Protein Array Service

Our protein array service with 2D DIGE and Mass Spectrometry is a powerful platform for studying the complex proteome and protein post-translational modifications (PTMs) of all biological systems.

Main applications:

  • Identifying therapeutic or diagnostic markers in different diseases
  • Identifying key regulators in major biological pathways
  • Studying post-translational modifications (PTMs) such as phosphorylation, glycosylation
  • Determining HCP antibody coverage and detecting HCP contaminants

Based on the total number of samples, you can choose one of the following study designs:

A. Identify proteins differentially expressed between 2 samples (Control, Test)

Study design:

  • Gel-1: Control, Test

Image report: Image of each sample and overlay image of 2 samples

Control

2D DIGE protein array of 2 samples: black/white image of control sample

Test

2D DIGE protein array of 2 samples: black/white image of test sample

Control / Test

2D DIGE protein array overlay image of 2 samples

Control

2D DIGE protein array of 2 samples: color image of control sample

Test

2D DIGE protein array of 2 samples: color image of test sample

Control / Test

2D DIGE protein array overlay image of 2 samples - changed spots are circled

Protein ratio report:

Assigned IDSpot No.Control/Test
1165-4.74
2340-4.33
3324-5.38
4116315.51
511488.86
613616.89
715763.36
818196.17
91841-6.79
1019006.41
11201829.00
122252-3.20

B. Identify proteins differentially expressed between 3 samples (Control, Test-1, Test-2)

Study design:

  • Gel-1: Control, Test-1, Test-2

Image report: Image of each sample and overlay image of 2 samples

Control

2D DIGE protein array of 3 samples: black/white image of control sample

Test 1

2D DIGE protein array of 3 samples: black/white image of test_1 sample

Test 2

2D DIGE protein array of 3 samples: black/white image of test_2 sample

Control

2D DIGE protein array of 3 samples: color image of control sample

Test 1

2D DIGE protein array of 3 samples: color image of test_1 sample

Control / Test 1

2D DIGE protein array overlay image of control/test_1

Control

2D DIGE protein array of 3 samples: color image of control2 sample

Test 2

2D DIGE protein array of 3 samples: color image of test_2 sample

Control / Test 2

2D DIGE protein array overlay image of control/test_2

Test 1

2D DIGE protein array of 3 samples: color image of test_1 sample

Test 2

2D DIGE protein array of 3 samples: color image of test_2 sample

Test 1 / Test 2

2D DIGE protein array overlay image of test_1/tes_2

Control / Test 1

2D DIGE protein array overlay image of control/test_1 - changed spots are circled

Control / Test 2

2D DIGE protein array overlay image of control/test_2 - changed spots are circled

Test 1 / Test 2

2D DIGE protein array overlay image of test_1/test_2 - changed spots are circled

Protein ratio report:

Assigned IDSpot No.Test 1 / ControlTest 2 / ControlTest 2 / Test 1
1300-1.02-2.31-2.21
2333-2.51-3.89-1.51
35707.888.981.17
46424.685.531.21
56705.256.671.3
6718-3.21-4.04-1.23
7875-3.46-5.91-1.66
89732.943.631.27
9997-2.61-3.86-1.44
1012774.345.041.19
111265-2.38-3.87-1.59
1213211.563.322.19
1317474.133.44-1.17
141534-2.24-3.17-1.38
151944-2.83-5.87-2.03
162049-2.11-4.31-1.99

C. Identify proteins differentially expressed between ≥ 4 samples

Study design:

2D DIGE Cross-gel will be used to compare samples from different 2D DIGE gels. An internal standard, containing equal amount of protein of each sample will be made and run each gel. Please view these 4 study designs to different project objectives.

Example: 2D DIGE analysis of 6 mouse liver tissues (3 WT and 3 Treated)

Proteins were extracted and 2D DIGE was performed using Applied Biomics’ protocol. Gel images were analyzed by ImageQuant followed by quantitative analysis using DeCyder 2D software.

