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BIO RAD EXQuest Spot Cutter manuals

Owner’s manuals and user’s guides for Accessories for water BIO RAD EXQuest Spot Cutter.
We providing 2 pdf manuals BIO RAD EXQuest Spot Cutter for download free by document types: User Manual


Bio rad EXQuest Spot Cutter User Manual (81 pages)


Brand: Bio-rad | Category: Accessories for water | Size: 1.67 MB |

 

Table of contents

Spot Cutter

1

Instruction Manual

1

1.0 INTRODUCTION

5

Gel Cutting Head

8

Gel Tip Wash Station

10

Membrane Tip Wash Station

10

Figure 1-7. Microplate rack

10

INTRODUCTION

10

Figure 1-9. Robotics

11

Manual Excision Tool

13

2.0 SYSTEM INSTALLATION

14

SYSTEM INSTALLATION

15

Figure 2-1. Spot cutter leg

16

Closely spaced tabs

17

Widely spaced tabs

17

EXQUEST CALIBRATION WIZARD

23

Camera Focus

25

Head Height Calibration

26

Flat Field Calibration

27

Lens Calibration

28

System Position Calibration

28

Plate Position Calibration

29

Calibration Complete

32

4.0 GEL AND BLOT PREPARATION

34

GEL AND BLOT PREPARATION

35

5.0 MANUAL EXCISION TOOL

36

MANUAL EXCISION TOOL

38

Microplate Imaging

39

Gel Imaging

39

ANALYSIS SET EXCISION TOOL

43

Manual Gel Selection

45

Automatic Gel Selection

46

Plastic-backed Gels

59

Glass-backed gels

59

7.0 LANE/VOLUME EXCISION TOOL

60

LANE/VOLUME EXCISION TOOL

61

Right, Horizontal = 0

63

8.0 EXCISION TOOL CONTROLS

65

Frequency Distribution

66

Histogram

66

Transform Plot

66

Preview Window

66

ACCESSORIES

72

10.0 MAINTENANCE

73

MAINTENANCE

74

Figure 10-4. Spot cutter fuse

75

11.0 TROUBLESHOOTING

76

TROUBLESHOOTING

77

12.0 WARRANTY

79

Life Science

81

Bio-Rad

81

Laboratories, Inc

81

Bio rad EXQuest Spot Cutter User Manual (564 pages)


Brand: Bio-rad | Category: Accessories for water | Size: 11.87 MB |

 

