analytical steps, platform performance, and normalization; (iv) enable comparison of data sets; and (v) be freely available to all laboratories working in the field of urinary proteomics.

Here, we report on the generation and extensive characterization of two reference “standard” samples, representing “normal” pooled urine samples from healthy females and males, respectively.

2 Materials and methods

2.1 Urine samples

The two “standard” samples consisted of pooled midstream morning urine (collected between 8 and 10 am) from multiple collections from seven male and eight female healthy volunteers, respectively. There were no specific dietary or, in the case of females, menstrual cycle requirements (with the exception of absence of menstruation) for inclusion in the study. The use of pooled versus individual urine was favoured due to the need for large volumes, which renders the collection of the latter less practical and technically more demanding. All subjects in the study were healthy volunteers; only urine was collected and all samples were provided anonymously. All samples were collected in Germany, and under German law this study does not require IRB approval. Informed consent was obtained from participating individuals. The study complied with the guidelines of the Declaration of Helsinki (www.wma.net/en/30publications/10policies/b3/index.html). The collection in all cases followed the procedure that was used in several recent studies (e.g.10–12, full details on the collection protocol are also provided at www.eurokup.org: collection protocol for peptidomics analysis). This urine collection protocol is in agreement to a “standard protocol for urine collection” currently under development by the Human Urine and Kidney Proteome Project and European Kidney and Urine Proteomics COST Action (EuroKUP) networks (for more information please visit: www.eurokup.org; www.hukpp.org). To ease later comparison with samples collected at other centres and in agreement with the recently reported suggestions for gel-based urine proteomics 13, 14, no protease inhibitors were added and the pH was not adjusted. In addition, no phosphatase inhibitors were included. Demographical/clinical data on the volunteers are given in Table 1. Collected samples (between 40 and 100 mL per collection) were frozen immediately at −20°C. Upon completion of collection, all frozen samples were thawed on ice, sonicated, combined (total volume >2500 mL per gender group), divided into several 1, 10, and 50 mL aliquots, and frozen again at −80°C. The urinary proteome is not affected significantly by up to three freeze/thaw cycles following initial freezing (15 and unpublished data).

Table 1. Demographical data of subjects involved and concentration of clinically relevant analytes in the male and female urine standard
Analyte or parameterMaleFemale
  1. a

    Upper part of the table in bold: Demographic characteristics include average age, body mass index (BMI), glomerular filtration rate (in mL/min, estimated based on the Cockroft-Gould), and diastolic and systolic blood pressure (in mmHg). Lower part of the table: protein/peptide identity (name or sequence), and average concentration (in ng/mL) and standard deviation are given. n.d.: not detectable. The urinary peptides (see sequences in italic type) could be quantified with use of external stable isotope-labelled peptide standards 11. Hydroxylated proline sites are annotated by a “p”. For further sequence information see Supporting Information “Detailed Tables”).

Age36±628±6
BMI22.5±1.122.4±2.8
GFR (CG)108±6104±9
Diastolic BP77±471±6
Systolic BP126±4112±7
Creatinine879 000±26370787 000±23 610
Total protein14 600±36518 400±460
IgA557.7±23.3258.2±14.1
HAA-IgA0.224±0.0080.186±0.012
CD1410.15±0.3616.37±0.41
Ngal2.20±0.088.89±0.36
MGPRGPpGPpG1.82±1.002.84±1.42
ApGDRGEpGPp23.86±13.0929.19±12.34
GDPGPPGpPGpPGpPAI18.01±23.1922.17±13.11
SpGSpGPDGKTGPPGpAG3.75±1.46.29±2.16
PpGEAGKpGEQGVPGDLG0.79±0.571.39±1.02
EAIPMSIPPEVKFNKPFn.d.n.d.
NGDDGEAGKpGRpGERGPpGP8.24±6.0921.47±20.49
DAGApGApGGKGDAGApGERGPpG23.01±21.5131.65±16.65
AGPpGEAGKpGEQGVpGDLGAPGP1.59±0.933.28±1.57
AGPpGEAGKpGEQGVpGDLGApGP5.18±2.8912.45±2.75
ADGQpGAKGEpGDAGAKGDAGPpGPA8.70±4.1416.44±7.32
GKNGDDGEAGKpGRpGERGPpGPQ3.45±2.9911.09±6.67
TGPIGPpGPAGApGDKGESGPSGPAGPTG1.19±1.123.01±1.13
PpGESGREGApGAEGSpGRDGSpGAKGDRGETGP56.04±37.67193.30±87.88
MIEQNTKSPLFMGKVVNPTQKn.d.n.d.

2.2 2-DE analysis: Processing, separation, and identification of urinary proteins

Fifty millilitres of urine sample was concentrated approximately tenfold using the Millipore (Bedford, MA, USA) stir-cell apparatus with a PLBC Regenerated Cellulose membrane (3000 Da cut-off) under nitrogen pressure (4.5 bar). The protein content in the concentrated sample was determined to be 0.972 mg for the male sample and 1.242 mg for the female sample by the Bradford assay (Biorad, Hercules, CA, USA).

The concentrated urine samples were further subjected to protein precipitation using 7.5% trichloroacetic acid and 0.1% N-lauroylsarcosine sodium salt 16. Typical yields for this precipitation approach are 85–95% (Vlahou, unpublished data). Following an overnight incubation at −20°C, the samples were centrifuged at 10 000×g for 30 min. The supernatant was removed and the pellet washed twice with cold tetrahydrofuran. The pellet was resuspended in 800 μL sample buffer (7 M urea, 2 M thiourea, 4% w/v CHAPS, 1% w/v DTE, 50 mM Tris, pH 6.8), aliquoted in 150 μg aliquots, and stored at −20°C.

