A simple and reliable protocol for mouse serum proteome profiling studies by use of two-dimensional electrophoresis and MALDI TOF/TOF mass spectrometry

1477-5956-6-25 1477-5956 Research A simple and reliable protocol for mouse serum proteome profiling studies by use of two-dimensional electrophoresis and MALDI TOF/TOF mass spectrometry Ritorto Stella Maria ritorto@item.fraunhofer.de Borlak Jürgen borlak@item.fraunhofer.de

Department of Drug Research and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Nikolai-Fuchs-Str 1, 30625, Hanover, Germany

Centre for Pharmacology and Toxicology, Hanover Medical School, Carl-Neuberg-Str 1, 30625, Hanover, Germany

Proteome Science 1477-5956 2008 6 1 25 http://www.proteomesci.com/content/6/1/25 18789141 10.1186/1477-5956-6-25 21 5 2008 12 9 2008 12 9 2008 2008 Ritorto and Borlak; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

Unravelling the serum proteome is the subject of intensified research. In this regard, two-dimensional electrophoresis coupled with MALDI MS analysis is still one of the most commonly used method. Despite some improvements, there is the need for better protocols to enable comprehensive identification of serum proteins.

Here we report a combination of two proteomic strategies, zoom in acidic and neutral part of 2-D gels and an application of two optimised matrix preparations for MALDI-MS analyses to simplify serum proteome mapping.

Results

Mouse serum proteins were separated by 2-D electrophoresis at the pH ranges 3–10 and 4–7, respectively. Then in gel tryptic digests were analysed by MALDI-MS. Notably, sample-matrix preparations consisted of either a thin-layer α-ciano-4-hydroxycinnamic acid (CHCA) matrix deposition or a matrix-layer 2,5-dihydroxybenzoic acid (DHB). This enabled an identification of 90 proteins. The herein reported method enhanced identification of proteins by 32% when compared with previously published studies of mouse serum proteins, using the same approaches. Furthermore, experimental improvements of matrix preparations enabled automatic identification of mouse proteins, even when one of the two matrices failed.

Conclusion

We report a simple and reliable protocol for serum proteome analysis that combines an optimized resolution of 2-D gels spots and improved sample-matrix preparations for MALDI-MS analysis. The protocol allowed automated data acquisition for both CHCA and DHB and simplified the MS data acquisition therefore avoiding time-consuming procedures. The simplicity and reliability of the developed protocol may be applied universally.

Background

From a disease diagnostic and drug monitoring point of view there is great interest in serum proteome mapping of humans and of laboratory animals. Indeed, various mouse strains and genetically engineered animals are considered to be good models for human diseases as they offer unprecedented opportunities for mechanistic studies with new experimental medicines. There is hope that serum proteomics enables an identification of biomarkers of disease and drug safety and serum proteins can be used for therapeutic monitoring. In the past 2-D maps for human serum have been reported 1234. And very recently a map for the C57BL6 mouse serum proteome was published 5.

In general, serum proteome profiling is challenging, because of interference by high-abundance proteins such as albumin, immunoglobulins, antitrypsin and transferrin, which typically constitute greater than 90% of total protein mass 126789. These abundant proteins may hinder the detection of low-abundance proteins that can be of specific interest in the search of biomarkers of disease. Additionally, protein biochips have been applied to proteomic studies with antibody microarrays offering new possibilities in the simultaneous identification of analytes from complex samples 10.

So far, only a handful of plasma proteins are routinely measured for diagnostic purposes, because an effective technology that rapidly detects and quantifies specific changes of proteins including low-abundance proteins of serum is not available. As summarized elsewhere 11, the most common methods for serum proteome studies include separation of proteins by gel electrophoresis, excision of spots from the gel, enzymatic digestion and analysis by mass spectrometry. In particular, pre-fractionation techniques such as serum albumin depletion are useful procedures in proteome profiling studies, but they may introduce bias as well. There is substantial run-to-run variation after albumin depletion with IgY immunoaffinity spin columns. Likewise, pre-fractionation increases the risk of depletion of low-abundance proteins as has been shown for paraneoplastic antigen MA I, coagulation factor VII precursor, prostate-specific antigen, as a result of multiple protein-protein interactions with IgG, transferrins, and/or gelsolin 1112.

In this regard, MALDI-MS is considered to be one of the most powerful techniques for the analysis of proteins and peptides 131415, but the sample matrix preparation greatly influences the quality of MALDI-MS spectra of peptides and therefore protein identification. Despite considerable knowledge in the use of MALDI-MS 15161718, sample-matrix preparations are basically empirical.

Here we report a protocol for serum proteome profiling based on zoom in gels in the acidic and neutral pH that enabled detection of many serum proteins. Moreover, the developed protocol allowed for an automated data acquisition, and the sample protocol was optimised by the use of two different matrix-sample preparations in sequence 19. We thus applied tryptic in-gel digest matrix preparation to either α-ciano-4-hydroxycinnamic acid (CHCA) or 2, 5-dihydroxybenzoic acid (DHB) as recently reported by us 19.

Materials and methods

Serum sample preparation

C57/BL6 mice (healthy mice) were obtained from Harlan Winkelman (Borchen, Germany) and kept in an animal house with 12 hour of light and dark cycled. Food and water was given ad libitum. Blood serum was collected from vena cava and allowed to clot for 2 hours at room temperature. The clotted material was removed by centrifugation at 3000 rpm for 15 min. Hemolytic material was not observed. The sera obtained from the blood samples were frozen immediately without any further treatment in liquid nitrogen and stored at -80°C until further analysis. The protein concentration of serum was determined with the Bradford protein assay (Bio-Rad Protein Assay Dye Reagent Concentrate, Bio-Rad), using bovine gamma globulin as the standard. The protein concentration ranged from 80 to 90 μg/μl for wild type mouse serum samples.