Gel layout:

  • Gel_01: Internal Standard, WT_1, Treated_1
  • Gel_02: Internal Standard, WT_2, Treated_2
  • Gel_03: Internal Standard, WT_3, Treated_3

Image report: Image of each sample and overlay image of 2 samples from the same gel

WT_1

2D DIGE protein array of large sample set: WT sample_1

Treated_1

2D DIGE protein array of large sample set: Test sample_1

WT_1 / Treated_1

2D DIGE protein array of large sample set: overlay image WT_1/T_1

WT_2

2D DIGE protein array of large sample set: WT sample_2

Treated_2

2D DIGE protein array of large sample set: Test sample_2

WT_2 / Treated_2

2D DIGE protein array of large sample set: overlay image WT_2/T_2

WT_3

2D DIGE protein array of large sample set: WT sample_3

Treated_3

2D DIGE protein array of large sample set: Test sample_3

WT_2 / Treated_3

2D DIGE protein array of large sample set: overlay image WT_3/T_3

Gel-01: Internal Standard

2D DIGE protein array of large sample set: Internal Standard_1

Gel-02: Internal Standard

2D DIGE protein array of large sample set: Internal Standard_2

Gel-03: Internal Standard

2D DIGE protein array of large sample set: Internal Standard_3

WT_1 / Treated_1

2D DIGE protein array of large sample set: overlay image WT_1/T_1 with circles

WT_2 / Treated_2

2D DIGE protein array of large sample set: overlay image WT_2/T_2 with circles

WT_3 / Treated_3

2D DIGE protein array of large sample set: overlay image WT_3/T_3 with circles

DeCyder Analysis: Spot matching across 3 gels

2D DIGE spot matching for cross-gel analysis

DeCyder Analysis: Selected spots with significant changes across all 3 pairs

2D DIGE cross gel analysis of selected spot

Protein ratio report will contain:

  • Protein ratios between any of the 2 samples (on the same or different gels)
  • Protein ratios between any of the 2 sample groups (on different gels) and the associated p-values
Assigned #Original No.AppearanceTreated / WT
Av. RatioP-value
13429 (9)3.520.001
25399 (9)5.440.001
35939 (9)5.050.001
46119 (9)4.090.000
55819 (9)-2.830.001
66569 (9)-4.400.011
77579 (9)3.920.001
88639 (9)-3.080.002
910539 (9)-4.390.001
1011049 (9)5.290.002
1111079 (9)4.620.002
1214539 (9)-2.420.003
1315789 (9)-2.240.031
1417579 (9)-1.860.170
1518029 (9)2.560.005
1619939 (9)-14.380.001

Protein Array Applications

Clinical ResearchBasic Research
Tumor Marker MonitoringTransgenic Mouse Protein Profiling
Tumor Biomarker ScreeningSiRNA Protein Profiling
Drug Toxicity MarkersMonitoring Protein Expression
Drug Biomarker PathwaysTime-Dependent Profiling
Disease BiomarkersKinase Target / Substrate
Therapeutic TargetsGene Function Analysis
Diagnostic MarkersGene Knockout
Quality Control (QC) TestingYeast Protein Profiling

Tumor Marker Monitoring

Identify tumor markers from human liver cancer patients: differential expression between normal, early stage, and late stage liver tumor.

Normal human liver

2D DIGE tumor marker monitoring by 2D DIGE protein array: black/white image of normal liver tissue proteome

Early-stage liver tumor

2D DIGE tumor marker monitoring by 2D DIGE protein array: black/white image of early liver tumor proteome

Late-stage liver tumor

2D DIGE tumor marker monitoring by 2D DIGE protein array: black/white image of late liver tumor proteome

Figure 1: Human liver proteome from normal liver, early and late stage liver tumor.

Normal / Early stage

2D DIGE tumor marker monitoring by 2D DIGE protein array: overlay liver proteome image of normal/early liver tumor

Normal / Late stage

2D DIGE tumor marker monitoring by 2D DIGE protein array: overlay liver proteome image of normal/late liver tumor

Figure 2: Overlay images of Normal/Early stage and Normal/Late stage. The green and red spots are proteins with decreased and increased expressions, respectively, due to early/late stage tumor, which are potentially tumor monitoring markers.

Tumor Biomarker Screening

Identify commonly changed proteins in patients with late stage liver cancers.