Table of contents

User Guide for Version 7.1

2

Windows and Macintosh

2

Table of Contents

4

Contents

6

1. About This Document

10

Proteomics Applications

11

Medical Applications

12

3. Bio-Rad Listens

13

1. Introduction

14

Mass Spec Analysis

15

And More

15

Introduction

16

1.3 PDQuest Workflow

17

Spot Identification

18

Matching and Editing

19

Data Analysis

19

1.4 Computer Requirements

20

Macintosh

21

1.5 Installation

22

1.7 Starting the Program

25

1.8 Software License

26

Registering by Internet

27

Registering by Fax or E-mail

28

Entering a Password

28

1.10 PDQuest Basic

30

1.11 Contacting Bio-Rad

30

2. General Operation

32

2.1.b Main Toolbar

33

2.1.c Status Boxes

34

2.1.d Secondary Toolbars

34

2.1.e Quick Guide

35

2.2 Keyboard Shortcuts

36

2.3.a File Types in PDQuest

38

Scansets

39

General Operation

40

2.3.c Opening Files

41

Opening TIFF Images

43

Export Image as TIFF

44

2.3.d Closing files

46

2.3.e Saving Files

47

2.3.f Revert to Saved

47

2.3.g Image Info

48

2.3.h Reduce File Size

49

2.4 Printing and Exporting

51

2.5 Printing

52

2.5.b Print Actual Size

53

2.5.c Image Report

54

2.5.d Video Printing

55

2.6 Exporting

56

2.6.a Exporting an Image

57

Analysis Export Mode

58

Publishing Export Mode

58

Exporting the Image

58

2.6.b MatchSet Data

59

Basic Export MatchSet

62

2.6.c Exporting Annotations

64

2.7 Preferences

66

2.7.b Path Preferences

67

2.7.c Display Preferences

70

2.7.d Toolbar Preferences

72

2.7.e Application Preferences

73

2.7.f Imagers

74

2.8 Mouse-assignable Tools

76

3. Viewing and Editing

80

Assigning Images

82

Interchanging Images

82

3.4 Tiling Windows

83

3.5 Magnifying Images

83

Zoom Box

84

Zoom In/Zoom Out

85

View Entire Image

85

3.6 Positioning Images

86

Arrow Keys

87

3.6.a Advanced View

88

3.7 Hiding Overlays

89

3.8 Density Tools

90

Plot Density Distribution

91

Plot Cross-section

91

3.9 Colors

92

Changing a Color

93

3.10 Multi-Channel Viewer

95

Viewing Options

96

3.11 3D Viewer

97

3.12 Transform

99

Viewing and Editing Images

100

PDQuest User Guide

101

3.12.a Transform Controls

102

Gamma Slider

103

3.13 Cropping Images

105

3.13.a Advanced Crop Commands

107

Flipping

109

90° Rotations

109

Custom Rotation

109

3.15 Filtering Images

111

3.15.a Filter Wizard

112

Step 2: Select Filter Size

114

Step 3: Begin Filtering

115

3.16 Invert Data

117

3.17 Text Overlays

117

Creating a Text Overlay

118

Editing a Text Overlay

118

Line Tool

119

4. Detecting and Editing

122

Detecting and Editing Spots

124

4.1.b Step 2. Test Settings

125

Sensitivity

126

4.1.c Advanced Tab

127

Background

128

Smoothing

128

Speckles

129

4.2 Detecting Spots

130

Automated Detection dialog

131

Step 2 - Detect Spots on Gels

132

Step 3 - Create MatchSet

132

Step 4 - Match Gels

132

Spot Detection Report

132

What Are Gaussian Spots?

134

4.5 Adding and Removing Spots

136

Adding Spots

137

Removing Spots

138

4.6 Spot Boundary Tools

139

Spot Contour Tool

140

Spot Freehand Tool

141

4.7 Cancelling Spots

143

4.9 Saturated and Faint Spots

144

4.8 Combining Spots

144

4.10 Spot Quantity

145

Low Quantity Spots

146

4.11 Spot Quality

147

Low Quality Spots

148

4.12 Spot Parameters

149

4.13 Finding Spots

149

5. MatchSets

152

5.1 Creating a MatchSet

154

5.1.a Create a MatchSet

155

Matchsets

156

5.1.b Member Sharing

157

Matching

158

5.2 Selecting the Master

160

5.3 Matching Spots

161

5.3.a Editing MatchSets

163

5.4 Landmarking Spots

165

5.5 Automated Matching

168

Getting started

169

Classic Matching

169

Primary Matching

171

5.5.a Show Symbols

172

5.5.b Show Vector Offsets

173

5.6 Cybergels

174

Auto-Adding Spots

177

Selection Criteria

178

Manually Adding Spots

179

5.8 Edit Match Submenu

180

Manual Matching

181

Unmatched Spots

182

Partial Matches

182

Erratic Spots

183

5.8.a Colony Matching

184

5.8.b Higher Level MatchSets

185

5.9 Matching Summary

188

MatchSet Information

189

Replicate Group Information

190

Other Features

190

6. Analysis Tools

192

Analysis Tools

194

6.2 Image Stack Tool

196

6.3 Scatter Plot Tool

198

6.4 Replicate Groups

200

6.5 Group Consensus

204

6.5.a Review Individual Spots

206

6.5.b Achieving Consensus

207

6.6 Sample Database

208

Adding Attributes

210

6.6.b Classes

211

MatchSet

212

6.6.d Sample Pairs

212

6.7 Normalization

214

Normalization Formula

215

6.7.a Scaling Factor

216

6.7.b Normalization Methods

216

Total Quantity in Valid Spots

218

Total Density in Gel Image

218

Specified Value

218

Counts Loaded from Gel Record

219

Pipetting Error Compensation

219

6.8 MrpI Data

220

Displaying MrpI Data

221

6.9 Standard Spot Numbers

223

6.10 Database Spot Numbers

225

Assigning DSNs

226

7. Analysis Sets and

228

Annotations

228

7.1.a Analysis Set Manager

229

Analysis Sets and Annotations

230

No Spots

243

7.1.g Boolean Analysis Sets

244

7.1.h Matching Analysis Sets

247

7.2 Annotation Tool

249

7.2.b Annotation Categories

251

URL Categories

252

File Name Categories

253

7.2.c Selecting a Category

254

7.2.d Selecting Spot(s)