Two-dimensional separation of urinary proteins was performed as described previously 17 with the following modifications: the samples were loaded on IEF strips, pH 3–10 NL (18 cm; Biorad). Four hundred and fifty micrograms protein (for Coomassie staining) or 150 μg protein (for silver staining) was loaded onto the strips. Silver staining was performed according to Chevallet et al., Protocol B 18. To confirm reproducibility of profiles, urinary proteins from male and female samples were analysed in at least three replicates each. The gel with the female urine sample was used as master for the demonstration of spot identifications. Gels were scanned using GS-800 calibrated densitometer.

Protein spots were excised manually or automatically using Proteineer Sp Protein picker (Bruker Daltonics, Bremen, Germany). Tryptic digest and PMF were performed as previously described 17. In brief, peptide masses were analysed by MALDI-TOF-TOF MS (Ultraflex, Bruker Daltonics), peak lists were created with FlexAnalysis v2.2 software (Bruker), smoothing was applied with Savitzky-Golay algorithm (width m/z 0.2, cycle number 1), and a signal/noise threshold ratio of 2.5 was allowed. Resolution for the mass range of collected data (m/z 900–3000) was at least 6000 and for the calibrants at least 8000. For calibration, internal standard peptides des-Arg-bradykinin (Sigma, St. Louis, MO, USA 904.4681 Da) and adrenocorticotropic hormone fragment 18–39 (Sigma, 2465.1989 Da) included in the peptide mixture were utilized. The probability score with p<0.05 defined by the software was used as the criterion for the affirmative protein identification. Peaks corresponding to trypsin auto-proteolysis, matrix, and keratin fragments were not considered for protein search (MALDI-TOF MS spectra as well as peak list excluded from the analysis are provided in the Supporting Information “MALDI-TOF-MS PMF spectra” file).

For peptide matching (MASCOT Server 2.2.01; Matrix Science, London, UK), the following two settings were used for the MALDI-TOF MS data analysis:

  • (i)Standard parameters- MASCOT search: Database: Swiss-Prot; Taxonomy: Human; Enzyme: Trypsin; Mis-cleavages: 2; Mass tolerance: 25 ppm; Monoisotopic mass; Fixed modifications: carbamidomethylation (Cys); Variable modifications: Oxidation (Met).
  • (ii)Many variable modifications -MASCOT search: Database: Swiss-Prot; Taxonomy: Human; Enzyme: Trypsin; Mis-cleavages: 2; Mass tolerance: 25 ppm; Monoisotopic mass; Fixed modifications: none; Variable modifications: N-acetyl (protein), Cysteic acid (Cys), Oxidation (Met), Phospho (STY), Sulfonate (Met), Pyro-glu (N-term E), Pyro-glu (N-term Q).

The resulting protein and peptide identifications were manually filtered by detailed examination of the MALDI-TOF MS spectra for the occurrence of the peaks and comparison of the search results (i and ii, above). A delta mass of 0.03 was used as threshold for peptide identification. Data were searched against human entries in the Swiss-Prot (release 56.0; 20 402 entries database). Analysis of the data using a sequence-scrambled version of Swiss-Prot generated by the decoy-generating script available at Matrix Science (http://www.matrixscience.com/downloads/decoy.pl.gz) and using the settings described above provided no identifications.

Additionally, tryptic digests of selected spots identified by MALDI-TOF-MS as albumin and serotransferin isoforms were also analysed by CE-MS and similarly processed for their direct comparison to the former. The CE-MS identified peak lists are included in Supporting Information “Detailed Tables”, Spreadsheet “2DEspots-CEMS Analysis” and Supporting Information Fig. 1.

2.3 ELISA

CD14 levels were determined using Human sCD14 Quantikine ELISA Kit (R&D Systems, Minneapolis, MN, USA) and neutrophil gelatinase-associated lipocalin levels were measured with neutrophil gelatinase-associated lipocalin ELISA kit (BioPorto, Gentofte, Denmark). Urinary concentration of IgA and galactose-deficient IgA1 were measured by capture ELISA as described previously 19.

2.4 Urine sample processing, nano-HPLC FTMS/MS, and database search for 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra)

One millilitre of sample was deposited on a vivaspin 5 kDa cut-off microconcentrator (Sartorius group) and centrifugated (5000×g) to a volume of ∼100 μL. Two millilitres of deionized water (ELGA 18.2 MΩ) were added to the tube for desalting and the sample was centrifuged again to a volume of ∼30 μL. The concentrated sample was completed to 75 μL with Laemmli buffer 5× to redissolve proteins that may have adsorbed on the ultrafiltration membrane. Thirty microlitres of the sample were deposited on a 4–12% Bis-Tris precast 1-D gel (Invitrogen, Carlsbad, CA, USA) and separated. Following gel staining with Coomassie blue, 22 bands were cut and proteins were oxidized using H2O2 before in-gel trypsin digestion. The resulting peptide mixtures were vacuum-dried.

Before analysis, the peptide mixtures corresponding to each gel band were resuspended in 15 μL H2O-ACN-formic acid (97.8:2:0.2) spiked with 0.1% TFA.