Patient 1: Normal tissue / Tumor tissue

Tumor marker screening by 2D DIGE protein array: overlay image of normal/tumor_1 liver tissue proteome with tumor markers circled

Patient 2: Normal tissue / Tumor tissue

Tumor marker screening by 2D DIGE protein array: overlay image of normal/tumor_1 liver tissue proteome with tumor markers circled

Figure 1: Differential protein expression was analyzed by 2D DIGE between normal liver and 2 patient livers with late stage liver cancer. Circled spots are proteins with common changes in 2 patients vs. normal. These proteins could be candidate markers to screen people with liver cancer.

Drug Toxicity Markers

Identify common proteins causing drug toxicity: 2D DIGE was used to analyze the protein expression changes induced by the different drug treatment on human embryonic body (EB) cells . Data showed that 2D DIGE can be used to evaluate drug toxicity and identify the potential toxicity biomarkers.

Control / Drug 1

Identify drug toxicity markers by 2D DIGE protein array: overlay image of control and drug_1 treated human embryonic body cell proteome

Control / Drug 2

Identify drug toxicity markers by 2D DIGE protein array: overlay image of control and drug_2 treated human embryonic body cell proteome

Drug 1 / Drug 2

Identify drug toxicity markers by 2D DIGE protein array: overlay image of drug_1 and drug_2 treated human embryonic body cell proteome

Control / Drug 3

Identify drug toxicity markers by 2D DIGE protein array: overlay image of control and drug_3 treated human embryonic body cell proteome

Control / Drug 4

Identify drug toxicity markers by 2D DIGE protein array: overlay image of control and drug_4 treated human embryonic body cell proteom

Drug 3 / Drug 4

Identify drug toxicity markers by 2D DIGE protein array: overlay image of drug_3 and drug_4 treated human embryonic body cell proteome

Figure 1: Protein expression changes between control and drug treatment. Here we only showed 4 out of 18 drugs tested.

Heat map of human cell proteome treated with 3 groups of drugs of different toxicity: data collected from 2D DIGE protein array

Figure 2: 18 drugs are divided into 3 groups based on their toxicity: Liver and kidney toxic, liver toxic and liver non-toxic. A total of 1480 proteins are shown for each of the 18 drugs. Cluster analysis was performed with Genespring software (Redwood City, CA) on the expression change (obtained from 2D DIGE experiment) between normal and drug on 1480 proteins for each drug. Blue and red indicated down- and up- regulation, respectively. Similar protein patterns are observed within each toxicity group.

Drug Biomarker Pathways

Understand the mechanism, effective dose, and toxicity of drugs

Type A

Drug toxicity pathways by 2D DIGE protein array: 2D image of human cell proteome treated with type A drug

Type B

Drug toxicity pathways by 2D DIGE protein array: 2D image of human cell proteome treated with type B drug

Figure 1: Two compounds of each type (A1, A2 and B1, B2) were used to treat a human cell line. The toxicity indicators (proteins) were analyzed by 2D DIGE cross-gel analysis.

Type A

Heat map of human cell proteome treated with type A drug

Type B

Heat map of human cell proteome treated with type B drug

Fold Change

Fold change for protein expression

Figure 2: Clustering analysis of differentially expressed proteins. The data illustrate different protein pathways for each type of compound. The protein pathway helps to understand compound’s mechanism of action, effective dose and toxicity.

Disease Biomarkers

Identify biomarkers of different liver diseases

  • Normal: normal liver (control mice)
  • Disease models: MDB (DDC+), fatty liver, CH7

Normal Liver

Identify liver disease marker by 2D DIGE protein array: Black/white image of normal liver proteome

MDB (DDC+)

Identify liver disease marker by 2D DIGE protein array: Black/white image of MDB liver proteome

Normal / MDB (DDC+)

Identify liver disease marker by 2D DIGE protein array: overlay color image of normal/MDB liver proteome

Figure 1: Black/white 2D DIGE image of Normal, MDB (DDC+) liver proteome and color overlay image of Normal/MDB (DDC+)

Normal Liver

Identify liver disease marker by 2D DIGE protein array: color image of normal liver proteome

MDB (DDC+)

Identify liver disease marker by 2D DIGE protein array: color image of MDB disease liver proteome

Normal / MDB (DDC+)

Identify liver disease marker by 2D DIGE protein array: overlay color image of normal/MB liver proteome

Figure 2: Color 2D DIGE image of Normal, MDB (DDC+) liver proteome and color overlay image of Normal / MDB (DDC+)