Materials

IPG strips of pH 3 to 10 and 4 to 7 (ReadyStrip, 0.5 × 3 × 170 mm; BioRad, Germany), Bio-Lyte (pH 3 to 10), SDS, acrylamide, methylenebisacrylamide, TEMED, ammonium persulfate, DTT, urea, Tris, glycine, glycerol, and CHAPS were purchased from Bio-Rad. Alpha-cyano-4-hydroxycinnamic acid (CHCA) and 2,5 dihydroxybenzoic acid (DHB) from Bruker Daltonics. Methanol, ethanol, phosphoric acid, acetic acid, and formaldehyde were purchased from Merck (Darmstadt, Germany). Sequencing grade modified trypsin was obtained from Promega (Madison, WI, USA).

Coomassie Brilliant Blue G-250, TCA, iodoacetamide and other reagents were obtained from Sigma (St. Louis, MO, USA).

Two-dimensional electrophoresis

IEF was carried out using commercially available, dedicated apparatuses: IPGphor Protean IEF Cell (Bio-Rad). IPG strips were used according to manufacturer instructions [see also 20]. About 500 μg of serum for gel were diluted to 350 μL with re-hydration solution (5 M urea, 2 M Thiourea, 2% CHAPS, 100 mM DTT, 0.5% v/v pH 3 to 10 IPG buffer, 40 mM Tris Base, 2% SB 3–10 and trace bromophenol blue), and applied to immobilized pH 3 to 10 nonlinear and pH 4 to 7 linear gradient strips by overnight re-hydration at 50 V. With Protean IEF Cell, focusing was done initially at 250 V for 15 min, then the voltage was increased to 10 000 V within 3 h, and maintained at 10 000 V for 7 h for a total of 70 kVh. All IEF steps were carried out at 20°C. After the first-dimensional IEF, IPG gel strips were placed in an equilibration solution (6 M urea, 2% SDS, 30% glycerol, 50 mM Tris-HCl, pH 8.8) containing 1% DTT for 10 min with shaking at 50 rpm on an orbital shaker. The gels were then transferred to the equilibration solution containing 2.5% iodoacetamide and shaken for a further 10 min before placing them on 12% polyacrylamide gel slab (185 × 200 × 1.0 mm).

Separation in the second dimension was carried out using Protean II electrophoresis equipment and Tris-glycine buffer (25 mM Tris, 192 mM glycine) containing 0.1% SDS, at a current setting of 5 mA/gel for the initial 1 h and 10 mA/gel thereafter. The second-dimensional SDS-PAGE was developed until the bromophenol blue dye marker had reached the bottom of the gel.

Protein visualization and image analysis

Following second-dimensional SDS-PAGE, analytical gels were fixed three times in 30% ethanol containing 2% phosphoric acid for 20 min and rinsed three times in 2% phosphoric acid. Gels were then equilibrated in a solution containing 18% ethanol, 2% phosphoric acid, and 15% ammonium sulfate for 30 min and Coomassie Brilliant Blue G-250 was added to a final concentration of 1%. Staining was carried out overnight. Protein patterns in the gels were recorded as digitalized images using a high-resolution scanner (Pharox FX, Bio-Rad). Gel image matching was done with PDQuest software (Version 8.01.40; Bio-Rad). Scanned gel images were processed to remove backgrounds, staining on the gel borders and to automatically detect spots. For all spot intensity calculations, normalized values were used. Normalization of spot intensity was done with Loess Regression Method and normalized spot intensities were expressed in ppm.

In-gel digestion

In-gel digestion of protein spots on Coomassie gels was carried out with 160 ng of Porcine Modified Trypsin (Sigma) in 10% ACN and 25 mM NH₄HCO₃and performed essentially as described below.

Briefly, after the completion of staining, the gel were washed twice with water for 15 min, and then twice with water/ACN (1:1 v/v) for 15 min. The solvent volumes were about twice the gel volume. Liquid was removed, ACN was added to the gel pieces and the mixture was left for 5 min. Liquid was removed and the gel pieces were re-hydrated in 0.1 M NH₄HCO₃for 5 min. ACN was added to give a 1:1 v/v mixture of 0.1 M NH₄HCO₃/ACN and the mixture was incubated for 15 min. All liquid was removed the digestion buffer containing 25 mM NH₄HCO₃and 10 ng/μL of trypsin was added and all was incubated for 4 hours at 37°C. The supernatant was recovered and the extraction was carried out with 1% TFA/ACN (1:1 v/v).

MALDI-TOF-MS, MS/MS and database search

Tryptic peptides were spotted directly onto a 600 μm/384 well AnchorChip™ sample target (Bruker Daltonics). The matrix CHCA was saturated in 97% Acetone/0.1% TFA solution; DHB matrix was solved in 30% ACN/0.1% TFA solution (5 mg/ml). The matrix-analyte preparations were loaded onto the MALDI plate (AnchorChip™ 600 mm 384 well, Bruker Diagnostic) by the thin layer and the matrix layer (ML) method for CHCA and DHB respectively. A further re-crystallization approach was tested on peptide calibration standard preparation (Bruker Daltonics) and applied for the samples on the AnchorChip™ 19. An external peptide calibration standard containing the following fragments was used to calibrate the instrument: angiotensin II ([M+H]+ 1046.54); angiotensin I ([M+H]+ 1296.680); substance P ([M+H]+ 1347.740); bombesin ([M+H]+ 1619.820); ACTH clip 1–17 ([M+H]+ 2093.090); ACTH clip 18–39 ([M+H]+ 2465.200); somatostatin 28 ([M+H]+ 1347.470) (Bruker Daltonics). Furthermore, the spectra were calibrated using trypsin autolysis products (m/z_s1045.564, 2211.108 and 2225.119) for three points internal calibration resulting in a mass accuracy of <50 ppm.