All Nano-HPLC FTMS/MS experiments were performed on a 7-tesla hybrid linear ion trap Fourier transform mass spectrometer LTQ-FT Ultra (Thermo Electron, Bremen, Germany) coupled to an Ultimate 3000 (LC-Packings, Amsterdam, The Netherlands) high-performance liquid chromatographer. Samples were loaded on an LC-Packing Acclaim Pepmap 100 C18 precolumn (300 μm id, 5 mm long, 5 μm particles, 100 Å pores) and separated on an LC-Packings Pepmap nano-column (75 μm id, 15 cm long, 3 μm particles, 100 Å pores) coupled with a New Objective (Woburn, MA, USA) PicoTip electrospray emitter (30 μm). The nanoflow rate was set to 300 nL/min. Mobile phases consisted of (A) 0.1% formic acid, 97.9% water and 2% v/v/v ACN and (B) 0.08% formic acid, 20% water in 79.92% v/v/v ACN. The loading buffer (C) was composed of 0.2% formic acid 97.8% water and 2% v/v/v ACN. Ten microlitres of sample were loaded onto the precolumn during a 1 min injection event at a flow rate of 20 μL/min before the gradient was applied. The gradient profile was the following: from 4 to 50% B in 60 min; from 50 to 90% B in 5 min; constant 90% B for 5 min and return to 4% B in 1 min. The column was re-equilibrated for 28 min at 4% B between runs. MS data were acquired in the FTMS detection mode of operation (reduced profile) on an m/z 450–1800 range with resolution settings 50 000 at target 5e5. MS/MS spectra were obtained concomitantly with the FTMS detection for the three most-abundant ions on the LTQ ion trap at 35% collision energy. Dynamic exclusion was set to avoid reselecting the same ion multiple times, using a 5 ppm tolerance window and 3 min exclusion with one repeat during the first minute.

The MASCOT (version 2.2.03 Matrix Science) engine was used to perform searches against a database compiled from the Swiss-Prot (release 54.8) and Trembl (release 37.8) databases, using the following settings: taxonomy: human; mass tolerances: 10 ppm (MS) and 0.8 Da (MS/MS); enzyme: Trypsin/P; Variable modifications: N-Ac-protein, methionine oxidation and dioxidation, cystein trioxidation, and proline hydroxylation; allowed mis-cleavages: 2. The resulting peptide identifications were automatically filtered using the home-made software IRMa and consolidated into an MS identification database (msiDB). The criteria used to filter identifications were: Rank = 1, peptide score >identity threshold (p<0.05). The target-decoy approach was used to estimate false-positive identifications rates. The average false discovery rate (FDR) received during this analysis was below 2%.

2.5 CE-MS sample preparation, analysis, and data processing

The urine samples were prepared as described previously 20. Shortly, 0.7-mL aliquots were diluted 1:1 with an aqueous solution containing 2 M urea, 10 mM NH4OH, and 0.02% SDS. For removal of high-molecular mass proteins, ultrafiltration using Centrisart ultracentrifugation filter devices (20 kDa molecular mass cut-off; Sartorius, Goettingen, Germany) was used. Centrifugation was carried out at 3000×g until 1.1 mL of filtrate was obtained. After desalting on PD-10 columns (GE Healthcare, Munich, Germany) pre-equilibrated with 0.01% NH4OH, samples were lyophilized and stored at 4°C. Before CE-MS analysis, samples were reconstituted in 9 μL water (plus, if applicable, 1 μL external standard stock solution; see below) irrespective of protein content to keep reference standards constant.

CE-MS analysis was performed in two different laboratories (Hannover and Glasgow) essentially as described previously 21. A P/ACE MDQ capillary electrophoresis system (Beckman Coulter, Fullerton, CA, USA) was coupled to either a micrOTOF MS (Bruker Daltronic, Bremen, Germany) in Hannover, Germany or to a micrOTOF-Q MS/MS (Bruker Daltronic) in Glasgow, UK. Twenty percent ACN (Sigma-Aldrich, Taufkirchen, Germany) in HPLC-grade water (Roth, Karlsruhe, Germany) supplemented with 0.94% formic acid (Sigma-Aldrich) was used as running buffer. For CE-MS analysis, the ESI interface from Agilent Technologies (Palo Alto, CA, USA) was used. Spectra were recorded over an m/z range of 350–3000 and accumulated every 3 s. The MosaiquesVisu software was used to deconvolute mass spectral ion peaks from the same molecule at different charge states into a single mass 22. To achieve high mass accuracy, deconvoluted TOF signals were calibrated based on FT-ICR-derived accurate masses (mass deviation <1 ppm) as described previously 23. After calibration, mass deviation of TOF-MS data was found to be 2±8 ppm. A probabilistic clustering process was implemented in parallel for normalization of CE-retention times and calibration of signal intensities. This was accomplished by local regression analysis of each analysis to specific urinary calibrants that serve as internal standards 11. All detected peptides were deposited, matched, and annotated in a Microsoft SQL database.

The analytical characteristics of the CE-MS system were extensively investigated and described by Theodorescu et al. 20; and Haubitz et al. 10. Briefly, the average recovery of the sample after preparation was 85%. The limit of detection was found to be approx. 1 fmol. Resolution >8000 ensured the detection of monoisotopic mass signals for z≤6.

2.6 Quantification using stable isotope-labelled external standards by CE-MS analysis

For absolute quantification, stable isotope-labelled peptides were used as described previously 11. Samples (9 μL) were spiked with 1 μL of a stable isotope-labelled external standard solution (for concentration of the different peptides see 11), and 290 nL of this sample was injected into the CE, resulting in between 0.09 and 20 ng of each synthetic peptide being injected. Resulting MS signal (ion counts) were correlated with the known concentration of the standard peptides. Amount of endogenous peptide was assessed using the calibration curves previously established. The analysis was repeated 15 times, and the mean and standard deviation of the results are reported in Tables 1 and 2.