Normal / MDB (DDC+)

Identify liver disease marker by 2D DIGE protein array: zoomed view of overlay color image of normal/MDB disease liver proteome

Normal / Fat liver

Identify liver disease marker by 2D DIGE protein array: zoomed view of overlay color image of normal/fatty liver proteome

CH7 / MDB (DDC+)

Identify liver disease marker by 2D DIGE protein array: zoomed view of overlay color image of CH7/MDB disease liver proteome

Figure 3: Zoomed-in view of overlay color images of Normal/MDB, Normal/Fat liver, and CH7/MDB

Therapeutic Targets

Identify therapeutic targets: detect common protein changes

  • T-cells Tmart-1 D20 and D27: displays the therapeutic functions
  • T-cells Tmart-1 D13: without the therapeutic functions

Tmart-1-D13 / Tmart-1-D20

Identify therapeutic markers by 2D DIGE protein array: color overlay image of D13/D20 Tmart-1–specific CD8+ T-cell proteome

Tmart-1-D13 / Tmart-1-D27

Identify therapeutic markers by 2D DIGE protein array: color overlay image of D13/D27 Tmart-1–specific CD8+ T-cell proteome

Figure 1: T cells play a pivotal role in the immune response. Here we use 2D DIGE to identify the commonly changed proteins from Day 20 and Day 27 Tmart-1–specific CD8+ T Cells versus Mart-1 Day 13. The circled spots clearly showed the change.

Diagnostic Markers

Identify prenatal diagnostic markers in human aminotic fluid: early prenatal diagnostic markers from human aminotic fluids can be used as the genetic and/or developmental markers to monitor the embryo development.

Normal / Disease

Identify diagnostic markers in aminotic fluid by 2D DIGE protein array: color overlay image of normal/disease sample. The circled proteins are potential disease diagnostic markers in human amniotic fluid.
Figure 1: 2D DIGE is used to analyze the Normal and Disease human amniotic fluid samples. The overlay images clearly showed a few differentially expressed spots (circled). These proteins are potential disease diagnostic markers of human amniotic fluid.

Quality Control Testing

Detect Batch-to-Batch Variations: Another important application of 2D DIGE allows comparing different batches of any protein samples. Such analysis provides direct visual comparisons as well as accurate quantification of the differences.

Quality control of batch to batch variations using 2D DIGE protein array. The circled proteins are the main differences due to temperature.
Figure 1: The example here shows 2 different batches of cell lysate stored at different temperature. The green spots (circled) at the bottom of the gel are the main differences due to temperature.

Transgenic Mouse Protein Profiling

Transgenic mouse is widely used in studying gene functions or as animal models of human diseases. 2D DIGE protein array on transgenic mouse proteome will identify differential protein expressions due to the gene alteration, providing in-depth knowledge of protein functions and pathways.

2D DIGE protein array of wild type and transgenic mouse liver proteome.
Figure 1: Top panel shows the black/white images of WT (wildtype animal), TG (transgenic animal) and color overlay image. Bottom panel shows color images of WT, TG and color overlay image of a zoom-in area. Spot 1218 (green) and 1266 (red) represents decreased and increased expressed protein, respectively. Right panel shows 3D view of spot 1218 and 1266 from DeCyder software.

SiRNA Protein Profiling

Small interfering RNA (siRNA) is widely used to study the function of specific genes by preventing the gene translation. 2D DIGE protein array on samples with siRNA will identify differential protein expressions due to siRNA interference, providing in-depth knowledge of protein functions and pathways.

Control

Analyze siRNA induced proteome change by by 2D DIGE protein array: black/white image of Control proteome

+siRNA

Analyze siRNA induced proteome change by by 2D DIGE protein array: black/white image of siRNA+ proteome

Control / +siRNA

Analyze siRNA induced proteome change by by 2D DIGE protein array: color overlay image of control/siRNA+ proteome showing changed proteins caused by siRNA

Figure 1: Black/white images of Control, sample with siRNA and color overlay image.

Analyze siRNA induced proteome change by by 2D DIGE protein array: zoomed view showing the protein expression knocked out by siRNA
Figure 2: Spot view (left), zoomed view (middle) and 3D view of the protein expression knocked out by siRNA.