The MALDI mass spectra were obtained using an Ultraflex II TOF/TOF mass spectrometer equipped with a 384-sample scout source (Bruker Daltonics) and AutoXecute^®software for automatic spectra acquisition (Bruker Daltonics) was used. Peptide masses were searched against SwissProt database employing Mascot (in-house MASCOT-server) for protein identification. Database searches were performed taking into account carbamidomethyl modification of cysteines and possible oxidation of methionine and allowing one missed cleavage. The mass accuracy required for PMF and MS/MS was basically chosen according to peptide mass-tolerance defined by Root Mean Square (RMS) error, since it defines the limit of peptide mass tolerance (Peptide tol +-) for respectively Mascot Peptide Mass Fingerprint and Mascot MS/MS Ion Search to obtain a significant score (p < 0.05) of matched peptides to select protein entry 21.

Peptides were identified using ProteinScape™ database (Protagen, Bruker, Germany) and Mascot search engine to cross-validate or consolidate the identification results through the complementary use of several software packages. We use ProteinScape™ ScoreBooster feature to improve database search results by automatic iterative recalibrations and background eliminations. Identified proteins were checked individually for further considerations.

The criteria used to accept identifications included the extent of sequence coverage, the number of matched peptides, the Mascot score, i.e. the Top Score obtained after Mascot has incorporated the Mowse score into a probabilistic framework. It is defined as -10*LOG₁₀(P), where P is the absolute probability that the observed match is a random event 21. In case of SwissProt as selected protein sequence database, protein scores greater than 53 were significant (p < 0.05). In addition we requested mouse protein as the top candidates in the first pass search when no restriction was applied to the species of origin. Moreover, when the identification was not possible to reach from PMF, MS/MS data were collected and used as result, if Significant hits were obtained by Probability Based Mowse Score (individual ion scores >25 that indicate identity or extensive homology-p < 0.05-) 21. In general, false positive evaluation was done by software with randomized searches to remove redundant peptide and protein identification.

The new identifications were furthermore searched in PeptideMap free software (ProWL free software programs, National Resource for the Mass Spectrometric Analysis of Biological Macromolecules, the Rockefeller University) 22 and compared with Mascot results (for details, please refer to Additional files 1, 2).

Additional file 1

Validation of the new protein entries. We analysed the same spectra with Mascot search engine in ProteinScape™) and PeptideMap (PROWL free softwares). The ionized tryptic peptides resulted matched to the same protein sequences.

Click here for file

Additional file 2

Mascot and PeptideMap. Single entries from both Mascot and PeptideMap for the new identifications.

Click here for file

Results and discussion

Two-dimensional electrophoresis of serum proteins

We found narrow 2-D gels to improve detection of low abundant proteins in sera, thereby avoiding any pre-fractionation. The 2-DE proteomics carries the advantage of visualizing changes in Mw and pI of a protein, which we find helpful in highlighting biologically significant processes. This electrophoresis technique has been applied successfully to identify oncoproteins in human serum and tissues 11132023. Notably, mouse serum proteins were separated by 2-D electrophoresis (2-DE) and resolved in the first dimension in a broad pH range with IPGphor strips (pH 3 to 10 NL), and subsequently in a 12% gradient polyacrylamide SDS gel in the second dimension. On average, 350 spots could be detected and 77 unique mouse proteins were identified, of which more than 30% were in the basic region of the gel (Figure 1). Among them, we identified some proteins already known or evaluated as potential biomarkers for human malignancies. For instance, previous studies have shown the benefit of studying complement factors in human cancer, i.e. elevated CO3 levels identified in pancreatic cancer patients. Consequently, monitoring activity of CO3/CO4 is clinically relevant 242526. Moreover, heme in tissues and circulation may be come toxic due to oxygen radical formation. Hemopexin, a plasma protein binds heme with high affinity, and therefore limits its reactivity thereby facilitating its catabolism via receptor-mediated endocytosis. Furthermore, the heme-hemopexin complex is glycosilated at specific Hys residues. Obviously, monitoring the precursor at basic pH and its glycosilated form at acidic pH can be informative as biomarker of disease 2728. Likewise, we identified tryptophan 5-hydroxylase 1 (TPH1_MOUSE) in the serum proteome. This protein promotes the synthesis of 5-HT (serotonin). Intriguingly, a recent investigation has found its involvement in the regulation of the immunosystem and aberrant activity in cancers 2930.

Figure 1

Protein entries at basic region of 3–10 pH range

Protein entries at basic region of 3–10 pH range. An amount of 23 proteins were identified at basic region of gels at pH range 3–10. As discussed in the text, most of those proteins could be relevant in biomarker discovery research because of their involvement in inflammation or in mechanisms that could bring toward the development of cancer.

As shown in Figure 2 the sample complexity was further reduced by the use of IPG strips in the pH range of 4 to 7. The number of spots was increased by 2-fold. Approximately 660 spots were detected and 59 proteins were identified in this pH range. When compared with gels of the 3 to 10 pH-range, multiple isoforms of proteins can now be visualised and may have arisen from a combination of post-translational modifications as well as chemical modifications that occur during sample preparation (Figure 2) 2031. Apart from high abundant proteins, on average three spots for each protein at pH of 4 to 7 could be detected, when compared to one spot for each entry or smears observed with gels at pH of 3 to 10 (Figure 2). Altogether, the spot detection was improved and a total of 16 of these proteins were novel gene products resolved at pH 4 to 7 (Table 1, italic font). Notably, 4 of them had not been reported so far in mouse serum 567893233.

Table 1

Mouse serum protein map

No.