Table 2. Summary of methods and technologies employed for the analysis of the standard urine samples
TechniqueSamplepreparationSeparationDigestionMS Identification Quantification
     EngineModificationsAccuracy 
  • a

    UF: ultrafiltration; MWCO: molecular weight cut-off; N/A: not applicable; H: Hannover; G: Glasgow.

  • a)

    a) An alternative search method with multiple variable modifications was also tested as described in Section 2 (2-DE analysis).

2-DEUF (3000 MWCO) trichloroacetic acid/N-lauroylsarcosine sodium salt precipitationIEF 3–10, NL 11% PAGETrypsinMALDI-TOF/TOFMASCOT 2.2.01Fixed modification: carbamidomethylation (Cys); variable: oxidation (Met)a)25 ppm (MS)N/A
GeLCMSUF (5000 MWCO)4–12% Bis-Tris PAGE and Ultimate 3000 coupled to MSOxidation trypsinLTQ-FT UltraMASCOT 2.2.03Variable modifications: N-Ac-protein, methionine oxidation, and dioxidation, cystein trioxidation and proline hydroxylation10 ppm (MS), 0.8 Da (MS/MS)N/A
CE-MSUF (20 000 MWCO), desalting (PD-10), lyophilizationP/ACE MDQ CE coupled to MSNonemicrOTOF MS (H) or micrOTOF-Q MS/MS (G)MASCOT Internet version, OMSSA 2.1.4Variable modifications: oxidation of methionine, lysine, and proline0.5 Da (MS), 0.7 Da (MS/MS)Internal standards and spiked isotope labelled peptides
LC-MS and MS/MSUF (20 000 MWCO), desalting (PD-10), lyophilizationUltimate3000 coupled to MSNoneLTQ-OrbitrapMASCOT 2.2.03Variable modfications: oxidation of methionine, lysine and proline10 ppm (MS), 0.8 Da (MS/MS)Internal standards

2.7 LC-MS sample preparation, analysis, and data processing

LC-MS analysis of endogeneous peptides was performed with an Ultimate3000 system (Dionex, Amsterdam, The Netherlands) coupled to an LTQ-Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany). High-resolution MS scans were acquired in the Orbitrap analyser while MS/MS scans were triggered in parallel in the LTQ ion trap. Urine samples were prepared as described above (see Section 2.5). Lyophilized peptides were reconstituted in 14 μL of 2% ACN, 0.05% TFA, and an aliquot of 5 μL (approximatively 7 μg total peptide) was loaded onto a C18 precolumn (300 μm id×5 mm, Dionex) at 20 μL/min in 2% ACN, 0.05% TFA. After desalting, the precolumn was switched online with the analytical column (75 μm id×15 cm PepMap C18, Dionex) and equilibrated in solvent A (5% ACN, 0.2% formic acid). Peptides were eluted using a 0–60% gradient of solvent B (80% ACN, 0.2% formic acid) for 60 min at 300 nL/min flow rate. The LTQ-Orbitrap was operated in data-dependent acquisition mode. Survey full scan MS spectra (m/z mass range 300–2000) were acquired in the Orbitrap with the resolution set to a value of 60 000 at m/z 400 (target value of 1 000 000 charges in the linear ion trap). The five most intense ions per survey scan (excluding singly charged) were selected for MS/MS fragmentation using CID and the resulting fragments were analysed in the linear ion trap (parallel mode, target value 10 000). Collision energy was set to 35% for MS/MS. Dynamic exclusion was employed within 60 s to prevent repetitive selection of the same peptide. For each peptide mixture (male and female), seven replicate LC-MS runs were performed. RAW files were converted into mzxml files with the use of ReAdW (version 4.2.0). For further comparisons this file format was used with msInspect (version 2.0) (http://proteomics.fhcrc.org/CPL/msinspect/) to generate a peaklist of the MS data. For matching of the various LC-MS data, these were calibrated with respect to abundance based on the 29 internal standards and using the same procedure as described above for CE-MS.

Database search from MS/MS data acquired with the LTQ-Orbitrap was performed using the MASCOT Daemon software (version 2.2.03, Matrix Science). The following parameters were set for creation of the peak lists: parent ions in the mass range 400–4500, no grouping of MS/MS scans, and threshold at 1000. Data were searched against human entries in the Uniprot database (release 14.0, 72 400 sequences, compiled from the Swiss-Prot (release 56.0) and Trembl (release 39.0) databases), without any enzyme specificity. No fixed modification was selected, and oxidation of methionine and proline were set as variable modifications. The mass tolerance was set to 10 ppm and 0.8 Da for MS and MS/MS, respectively. MASCOT results were parsed with the in-house developed software MFPaQ version 4.0 (http://mfpaq.sourceforge.net/) and top ranking peptides with a MASCOT score of more than 35 were automatically selected. In order to calculate the FDR, the search was performed using the “decoy” option in MASCOT, and MFPaQ used the same threshold to validate decoy and target hits. The FDR was calculated for each database search at the peptide level (FDR = number of validated decoy hits/(number of validated target hits + number of validated decoy hits)×100), and the average value for all samples analysed was 2.8 % for a MASCOT score of 35. In addition, criteria related to the mass accuracy and the frequency of detection in all replicate samples were also used to validate peptides reported in the final list. Deviation between the experimental m/z and the theoretical m/z of the identified sequence was calculated for all peptides, boxplot analysis was performed to detect the outliers. The median mass shift was 2.2 ppm, peptides identified with a mass deviation >2.5 ppm from this value were removed from the list. The MS signal intensity of the sequenced peptides was extracted from each replicate run of male and female samples using MFPaQ. Only peptides for which MS signal was found in at least four of the seven analysis for each sample were provided in the list of sequenced peptides.