Monitoring Protein Expression

2D DIGE protein array is very useful in monitoring protein expression changes under different conditions. The following 12 images showed how different treatments can change the proteome in different ways.

Monitor mouse liver proteome change under different treatments by 2D DIGE protein array
Figure 1: 2D DIGE color overlay images of control (green) and treated (red) mouse liver proteome.

Time-Dependent Profiling

Due to the multiplexity nature, 2D DIGE protein array has been widely used in time course studies. Here we show an example of monitoring time-dependent proteome changes during stem cell differentiation by 2D DIGE protein array.

Time course study by 2D DIGE protein array to show proteome change during stem cell differentiation: Day 0-18
Figure 1: Embryonic stem (ES) cells were allowed to differentiate under controlled conditions. The overlay images between different time points showed differential protein expressions on days 0, 2, 4, 6, 8, 10, 15 and 18.
Time course study by 2D DIGE protein array to show proteome change during stem cell differentiation: Zoomed view of day 0-10
Figure 2: Zoomed view of a specific area showing changes of 5 spots during the time course.
Time course study by 2D DIGE protein array to show proteome change during stem cell differentiation: 3D view and quantitation
Figure 3: Top panel shows the 3D view of the 5 spots in Figure 2. Bottom table shows the protein ratios over the time course.

Kinase Target / Substrate

Protein phosphorylation by kinase shifts the protein spot to the acidic side. 2D DIGE is the only platform that enables visualization of both unmodified and phosphorylated protein spots between Control and Kinase-stabilized cell proteome. The example here can be used to monitor kinase activity and identify kinase substrates.

Identify kinase substrates by 2D DIGE protein array
Figure 1: 2D DIGE color overlay images of Control (green) and Kinase-stabilized cell (red) proteome. The circled areas shows proteins phosphorylated by kinase.

Gene Function Analysis

Transfection is a powerful tool for study of gene and protein functions. 2D DIGE protein array allows comparing the protein profiling before and after gene transfection, and identifying proteins that are changed due to transfection. The data provides great insight into the function of the transfected gene.

Mock

Study gene function by comparing transfected cell proteome using 2D DIGE protein array: Control cell proteome image

Transfected

Study gene function by comparing transfected cell proteome using 2D DIGE protein array: Transfected cell proteome image

Mock / Transfected

Study gene function by comparing transfected cell proteome using 2D DIGE protein array: overlay image of control/transfected cell proteome

Figure 1: 2D DIGE color images of Mock (green), Tranfected (red) and their overlay images. The red and green spots in the overlay image represent increased and decreased expressed proteins due to gene transfection.

Gene Knockout

Gene knockout (KO) is a genetic approach to inactivate a specific gene in order to understand it functionality. 2D DIGE protein array can compare the proteome between the knockout and normal individuals, in order to identify proteins changed due to the gene knock-out, thus providing in-depth knowledge of functions and pathways of the targeted gene.

Example 1: Effects of gene knockout on 4 different mouse tissue proteomes

2D DIGE color overlay images of Parental (P) and Knock-out (KO) on 4 different mouse tissue proteomes: liver, colon, pancreas and small intestine
Figure 1: 2D DIGE color overlay images of Parental (P) and Knock-out (KO) on 4 different mouse tissue proteome. The red and green spots represent increased and decreased expressed proteins due to gene knockout.

Example 2: Effects of gene knockout on a bacteria proteome

WT / KO

Effects of gene knock-out on bacteria proteome by 2D DIGE protein array
Figure 2: 2D DIGE color overlay images of WT and KO of bacteria proteome. The arrows point to the red and green spots, which represent increased and decreased expressed proteins due to gene knockout.

Yeast Protein Profiling

2D DIGE analysis of Yeast (S. cerevisiae) proteome before and after treatment

Control

Treated

Control / Treated

2D DIGE protein array of Yeast (S. cerevisiae) proteome before and after treatment
Figure 1: Top panel shows the black/white images of Control, Treated and their color overlay image. Bottom left shows DeCyder screenshot of a zoomed area. In the middle is the overlay image of a zoomed area with an up-regulated spot circled. On the right is the 3D view of the circled spot.

Sample Info

Please follow these general principles regarding biohazardous material and buffer condition in getting your samples ready.