SwissProt entry

SwissProt accession

Mw (KDa)

Mascot score

sequence coverage (%)

msms (m/z)

matrix

Our Map 1 (matched peptides)

Ref Map 2 (matched peptides)

Ref Map 3 (matched peptides)

Ref Map 4 (matched peptides)

Ref Map 5 (matched peptides)

Ref Map 6 (matched peptides)

A1AG1 MOUSE

Q60590

5.6

124

1703.91

CHCA DHB

not present

5 (up regulated)

present

AMBP MOUSE

Q07456

1669.85

CHCA

not present

APOM MOUSE

Q9Z1R3

21.6

105

938.42

CHCA DHB

not present

present

MUP1 MOUSE

P11588

20.9

115

DHB

not present

MUP2 MOUSE

P11589

20.9

146

DHB

not present

MUP6 MOUSE

P02762

20.9

136

DHB

not present

MUP8 MOUSE

P04938

17.7

141

DHB

not present

A1AT1 MOUSE

P07758

46.1

5.4

145

981.56

1137.66

1232.70

2003.04

2327.09

2405.17

3498.80

CHCA DHB

10*

20 (up regulated)

not present

A1AT2 MOUSE

P22599

46.1

5.3

104

2405.17

2003.04

2327.09

3498.80

CHCA DHB

not present

3 (up regulated)

present

A1AT3 MOUSE

Q00896

5.3

146

981.56

1137.66

2003.04

2327.09

2405.17

3498.80

CHCA DHB

not present

A1AT4 MOUSE

Q00897

46.1

5.2

162

1232.74

2003.04

2327.09

3498.80

CHCA DHB

not present

present

A1AT5 MOUSE

Q00898

5.4

105

1232.71

2327.09

2405.17

CHCA DHB

not present

present

A1AT6 MOUSE

P81105

5.2

161

981.56

1137.66

1232.70

2003.04

2327.09

2405.17

3498.80

CHCA DHB

not present

present

ANT3 MOUSE

P32261

52.5

6.1

298

1198.70

1340.69

1359.67

1700.89

CHCA DHB

not present

present

A2AP MOUSE

Q61247

55.1

5.8

169

1591.80

1680.81

CHCA DHB

not present

present

CBG MOUSE

Q06770

44.9

148

CHCA DHB

not present

present

SPA3K MOUSE

P07759

113

CHCA DHB

not present

7 (up regulated)

present

A2MG MOUSE

Q61838

167

6.3

153

2068.21

CHCA DHB

16 (immuno depletion)

not present

present

10a

A2MG MOUSE C-term

Q61839

1031.50

1111.58

1216.61

1787.96

CHCA DHB

not present

16 (up regulated)

present

ADIPO MOUSE

Q60994

26.9

5.3

1504.72

DHB

not present

present

AFAM MOUSE

O89020

71.5

5.5

155

CHCA DHB

not present

present

ALBU MOUSE

P07724

70.7

5.7

426

1455.83

1479.70

1609.90

1882.96

1960.15

1981.98

CHCA DHB

26*

46'

12 (up regulated)

present

ALS MOUSE

P70389

67.7

6.1

DHB

not present

present

CPN2 MOUSE

Q9DBB9

61.3

5.5

131

CHCA

not present

present

ANGL6 MOUSE

Q8R0Z6

51.4

9.2

DHB

not present

ANXA2 MOUSE

P07356

38.8

7.5

CHCA

not present

APOA1 MOUSE

Q00623

30.5

5.6

207

1237.67

1318.61

1331.53

1340.77

CHCA DHB

18'

present

APOA2 MOUSE

P09813

11.3

6.6

1193.62

1831.98

CHCA DHB

3 (up regulated)

present

APOA4 MOUSE

P06728

5.4

223

1131.66

1231.61

1461.75

2023.05

CHCA DHB

6 (up regulated)

present

APOE MOUSE

P08226

35.9

5.6

166

968.52

1075.60

1599.82

CHCA DHB

16 (up regulated)

present

APOC3 MOUSE

P33622

10.9

4.6

140

1062.46

1078.45

1987.94

CHCA

not present

present

APOH MOUSE

Q01339

39.9

8.6

276

1325.68

1544.85

2719.48

CHCA DHB

not present

22 (up regulated)

present

CLUS MOUSE

Q06890

55.2

5.5

103

CHCA DHB

not present

present

C1R MOUSE

Q8CG16

81.5

5.4

CHCA

not present

CFAB MOUSE

P04186

86.3

7.2

269

CHCA DHB

not present

present

CFAI MOUSE

Q61129

69.5

7.4

103

1726.85

DHB

not present

HGFA MOUSE

Q9R098

72.9

6.6

DHB

not present

present

HPT MOUSE

Q61646

39.2

5.9

146

980.49

1320.74

1373.61

DHB

not present

14-3 (up and down regulated)

present

29a

HPT MOUSE

Q61646

1679.78

DHB

not present

PLMN MOUSE

P20918

93.4

6.2

387

1138.46

CHCA DHB

not present

present

CFAH MOUSE

P06909

144

6.6

269

CHCA DHB

not present

present

CS1A MOUSE

Q8CG14

78.3

DHB

not present

F13B MOUSE

Q07968

78.3

5.6

148

CHCA

not present

present

CO3 MOUSE

P01027

188

6.4

312

1886.93

CHCA DHB

23*

not present

17 (up regulated)

present

CO4 MOUSE

P01029

194

7.5

123

CHCA

not present

present

CO9 MOUSE

P06683

63.2

5.6

DHB

not present

C1QB MOUSE

P14106

8.6

CHCA

not present

present

EGFR MOUSE

Q01279

138

6.5

171

CHCA DHB

not present

present

FIBB MOUSE

Q8K0E8

55.4

6.7

112

CHCA DHB

not present

present

FINC MOUSE

P11276

276

5.4

CHCA

not present

present

FCN1 MOUSE

O70165

36.8

DHB

not present

FETUA MOUSE

P29699

38.1

135

1653.75 2138

CHCA DHB

not present

present

FETUB MOUSE

Q9QXC1

43.5

6.2

113

1382.89

1159.7

CHCA DHB

not present

present

GPX3 MOUSE

P46412

25.6

8.3

1955

CHCA DHB

not present

present

HA10 MOUSE

P01898

37.2

5.2

173

1671.86

CHCA DHB

not present

HBA MOUSE

P01942

1589.82

1819.93

CHCA

not present

present

HBB1 MOUSE

P02088

7.3

1274.72

CHCA DHB

not present

7 (up regulated)

present

HEMO MOUSE

Q91X72

7.9

188

1100.47

1212.63

1504.76

1516.71

1727.77

2472.12

CHCA DHB

3 (up regulated)