In addition, several peptides were also previously sequenced using LC-MS/MS analysis in other laboratories, as recently described in detail 23. Here, the average FDR received during these analyses was below 2%.

To enable comparison of CE- and LC-MS data, the identity of peptides in CE- and LC-MS was established on the basis of sequence, mass, and CE migration time. In the absence of sequence information, peptides were considered identical if the mass deviation was less than 30 ppm and the difference in abundance was less than fourfold.

3 Results

In a multi-institutional effort we have analysed the urinary proteome and peptidome of two “standard” human urine samples, representing pooled urine from healthy human male and female. The depth of the urinary proteome/peptidome covered by this multi-institutional analysis is reflected in Fig. 1. Analyses were performed in different laboratories using nearly all available state-of-the-art proteomics technologies and instruments, including 2-DE in combination with MALDI TOF MS, LC-MS and MS/MS using an LTQ-Orbitrap MS, 1-D gel in combination with nano-LC MS/MS using a hybrid linear ion trap Fourier transform MS (LTQ-FT Ultra; this method will be abbreviated as GeLC-MS) as well as CE coupled to MS (CE-MS. In all cases, participating laboratories applied their established protocols for sample preparation, analysis, and data processing (Summarized in Table 2).

Figure 1.

Representative examples of analysis of the human standard urine sample by different proteomics technologies. (A) 1-D gel used for fractionation in the GeLC-MS enables separation by mass and allows for ample material in the subsequent LC-MS/MS analysis of the respective tryptic fragments. The respective molecular weight zones that were excised are indicated on the right. (B) 2-DE-MS of the female sample, due to its high resolution, enables separation of isoforms/different PTMs. At the same time, representation of the entire gel in the subsequent MS/MS analysis, as in 1-DE, is generally not preformed, due to the size of the gel and the consequently high number of LC-MS/MS analyses required. (C) CE-MS (shown is the female sample) enables analysis of the lower molecular weight portion of the urinary proteome that cannot be addressed adequately by SDS-gel-based approaches. However, the evidently very high resolution can only be utilized in the analysis of molecules at lower mass, in general <15 kDa.

3.1 Clinical characterization of samples

In order to provide commonly used clinical reference points, volunteers were characterized for various clinico-pathological characteristics as presented in Table 1. In addition, the urine samples were characterized by conventional immunological assays (ELISA) for certain disease-specific biomarkers used in routine clinical laboratory testing. Specifically, biomarkers associated with IgA-Nephropathy (CD14, IgA and galactose-deficient IgA1) were examined by routine clinical ELISAs and results are provided in Table 1.

3.2 2-DE

The identification score, peptide coverage, and peptides for each of the identified protein spots (Fig. 1) are provided in Supporting Information “Detailed Tables”, spreadsheet “2DE Master”. In addition, identification and predicted modification data received from the analysis of the various peptides in comparison to those of the respective peptides identified during the GeLC-MS analysis and in a similar mass zone are provided (Fig. 2 and Supporting Information “Detailed Tables”, spreadsheet “2DE Master”). A total of 92 protein spots were identified using PMF, whose position in the gel and identity are in general agreement to published urinary data from normal individuals using similar sample preparation and electrophoretic protocols 3, 17, 24, 25.

Further, CE-MS analysis of tryptic peptides from spots identified by MALDI as albumin and serotransferin isoforms provided increased sequence coverage and predicted the presence of selected modifications per isoform (Supporting Information Fig. 1 a-h and Supporting Information “Detailed Tables”, spreadsheet “2DEspots-CEMS Analysis”).

3.3 GeLC-MS

Analyses of the 44 gel bands (see Fig. 1) corresponding to male and female urines resulted in ∼10 000 identifications pointing to ∼2450 protein accessions (including same and sub-sets). Results were compiled by sample and by band and proteins grouped in a similar way as MASCOT does. However, the protein representative of each group was selected on the basis of its emergence in the list of identifications. If two proteins shared the same set of peptides in a given analysis, the representative protein would be the one that appeared most frequently as master in all the analyses. The results by sample and by band are presented in Supporting Information “Detailed Tables”, spreadsheets “GeLC-MSMS Identification List” and “GeLC-MSMS Heat Map”, respectively. A table summarizing the different protein groups, their representatives, and the list of proteins belonging to each group, is also presented. (Supporting Information “Detailed Tables”, spreadsheet “GeLC-MSMS Protein Groups”).

3.4 CE-MS

CE-MS analysis of male and female standard samples was repeated 25 times in Hannover and seven times in Glasgow to ensure high confidence in the detected peptides. Only peptides that could be detected in at least 30% of these analyses (in either sample, using either instrumental setup) were accepted. A graphical depiction of the data is shown in Fig. 3A. The calibrated and annotated CE-MS data are available in Supporting Information “Detailed Tables”, spreadsheet “CE-(ESI)-MS male, female”. In the resulting CE-MS profiles, each peptide is identifiable by its mass and CE migration time, and ion signal intensity is used as measure for relative abundance. The sequences of 292 peptides (including PTMs) identified by LC-MS/MS are given. Identified peptides originate from 31 different protein precursors. Absolute quantification of some peptides was done using external stable isotope-labelled peptide standards. These results are provided in Tables 1 and 2.