Protein amount: 300-500 µg of total protein from each sample. This will be sufficient to cover the entire 2D DIGE procedure including analytical gel, preparative gel, spot picking and protein ID.

Protein concentration: 5-20 mg/ml is preferred.

Buffer: Please feel free to submit samples in whichever buffer that you would normally use. The standard sample preparation is covered by the DIGE gel cost. Such samples should have protein concentration in the range of 5-20 mg/ml. Additional charge may apply on samples that require extensive amount of the extra work such as protein eluting, concentrating, buffer exchange or serum abundant protein depletion.

Sample type: Please inform our scientists about your sample type. We will send you additional tips for each sample type.

Pricing

Services DescriptionAcademic/Governmental LabsIndustrial/Commercial Labs
CodePriceCodePrice
2D DIGE Analytical Gel (2 CyDye labeling)101A2$1200101N2$1500
2D DIGE Analytical Gel (3 CyDye labeling)101A3$1295101N3$1595

Price covers:

  • Experimental design
  • Standard sample preparation and protein concentration determination (2 samples for 2 CyDye labeling; 3 samples for 3 CyDye labeling)
  • Fluorescence dye labeling using CyDye
  • 1st dimension IEF and 2nd dimension SDS-PAGE
  • Gel image scan using Typhoon scanner
  • Data analysis covering image and DeCyder analysis (in-gel or cross-gel analysis)
  • Data report

Data will be presented as following

  • ImageQuant analysis: Gel images of individual samples and overlay of two sample images (example below)
  • DeCyder Analysis: Quantitative analysis and comparison of protein spots between different samples (example below)

Price does NOT cover:

  • Sample preparation that requires extensive amount of the extra work such as protein eluting, concentrating, buffer exchange or serum abundant protein depletion
  • Manual matching spots between different gels
  • Screen shots of 3D view of each spot
  • Preparative gel, spot picking, protein ID: Please note that Analytical gels do not contain sufficient amount of protein for protein identification. If you find some interesting spots you would like to move forward to perform Protein ID, we will need to run a Preparative gel. Please view here for differences between Analytical and Preparative gels.

2D DIGE Preparative Gel and Protein ID By Mass Spectrometry

Services DescriptionAcademic/Governmental LabsIndustrial/Commercial Labs
CodePriceCodePrice
2D DIGE Preparative Gel (1 CyDye labeling)* 1401A$800401N$960
2D DIGE Preparative Gel (2 CyDye labeling)* 1102A2$1200102N2$1500
2D DIGE Preparative Gel (3 CyDye labeling)* 1102A3$1295102N3$1595
Spot Picking per Gel* 2103$250 per 96 spots103$250 per 96 spots
Protein ID by Mass Spectrometry (MALDI-TOF/TOF) 3104A$125 per spot104N$140 per spot
Pathways Analysis After Protein ID 4203Acall for a quote203Ncall for a quote

* Prices are discounted and only apply for customers who perform protein identification at Applied Biomics

1. Price covers:

  • Experimental design
  • Sample preparation and protein concentration determination
  • Fluorescence dye labeling using CyDye (1 sample for 1 CyDye labeling; 2 samples for 2 CyDye labeling; 3 samples for 3 CyDye labeling)
  • IEF and SDS-PAGE
  • Gel image scan using Typhoon scanner
  • Spot picking design

2. Price covers:

  • Set up spot picking
  • Pick spots
  • Free storage at -80C for 6 months.

1-3. Turnaround time starting from Preparative gel to protein ID report is 7-10 business days. We offer high sensitivity protein identification from gel spots or bands using the latest technologies in mass spectrometry. In each run, four sensitivity standards in the amount of 1-10 femtomole are included. Our sensitivity is the range of 1-2 femtomole. Please view the protein ID procedure for detailed steps of this service. Price covers the following:

  • Gel treatment
  • In-gel trypsin digestion
  • Peptide extraction
  • Desalting
  • Spotting
  • MALDI-TOF
  • MALDI-TOF/TOF
  • Database search against NCBI database using MASCOT
  • Data report (example below)

4. Pathway Analysis Service is provided only for customers doing the 2D DIGE and Protein ID services with Applied Biomics. The report will include the major pathway list with the following information:

  • Functional groups
  • Genes in each functional group
  • Enrichment score
  • Statistic p-value and FDR