present

IGHG1 MOUSE

P01868

36.2

7.2

DHB

not present

KNG1 MOUSE

O08677

74.1

164

1010.56

1060.56

1515.68

CHCA DHB

5 (up regulated)

not present

KLKB1 MOUSE

P26262

73.4

8.4

105

CHCA

not present

present

KV3A1/2/4 MOUSE

P01654

116

1616.89

1855.04

CHCA DHB

not present

present

KV3AD MOUSE

P01665

4.9

1155.46

1616.89

1855.04

CHCA DHB

not present

present

KV5AB MOUSE

P01644

7.9

1028.56

1926.92

2455.35

CHCA DHB

not present

KV5J MOUSE

P01645

11.9

9.2

1926.81

CHCA DHB

not present

present

KV3N MOUSE

P01666

4.5

DHB

not present

present

MUC MOUSE

P01872

6.6

184

1330.78

1603.91

CHCA DHB

not present

MUG1 MOUSE

P28665 (Q80XE6)

166.4

168

CHCA DHB

not present

present

PHLD MOUSE

O70362

93.8

6.6

151

CHCA DHB

not present

present

PON1 MOUSE

P52430

34.6

117

1853.9

CHCA DHB

not present

present

PROP MOUSE

P11680

8.4

CHCA

not present

present

RETBP MOUSE

Q00724

23.5

5.7

138

1226.63

1360.58

1789.84

2079.88

CHCA DHB

not present

present

SAMP MOUSE

P12246

26.4

2133.03

CHCA DHB

not present

present

THRB MOUSE

P19221

71.6

156

1189.56

CHCA DHB

not present

9 (up regulated)

present

TRFE MOUSE

Q921I1

78.8

308

1171.61

1419.86

1656.81

1990.82

2007.94

CHCA DHB

39*

not present

present

KAC MOUSE

P01837

11.9

990.51

CHCA DHB

not present

ZA2G MOUSE

Q64726

35.4

5.8

173

1274.60

1318.81

1409.72

1610.74

CHCA DHB

not present

present

VTDB MOUSE

P21614

55.1

5.4

266

1051.6

1303.77

2441.13

CHCA DHB

not present

present

TTHY MOUSE

P07309

15.9

5.8

122

1382.62

1554.89

2438.17

2517.22

CHCA DHB

not present

present

GELS MOUSE

P13020

86.3

5.8

233

1254.75

1275.73

CHCA DHB

not present

present

VTNC MOUSE

P29788

55.6

5.7

CHCA DHB

not present

present

GCAB MOUSE

P01864

8.5

31.5

1913.84

DHB

2 (membrane form)

not present

GCB MOUSE

P01866

37.3

7.2

1778.87

CHCA DHB

3 (membrane form)

not present

LAC1 MOUSE

P01843

11.7

5.9

DHB

not present

LAC2 MOUSE

P01844

11.4

5.9

DHB

not present

present

ACTG MOUSE

P63260

42.1

5.3

188

1198.75

1790.93

1954.14

CHCA DHB

not present

ACTB MOUSE

P60710

5.3

171

1198.75

1790.93

1954.14

CHCA DHB

not present

present

APC MOUSE

Q61315

313

7.4

CHCA

not present

present

CT160 MOUSE

Q8VCC6

9.5

CHCA

not present

CUL1 MOUSE

Q9WTX6

90.3

8.2

CHCA

not present

ESTN MOUSE

P23953

61.4

5.1

168

911.45

CHCA DHB

not present

present

ITIH2 MOUSE

Q61703

106

6.8

150

1337.73

CHCA DHB

not present

present

ITIH4 MOUSE

9055252

104.8

133

CHCA

not present

K2C5 MOUSE

Q922U2

7.6

DHB

not present

LIFR MOUSE

P42703

123.8

5.7

151

DHB

not present

present

MBL1 MOUSE

P39039

25.8

7.5

100

1544.89

CHCA

not present

8 (up regulated)

present

MBL2 MOUSE

P41317

26.3

1323.60

1522.72

1766.83

CHCA DHB

not present

OST5 MOUSE

Q8BSL4

40.7

9.7

CHCA

not present

SYT2 MOUSE

P46097

47.7

8.2

CHCA

not present

present

TPH1 MOUSE

P17532

51.9

CHCA

not present

KPYM MOUSE

P52480

DHB

not present

DYN2 MOUSE

P39054

CHCA DHB

not present

GAB2 MOUSE

Q9Z1S8

73.6

8.5

1794.8

DHB

not present

present

Mouse serum proteins identified by us in serum from C57BL6 mice (Our Mapping 1), in comparison with previous mouse serum maps (Ref Map 2: 9, Ref Map 3: 8, Ref Map 4: 732, Ref Map 5: ref 33 and Ref Map 6: 6). Exactly, 16 of them (italic font) were identified only by narrow IPGs of pH 4–7. In bold, we highlighted the proteins identified only with LIFT-MS/MS measurements. In case of TCA/methanol precipitation method (Ref Map 2: 9) we specified where the proteins were identified. (n*: precipitated fraction; n': supernatant fraction-). In the case of MUPs, we marked with 0 the entries, because there are evidences that those proteins are present just in C57BL6 mice and not in BALA/cj inbred strain 32.