To evaluate comparability between the male and the female sample, peptides that are among the 40 most-abundant (based on ion-counting) peaks from each sample were compared after calibration of the ion counts. Most of these 40 peaks were among the 40 most abundant in both samples. In total 47 peptides (33 of the 40 were found among the 40 most abundant in both samples) were compared. Further, and as evident from the comparison shown in Fig. 3C, most peaks were recorded with similar intensity in the male and the female samples, indicating the high quality of sample material. The intervariability between the labs is displayed by an overlap of 94.4% using the most abundant peptides, which demonstrated approximately 40% of the sample amount.

Notably, as these samples serve as “healthy human urine standards”, we also assessed their scoring versus previously established biomarker patterns for the following diseases: diabetes 26, diabetic nephropathy 27, chronic kidney disease 26, IgA nephropathy 28, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis 10, bladder cancer 20, and coronary artery disease 29, using CE-MS. In all of these biomarker models, both samples scored as normal healthy controls, confirming that they represent adequate baseline controls.

3.5 LC-MS and MS/MS

LC-MS profiling of male and female standard samples was performed on an LTQ-Orbitrap, and was repeated seven times to ensure high confidence in the detected peptides. The results of this analysis are shown in Fig. 3B and provided in Supporting Information “Detailed Tables”, spreadsheet: “LC-(ESI)-MS male, female”. As in the case of CE-MS analysis, we compared male and female data sets by aligning the 40 most-abundant peaks from each sample. Most of these 40 peaks were the same for the two samples and in total 46 peptides were compared and showed very similar intensity profiles (data not shown).

In parallel, MS/MS sequencing of the most abundant peptide ions was performed in the LTQ ion-trap. Two hundred and eighty-two unique peptides (detected in at least four of the seven analyses for each sample) were identified, with validation criteria based on MASCOT scoring, with a median mass shift of 2.2 ppm and a maximum standard mass deviation of ±2.5 ppm from this value. These sequenced peptides originate from 31 different protein precursors, among which are highly abundant collagens, but also other proteins already known to produce proteolytic fragments in urine. Matching of identified sequences to LC-MS peaks extracted with msInspect was performed based on accurate mass and elution time, as shown in Supporting Information “Detailed Tables”, spreadsheet “LC-(ESI)-MS male, female”.

3.6 Application of standard urine in inter-lab and platform comparability

To evaluate comparability between different instrumental setups in different laboratories, the 40 most abundant peaks in the individual samples analysed using CE-TOF (Hannover) and CE-Q-TOF (Glasgow) were identified and compared. Again, most of these 40 peaks were among the 40 most abundant in all of the data sets, resulting in a total of only 66 peptides. These 40 peaks account for approximately 40% of the total signal (see Supporting Information “Detailed Tables”, spreadsheet “CE-(ESI)-MS male, female”).

As a proof of principle for the application of these standard samples in estimating comparability of different MS platforms, we further compared data sets obtained on the two CE-MS platforms (see above) with those obtained using an Ultimate3000 nanoLC system coupled to an LTQ-Orbitrap mass spectrometer, sited in Toulouse (France). When comparing the 40 most-abundant sequenced peptides detected at the different sites, high consistency of the data sets was apparent (overlap: male 87%, female 89%), as well as some expected differences (see Supporting Information “Detailed Tables”, spreadsheet “Comparison CE-MS vs. LC-MS” and Fig. 3C). For example, several low molecular weight peptides detected by CE-MS were missing in the LC-MS data, likely due to their inability to bind to the LC column materials. Additionally, several high molecular weight peptides were absent in the LC-MS data, likely because of precipitation on the column material. This comparison highlights one advantage of CE in comparison to LC: selective loss of peptides is generally not observed. These results show that on the basis of a common standard a comparative analysis between data sets generated on different platforms and at different sites is possible after appropriate adjustment and recalibration of the data.

3.7 Data integration from different techniques

Data generated by different proteomics technologies are not always comparable and thereby combination of observations results in some information loss. For example, while GeLC-MS provides identification of tryptic peptides via sequence annotation, it generally does not provide a measure of abundance. In contrast, CE- or LC-MS gives measures of abundance, but not immediate sequence identification. In an effort to integrate the acquired data in an informative way, two tables were generated compiling respectively the proteomics (“bottom-up” approaches: 2-DE, GeLC-MS) and peptidomics data (LC-MS and CE-MS, “top-down” approaches; Supporting Information “Compiled Tables”). A detailed (within the limitations of each technique) description of the physicochemical properties of the identified proteins and peptides is provided. Specifically, in the case of the proteomics data (Supporting Information “Compiled Tables”, spreadsheet “GeLC-MS and 2DE combined”), the observed molecular weight and pI values of the proteins, as applicable, are shown. It should be noted that no homogenization of molecular weight calculations of the two techniques was made since rules for this were not always evident. For example, by 2-DE distinct isoforms of albumin were observed at 70, 68, 65 kDa, which could all correspond to the 69 kDa Albumin detected by GeLC-MS. It should also be noted that same identifications at adjacent molecular weight zones may not correspond to distinct isoforms but rather to cross-contamination. Since distinction of the two possibilities is impossible, we show all available information.