Figure 2

Improved resolution with zoom-in 2-D gels

Improved resolution with zoom-in 2-D gels. Details of the 2-D gel zoomed areas. We showed the improved separation and visualization of the mouse serum proteome. In fact, multiple isoforms for most identified proteins were found and other identified spots were detected only in 4–7 pH-range and not in 3–10 pH-range. Panel 1: 3–10 pH range (1 spot 1 id: mouse ceruloplasmin; 4 spots 1 id: mouse gelsolin) 4–7 pH range (14 spots 3 ids: mouse ceruloplasmin, mouse alpha-macroglobulin, mouse albumin; 6 spots 1 id: mouse gelsolin; 3 spots 1 id: mouse hemopexin).Panel 2: 3–10 pH range (1 smear 2 ids: mouse afamin and mouse hemopexin; 1 smear 1 id: mouse kininogen; 1 smear 2 ids: mouse antithrombin-III, mouse Alpha-2-HS-glycoprotein) 4–7 pH range (3 spots 1 id: mouse prothrombin; 3 spots 1 Id: mouse hemopexin; 3 spots 1 id: mouse kininogen; 6 spots 4 ids: mouse antithrombin-III, mouse Alpha-2-HS-glycoprotein, mouse vitamin D-binding protein and mouse fetuin-b).Panel 3: 3–10 pH range (3 spots 2 ids: mouse apolipoprotein A4 and mouse zinc-alpha-2-glycoprotein; 1 spot 1 id: mouse albumin) 4–7 pH range (1 spot 1 id: mouse serum paraoxonase/arylesterase 1; 1 spot 1 id: mouse H-2 class I histocompatibility antigen; 3 spots 1 id: mouse alpha-2-macroglobulin). Panel 4: 3–10 pH range (3 spots 1 id: mouse apolipoprotein A1) 4–7 pH range (1 spot 1 id: mouse mannose-binding protein2; 4 spots 1 id: mouse Ig kappa chain V-III region; 2 spots 1 id: mouse apolipoprotein A2). The spots 1 (alpha-2-macroglobulin); 2 (complement C1r-subcomponent); 3 and 3a (Apoliprotein A4 and Zinc-alpha-glycoprotein 2 respectively) and 4 (glutathione peroxidase 3) are examples discussed respectively in the text and in Figure 5.

Improved MALDI TOF-MS analysis of serum proteins

To increase the number of ionized tryptic-digested peptides, we took advantage of the properties of two commonly used matrices, CHCA and DHB 1519. To the best of our knowledge sample-matrix preparations with both matrices in sequence for serum proteome profiling has not been reported so far. These matrices differ considerably upon MALDI ionization. We combined a thin layer and the ML deposition on the AnchorChip™ to identify 2-D spots from mouse serum samples using a protocol recently described by us 19. Briefly, we used a Bruker MALDI target plate, equipped with hydrophilic patches ("anchors") in hydrophobic surroundings (AnchorChip™, Bruker Daltonics), and achieved signal uniformity, high sensitivity and an improved signal-to-noise ratio which gave rise to less complex MS spectra of which an example is given in Figure 2. Moreover, the re-crystallization of the sample-matrix mixtures loaded on the target increased considerably the number of identifiable peptide ions in an automated MS and MS/MS spectra acquisition mode (see also Table 1). Striking differences in the MALDI MS spectra of peptides were observed when the two matrices were compared (Figure 3). We observed better ionization of peptides from the tryptic-digested proteins with DHB as compared with CHCA. Indeed with CHCA, we frequently observed peaks at m/z 1044, 1060, 1066, 1082, 1249 and 1271 (Figure 3, azure cycles). We used matrix ion suppression in deflection mode of m/z 800. These abundant matrix clusters display high s/n ratio and resulted in poor acquired PMF spectra 1134. Previous reports had already highlighted differences in PMF because of different behaviour of the two matrices 151618. In particular, Zhu and Papayannopoulos tested several matrices and reported that DHB gave the best results without interferences from matrix ion peaks. Furthermore, common interferences from matrix-adducts of CHCA were observed, in particular in the range of m/z 800–1100 of the MALDI spectra 35.

Figure 3

Spectra comparisons between CHCA and DHB

Spectra comparisons between CHCA and DHB. (A, B) CHCA matrix vs DHB matrix. Considerably, in the case of DHB the peptide ions signals are less resolved than other signals in the spectrum, maybe connected to metastable decay of ions in the drift tube or "chemical noises" from matrix ions. On the other hand, CHCA was enabled to identify complement C1r-subcomponent (C1r_MOUSE) and alpha-2-antiplasmin (A2AP_MOUSE). Crosses represent matched peptides to the identification. (C, D) DHB matrix vs CHCA matrix. The spectra from DHB are notably rich of peptides ions fragments (crosses) which belong to the identification, i.e. glutatione peroxidase-secreted form (GPX3_MOUSE) and gelsolin (GELS_MOUSE). The blue circles on CHCA spectra, instead, represent matrix fragments which hide the peaks could be matched to the identifications. The pie chart represents our mouse proteome mapping, where both matrices have the almost same input in the identifications.

Nonetheless, there are obvious benefits in the use of the CHCA matrix in the MALDI MS analysis. This included a high uniform layer, which it forms, especially on the AnchorChip™ (data not shown). Its ability to induce desorption of ions at lower laser energies demonstrates transfer of sufficient energy for the pre-formation of ions. In some cases, metastable ions of matrix ion fragments were less formed when compared with DHB 36. This enabled acquisition of less ambiguous spectra for the identification of proteins. The different behaviours of both matrices are the subject of several published studies. In particular, Luo et al. 37 reported loss of internal energy of ions generated by MALDI and the role of the two matrices in desorption and ionisation processes.

Indeed, in a complex mixture such as serum, it is not really clear why in some cases diagnostic PMFs are obtained with DHB rather than CHCA and vice versa. Some examples, depicted in Figure 3, clearly demonstrate that it is difficult to predict which matrix would deliver best PMFs. For that reason, we exploited both matrices in order to redress any drawbacks of one matrix by the use of the other one especially in automatic data acquisition procedures.

Mapping of the mouse serum

As shown in Table 1, we were able to identify 90 unique proteins, some of which were reported to be identifiable only after sample pre-treatment or sophisticated and time-consuming procedures. For instance, several members of complement factor family [CFAB_MOUSE, CFAI_MOUSE, CO3_MOUSE, CO4_MOUSE, CO9_MOUSE and C1QB_MOUSE], properdin [PROP_MOUSE] and mannose binding protein A [MBL1_MOUSE] were identified at the basic pH region of the 2-D gels. None of them were reported in previous mouse serum proteome profiling studies using 2-DE and MS analysis 7832. Indeed, when the serum was albumin-depleted, other high abundance proteins were lost as well. Furthermore, complement factor 3 and transthyretin were found in both fractions, albumin-rich and depleted (Table 1) 9. This necessitated repetitive analyses. Indeed, complement factor 3 was shown to be up-regulated in human lung adenocarcinomas 33, as were increased serum levels of transthyretin and down-regulation of transferrin in human type-2 diabetes 38.

The application of our protocol enabled an identification of properdin [PROP_MOUSE] and adenomatous polyposis coli protein [APC_MOUSE]. Once again, in previous mouse serum maps these proteins were not identified 7893233 (Table 1). We were able to identify most of the proteins but some new proteins were identified as well (Table 1). Notably, with our optimized MALDI- matrix protocols, we were able to characterize the protein C1R complement [C1R_MOUSE] by the sequential use of DHB and CHCA (spot 2 in Figure 2, Figure 3). This is a serine protease that combines with C1q and C1s (which we had identified in our sample as well) to form C1, the first component of the classical pathway of the complement system. The spot corresponding to C1R is positional in the gel where the molecular weight and pH differs from the theoretical values, presumably because of glycosylation of this protein 39. Post-translational modifications (PTMs) do change the chemical characteristics of the protein that runs in 2-D gels at more acidic and higher mass ranges. Indeed, we identified glutathione peroxidase 3 [GPX3_MOUSE] (pI 8.3) in 2-D gel at pH 4–7 (spot 4 in Figure 2, Figure 3). The gene product GPX3_MOUSE is a secreted protein that protects cells and enzymes from oxidative damage, by catalyzing the reduction of hydrogen peroxide, lipid peroxides and organic hydroperoxide. This protein was reported to be regulated in various malignancies 40.

Without sample pre-treatments, we were able to identify proteins such as hemopexin [HEMO_MOUSE] and alpha-2-macroglobulin [A2MG_MOUSE]. Usually, an identification and quantification of these proteins requires time consuming procedures 932. Here we describe a simple protocol that allowed facile identification of the same proteins even with a higher number of matching peptides. For instance, spot 1 (see panel 1 in Figure 2) was identified as A2MG_MOUSE with high sequence coverage. Previously, pre-fractionation of the serum was needed to enable its identification 32. Likewise, with our protocol HEMO_MOUSE was identified with a Mascot score of 188 and 21 matched peptides, a result comparable to after immunodepletion (25 matched peptides), and pre-fractionation (14 matched peptides) but considerable better than with data from other mouse serum maps (8 matched peptides) 789. In Figure 4, we display identified proteins where the number of matched peptides amongst different strategies was compared; in general, we obtain a better protein score and comparable or even higher number of matched peptides of the protein sequence, without any sample pre-treatment (cylinders in Figure 4, Table 1).

Figure 4

Comparison of matched peptides

Comparison of matched peptides. We have depicted here a comparison of some identification (x-axis) from our work (azure-cylinder) and three different mouse serum maps (prisms) [see ref 978]. Note the number of matched peptides (y-axis) is higher or comparable with the pre-fractionation methods. Mouse protein identifications: A1AG1: alpha-1-acid glycoprotein, A2M: alpha-2-macroglobulin, HEMO: hemopexin, APOH: beta-2-glycoprotein 1, HPT: haptoglobin, PLMN: plasminogen, CFAH: complement factor H, FETUA: alpha-2-HS-glycoprotein-Fetuin-A, APOE: apoliproteinE.

When no significant PMF entries were obtained, we attempted identification by MS/MS spectra acquisition. For instance, we acquired the LIFT TOF-TOF spectrum of the peak yielded at m/z 1913.84 -the peptide sequence APQVYVLPPPAEEMTKK- with an ion score of 33 and error tolerance of 10 ppm. The peptide was then matched to Ig gamma-2A chain C [GCAB_MOUSE]. Additionally, we identified the secreted protein alpha-1-microglobulin (AMBP_MOUSE) by MS/MS with the parental ion at m/z 1669.85 and a peptide sequence of TIAACNLPIVQGPCR. We thus obtained the significant hit at ion score of 38 with 5 ppm as peptide mass tolerance; according to RMS error, and 0.5 Da as fragment mass tolerance 21.

Furthermore, we identified a number of proteins such as gamma actin [ACTG_MOUSE] which was believed to be primarily cytoskeletal and/or intracellular but was not reported so far for the mouse serum proteome. Three peaks belonging to ACTG_MOUSE were identified at m/z 1198.75 -peptide sequence AVFPSIVGRPR- 1790.93 -peptide sequence SYELPDGQVITIGNER- and 1954.14 -peptide sequence VAPEEHPVLLTEAPLNPK-, with an ion scores higher than 23. Further examples are listed in Table 1 (from number 74 to 90).

Taken collectively, our protocol enabled automated data acquisition and improved significantly the identification of proteins based on higher sequence coverage and the number of matched peptides. For instance, CFAH_MOUSE was identified with a Mascot score of 269, a 31% sequence coverage and 29 matched peptides, instead of 23% sequence coverage and 6 and 18 matched peptides as reported previously (Table 1). Similarly, the sequence coverage of apolipoprotein H (APOH_MOUSE) was increased by 17% with 5 additional peptides that could be mapped to this protein 79 (for sequence coverages, please refer to Additional file 3).

Additional file 3

Protein sequences. We listed all identified protein sequence, the PMF (MS analysis) and PFF (tandem-MS analysis). We chose representative tandem MS for every ion peak fitting with the protein sequence.

Click here for file

Newly identified proteins

Thirteen new mouse serum proteins were identified with our approach. Among them, some were recently confirmed by another group 5.

In their approach 5, however, matched peptides were less on average when compared to our data. Apart from this difference, a total of 6 new proteins are reported by us (italic font in Table 2).