In the case of the low molecular weight proteome and to display all data available, we combined the CE- and the LC-MS data (Supporting Information “Compiled Tables”, spreadsheet “CE-MS and LC-MS combined”). While this was possible with high confidence for the sequenced peptides, to do so in the absence of sequence was challenging. The second parameters that are used for identification, CE migration time or LC retention time, cannot be correlated to each other. This is also evident from Fig. 3, where no correlation can be found for the entire CE- and LC-MS analyses or the data that show distribution of the peptides from collagen α-1 (I), collagen α-1 (III), or uromodulin. As a compromise aiming at avoiding artificial duplication (a single peptide being listed as two different peptides), but at the same time avoiding reporting two different peptides as identical, we have considered peptides identical, if the mass deviation between the LC- and the CE-MS data was less than 30 ppm, and the difference between the normalized signal amplitude was below fourfold. The combined data are given in Supporting Information “Compiled Tables”, spreadsheet “CE-MS and LC-MS combined”.

Combination of the proteomics with peptidomics data in one table is impossible due to the completely different data representation. Nevertheless, an effort to combine sequence information received from the different techniques may be made: For example, mapping of the identified peptides of uromodulin (uromodulin spots detected by 2-DE are shown in Fig. 1; CE-MS uromodulin fragments detected by CE-MS and LC-MS are shown in Fig. 3) on the protein sequence reveals that the N- and C-termini of the protein have not been detected by any of the applied techniques (Fig. 4). The “native” peptides identified by the peptidomics approaches are located close to the C-terminus of the protein. In the case of albumin, even though very extensive sequence coverage is received by the combination of techniques, a peptide of the N-terminus of the protein remained undetected in the vast majority of applied techniques (Fig. 2B) with the only exception being the analysis of tryptic digests of 2-DE spot 24 by CE-MS (see Supporting Information Fig. 1e). These observations, even though not conclusive at this point, particularly in view of the expected continuous data accumulation from this sample, may form the basis for hypothesis-driven research questions relating to expected native peptides, “hot spots” for protein modifications, specific proteolytic sites, etc.

Figure 2.

Comparison of the identification results from GeLC-MS and 2-DE. (A) Graphical representation of the results from the analysis of the 56–69 kDa band zone by GeLC-MS and 2-DE referring to the number of unique protein identifications provided by each technique; using albumin as an example, a comparison of the number of detected isoforms, peptides, and respective cumulative sequence coverage (%) provided by each technique is also made. (B) The sequences of the identified peptides using GeLC-MS and 2-DE are also shown. Red characters indicate the identified peptides of the protein and blue characters indicate unique identifications by one approach. For comparison, regions of the protein detected as native peptides by CE-MS and/or LC-MS are underlined.

Figure 3.

Display of the low molecular weight proteome of the human urine standard. (A) Peptides and proteins detected using CE-MS: shown are compiled patterns of the individual analyses. The molecular mass on a logarithmic scale (0.8–20 kDa, indicated on the left) is plotted against normalized migration time (18–48 min, indicated on the bottom). Average signal intensity is encoded by peak height and color. Upper panel: all detected signals (corresponding to Supporting Information “Detailed Tables”, spreadsheet “CE-(ESI)-MS male, female”). Lower panels: Distribution of the collagen α-1 (I), the collagen α-1 (III), and the uromodulin peptides, as indicated on the left. (B) Peptides and proteins detected using LC-MS. Shown are compiled patterns of the individual analyses. The molecular mass on a logarithmic scale (0.8–20 kDa, indicated on the left) is plotted against retention time (18–48 min, indicated on the bottom). Average signal intensity is encoded by peak height and color. Upper panel: all detected signals (corresponding to Supporting Information “Detailed Tables”, spreadsheet “LC-(ESI)-MS female, male”). Lower panels: Distribution of the collagen α-1 (I), the collagen α-1 (III), and the uromodulin peptides, as indicated on the right. (C) Inter-laboratory and inter-platform comparisons of the 40 most-abundant sequenced peptides (based on ion counting) in the standard male and the female samples. These peptides account for ∼40% of the total signal. The majority of these peptides represent degradation products from collagen, uromodulin, and fibrinogen, as indicated on the bottom. As expected, a very high similarity between the data obtained on the two samples on an identical instrument can be observed, with most of these peptides being among the 40 most-abundant peptides in both samples. When comparing data obtained on similar, yet different, instruments (comparing upper two panels from CE-TOF with the middle two panels from CE-Q-TOF), good comparability can be observed, and most peptides can be detected with similar abundance. Analysis of the same samples on a completely different platform (LC-coupled Orbitrap) results in similar data. Most noticeable: the absence of very small and very large peptides in the LC-MS analysis. This is likely due to small and highly charged peptides not binding to the reversed-phase material and large peptides likely precipitating on the column, and thereby not eluting.

Figure 4.

Comparison of the identification results from the different techniques. Position of the uromodulin peptides detected by the employed techniques (2-DE, GeLC-MS, CE-MS, and LC-MS) on the protein sequence. The numeric labelling is based on the protein theoretical primary sequence (grey bar). The numbers in front of the bars correspond to the spot numbers of the 2-DE master gel (see Supporting Information “Detailed Tables”, spreadsheet “2DEMaster”) or to the gel band in the case of GeLC-MS (see Supporting Information “Detailed Tables”, spreadsheet “GeLC-MSMS Identification List”). The GeLC-MS female and male data are merged. In the case of the 2-DE and GeLC-MS approaches the detected peptides correspond to tryptic digests of the respective spots or bands. In the case of CE- and LC-MS analysis the naturally occurring peptides are shown, as identified by following MS/MS.

4 Discussion

We have generated two human urine samples that are available in large quantities, likely representative of the currently best-characterized urine specimens, and that can be used as “standards” in future urine proteomics analysis to enable inter-laboratory comparison of data sets.

In contrast to previous reports, analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs (within the limitation of the technologies employed), and the relative abundance of these compounds.

Proteins and peptides in urine generally are present in several different forms due to different posttranslational processing, including specific proteolysis 23. This is also evident from the data presented here, where we describe several different and distinct proteins and peptides that originate from the same parental protein. It is essential to accurately define these entities, as only some are biomarkers for disease (e.g. different, specific degradation products in renal pathology 30), and these different forms must be clearly distinguished.

The combination of different technologies allowed coverage of a wide mass range from the protein down to the peptide level, revealing the advantages of the different technologies and their complementarities. Specifically, and as expected, the various platforms and technologies yielded differences in the number of detected and identified peptides and proteins. However, both extensive overlaps and extensive complementarities in the information provided by different data sets were observed. For example, while the uromodulin protein was detectable in both, 2-DE and GeLC-MS experiments, naturally existing uromodulin peptides could only be identified by CE-MS or LC-MS analysis (Fig. 3). In addition, the presence of different uromodulin isoforms could be observed only on 2-D gels.

Due to the age of the participating volunteers (Table 1), and the increasing evidence supporting the presence of age-associated protein changes to urine 31, the reported proteome is considered more representative of younger age groups. In addition, while the two samples have been exhaustively analysed by current state-of-the art methods, they were not analysed “to completion”, i.e. not all of their compounds are currently known and quantified. Notably, the sample collection protocol that was followed is not compatible with the recommended procedure for the study of exosomal or other urine solid phase proteins 4, 9. In addition, the collection of more quantitative data is undoubtedly needed and is currently under way. Nevertheless, due to the combinatorial application of techniques, these samples likely represent the most extensively and comprehensively investigated urine samples reported.

These multi-institutional and multi-technology-based data sets of urinary proteins and peptides from two distinct standard samples are the foundation for the comprehensive compilation of the urine proteome. To facilitate this effort, the full list of identified peptides and proteins and pertinent separation and MS data are also available at the European Kidney and Urine Proteomics Action website (www.eurokup.org; 32) and Human ProteinPedia (accession number HuPA_000668). Importantly, future data sets that are obtained using these two samples will be also made freely available via the EuroKUP website. The development of unified systems for protocol and data reporting, processing, comparison, and mining for clinical urine proteomics is evident and mandatory for achieving clinical impact. This is under development in the EuroKUP consortium and will result in a continuous increase of the depth and breath of the characterization of these standard samples. Thus, they will be a resource of increasing value to the community and an invitation to optimize and complete the knowledge on the human urinary proteome/peptidome. Investigators interested in acquiring aliquots of the standard urine sample are invited to contact Harald Mischak (mischak@mosaiques.de).

Clinical Relevance

This manuscript describes the establishment and comprehensive analysis of two urine samples (male and female) in a multi-institutional study initiated within the Urine and Kidney Proteomics Cost Action (EuroKUP; www.eurokup.org). Analysed by all state-of the art technologies available to us (CE-MS, LC-MS, LC-MS/MS, 1-DE- and 2-DE-MS/MS), these samples likely represent the currently best-characterized urine specimens (both proteome and peptidome were investigated in depth). Further, we show that these specimens enable “inter-laboratory” and “inter-platform” comparison of data, and also allow pinpointing the advantages and complementarities of the different technologies.

Importantly, these urine samples will be freely available to laboratories worldwide via EuroKUP, laying the foundation for the continuous increase of the depth and breath of the proteome coverage and making them a resource of increasing value to the community. We are convinced that they will serve as reference in most future urinary proteomics studies, substantially increasing the data quality, especially in the context of clinical biomarker discovery studies.

  • 2

    University of Glasgow, Glasgow, UK

  • 3

    Beatson Institute for Cancer Research, Glasgow, UK

  • 4

    Biomedical Research Foundation Academy of Athens, Greece

  • 5

    CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse, France

  • 6

    Université de Toulouse; UPS; IPBS; Toulouse, France

  • 7

    CEA, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, Grenoble, France

  • 8

    Nephrology and Rheumatology UMG, Georg-August University Goettingen, Germany

  • 9

    Helmholtz Center for Infection Research, Braunschweig, Germany

  • 10

    University of Alabama at Birmingham, Birmingham, AL, USA

  • 11

    The Linnaeus Centre for Bioinformatics, SLU, Uppsala, Sweden

  • 12

    Hannover Medical School, Department of Pharmacology, Hannover, Germany

  • 13

    Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand

  • 14

    Institut National de la Santé et de la Recherche Médicale (INSERM), U858, Toulouse, France and Institut de Médecine Moléculaire de Rangueil, Université Toulouse III Paul-Sabatier, Toulouse, France

Acknowledgements

This work was funded in part by grants from the European Union through InGenious HyperCare (grant LSHM-C7-2006-037093) to H.M. and the EuroKUP COST Action (BM0702). A.V., M.A., M.M., J.Z. and J.G., C.M., M.C. acknowledge financial support from FP7 DECanBio (201333). In addition, D.B., C.L., A.G.P., B.M. and J.P.S. acknowledge financial support from the Agence Nationale pour la Recherche (ANR-07-PHYSIO-004-01). J.N. and H.S. acknowledge support by NIH grants DK075868 and DK078244.

The authors have declared no conflict of interest with the exception of H. M. who is a founder of Mosaiques-Diagnostics and developed CE-MS for proteomics clinical applications.

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