Table 2

New proteins, spectra interpretation and validation

No Table 1

Swiss Prot entry

Swiss Prot accession

putative PTMs

Subcellular location

Mw (KDa)

RMS error (ppm)

matrix

Swiss Prot

NCBInr

MSDB

Nr of matched peptides (Mascot)

Nr of matched peptides (Peptide Map)

ANGL6 MOUSE

Q8R0Z6

Secreted; highly expressed in the liver

51.4

DHB

ANXA2 MOUSE

P07356

Secreted, extracellular space, extracellular matrix, basement membrane. Melanosome

38.8

CHCA

C1R MOUSE

Q8CG16

Secreted

81.5

DHB CHCA

CS1A MOUSE

Q8CG14

Predominantly expressed in liver

78.3

DHB

LAC1 MOUSE

P01843

Secreted

11.7

DHB

ACTG MOUSE

P63260

Cytoplasm, cytoskeleton

42.1

DHB CHCA

188

CT160 MOUSE

Q8VCC6

CHCA

CUL1 MOUSE

Q9WTX6

Embryo fibroblasts and embryo preadipocytes

90.3

CHCA

K2C5 MOUSE

Q922U2

Expressed in epidermis

DHB

OST5 MOUSE

Q8BSL4

Golgi apparatus membrane; Single-pass type II membrane protein

40.7

CHCA

TPH1 MOUSE

P17532

Cytoplasmatic enzyme, pineal gland

51.9

CHCA

KPYM MOUSE

P52480

Liver, red cells, muscles, brain

DHB

DYN2 MOUSE

P39054

Cytoplasm

DHB CHCA

We listed here the 13 proteins which re not present in the previous mouse serum maps 67893233.

The SwissProt entries in Italic font are proteins not identified in mouse serum proteome so far 567893233. RMS (Root Mean Square) error is the calculated error for set of matched mass values (in ppm) in Mascot Search (matrix science, LTD, UK). It is measured in ppm. RMS error defines the limit of peptide mass tolerance (Peptide tol +-) for Mascot Peptide Mass Fingerprint to obtain a significant score (p < 0.05) of matched peptides to select protein entry.

The results were first searched in SwissProt databank and furthermore in NCBInr and MSDB databanks. The same criteria were applied (such as: mus musculus for the taxonomy, < +/- 50 ppm as peptide tolerance and one missed cleavage allowed for trypsin enzyme). In bold we highlighted the significant score (p < 0.05) according to the chosen database (SwissProt >53, NCBInr and MSDB >61) 2151.

We also specified if one matrix or the combination of them allowed the identification.

Post translation modifications (PTMs). P: phosphorylation; G: Glycosylation.

For instance, we identified members of complement cascade activation, a positive mediator for angiogenesis (ANGL6_MOUSE), proteins specifically regulated in several tumor cells such as [KPYM_MOUSE] and proteins playing an important role in protein degradation and protein ubiquitinylation, whose altered activity could allow for abnormal cell proliferation (CUL-1_MOUSE). Notably, some of these newly identified proteins may serve as cancer biomarkers 5414243.

In this regard, we identified heparan sulfate glucosamine 3-O-sulfotransferase 5 (OST-5_MOUSE), a sulfotransferase that catalyzes the transfer of a sulfo group from the sulfo donor, 3'-phosphoadenosine-5'-phosphosulfate (PAPS), to the 3-OH position of a glucosamine unit of the HS. It displays anticoagulant activity by interacting with antithrombin (AT) protein through sulfanation at the 3-OH position of HS-saccharide 444546. From recent studies, new biological functions of activated HS have emerged, for instance in regulation of cancer growth and inflammatory responses 4447.

Likewise, our identification of dynamin-2 (DYN2_MOUSE) in serum may be suggestive for extracellular matrix degradation, in case of invasive tumor cells (metastasis). Extensive studies are already published on the "invasive feet" enrichments in dynamin and actin and their involvement in extracellular matrix degradation in hepatocellular carcinoma 484950.

Conclusion

The combination of zoom in gels and the use of two different sample-matrix preparations in sequence improved protein identification of mouse serum proteins considerably and allowed for automated data acquisition as compared to previous methods using 2-DE and MALDI-MS (an example is given in Figure 4) 78. Moreover, we obtained a higher number of matched peptides, as compared to sample pre-fractionation methods coupled with LC-MS/MS or other proteomic approaches (Table 1) 93233. Finally, we report an improved mouse serum proteome map and an identification of 13 proteins that were not reported in previous 2-DE studies. Even with the comprehensive study reported in 5, six of them are still novel (Table 2) 567893233. We validated the newly identified proteins by repeating the searches against different databases (NCBInr and MSDB), as described above (Table 2) 51. Moreover, the same spectra were further analysed with PeptideMap free software 22. Altogether, identical results were obtained.

There is a need for a reliable characterization of serum proteomes to enable biomarker discovery. In our opinion, the strength of this work lies in the right combination of protocols and its simplification. We report a simple and reliable identification of mouse serum protein (for instance, see Figure 5) and as shown in Table 1, our work evidences an improved identification when compared with previous studies based on pre-treatments of serum or other sophisticated methods.

Figure 5

Fast and reliable identification of mouse serum proteins

Fast and reliable identification of mouse serum proteins. We have depicted here an example of improvement of data acquisition by the use narrow-pH IPG strips for the IEF. The data of score and matched peptides were chosen from the best outcome in MALDI-MS analysis by both matrices (CHCA and DHB) (ProteinScape™ database).

Taken collectively, we view our protocol to be useful in biomarker discovery.

List of abbreviations

ACN: acetonitril; DTT: dithiothreitol; IPG: immobilized pH gradient; MALDI-TOF-MS: Matrix Assisted Laser Desorption Ionization-Time of Flight-Mass Spectrometry; NH₄HCO₃: ammonium bicarbonate; SDS: Sodium Dodecyl Sulfate; TCA: trichloroacetic acid; TFA: trifluoracetic acid; TEMED: tetramethylenediamine.

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

MSR designed and carried out the 2-DE and MALDI MS analysis. MSR and JB were responsible for the design of the study and were involved in writing the manuscript. All authors have read and approved the final manuscript.

Acknowledgements

The authors thank Dott. Ignazio Garaguso for helpful discussions and support in MALDI MS analysis.

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