254

7.2.e Entering an Annotation

255

7.2.f Importing Annotations

255

7.3 Browsing Annotations

260

7.5 Printing Annotations

263

7.6 Transferring Annotations

264

8. Basic Excision Tool

266

8.1 Spot Cutter Setup

267

8.1.a Focus Cutter Camera

268

8.1.b Set Cutting Tip Height

268

8.1.c Spot Cutter Settings

269

Basic Excision Tool

270

Well A1 position

270

8.1.d Spot Cutter Calibration

271

8.2 Cutting Spots

273

Moving a Cut Circle

277

Removing Cuts

279

Display Options

279

8.2.e Performing a Cut Run

280

Confirming Cuts

281

8.2.f Recutting Spots

282

8.2.g Saving the Image

288

9. Integrated Excision Tool

290

9.1 Excision Gel Selection

291

Integrated Excision Tool

292

Table Options

295

9.1.c Step 3. Specify Cuts

296

9.2 Integrated Excision Tool

297

9.2.a Spot Cutter Setup

299

Set Cutting Tip Height

300

Spot Cutter Settings

300

9.2.b Spot Cutter Calibration

302

9.2.c Cutting Spots

304

Step 1. Select the Cut List

306

Switching Gels

317

Ending the Cut Run

317

Recutting Spots

317

9.2.d Exporting the Cut List

322

10. Mass Spectrometry

324

Analysis

324

Mass Spectrometry Analysis

326

Annotation Categories Created

327

10.3 Mass Spec Score Overlay

328

10.4 Protein Probe

329

10.5 Import Mascot Results

330

Set Search Filters

331

Select Search

332

10.5.a Options

334

11. Graphs and Reports

336

Graphs and Reports

338

11.2Histogram Graphs

339

11.2.b Types of Graphs

341

11.3 A-B Overlay

342

11.4 Quantity Table Report

344

Other Options

345

11.4.a Quantity Graph Report

346

11.5 Master Image Report

348

11.6 Scatter Plot Report

349

Appendix A

352

Simulation Mode

353

Appendix A. Gel Doc

354

A.2 Step I. Position Gel

355

A.4 Step III. Acquire Image

356

Manual Expose

357

A.5 Step IV. Optimize Display

359

A.6 Step V. Analysis

360

A.7 Step VI. Select Output

361

A.8 Exposure Status

362

A.9 Options

362

DAC Settings

363

Simple Acquisition Mode

365

Appendix B

366

Appendix B. ChemiDoc

368

B.2 Step I. Position Gel

369

B.3 Step II. Image Mode

370

B.4 Step III. Acquire Image

370

Auto Expose

371

Live Acquire

373

B.5 Step IV. Optimize Display

375

B.6 Step V. Analysis

377

B.7 Step VI. Select Output

377

B.8 Exposure Status

378

B.9 Options

378

Imaging Area

380

Auto Exposure Threshold

380

Reminder

380

Save Options

381

Appendix C

384

ChemiDoc XRS

384

Appendix C. ChemiDoc XRS

386

C.2.a. Custom Applications

387

C.3 Step II. Position Gel

388

C.4 Step III. Acquire Image

389

C.4.a. Exposure Status

392

Illumination Flat Fielding

392

C.5 Options

394

C.5.a. Imaging Area

395

C.5.b. Reminder

395

C.5.c. Dark Subtraction

396

C.6 Other Features

397

Highlight Saturated Pixels

398

File Size of Images

398

Appendix D

400

D.1 GS-700 Acquisition Window

401

Appendix D. GS-700

402

Choosing Your Own Settings

404

D.3 Step II. Select Scan Area

405

Selecting an Area

406

D.5 Acquire the Image

408

D.6 Calibration

409

D.6.a Editing the Step Tablet

410

Diffuse Versus Specular O.D

412

D.7 Other Options

413

Auto Save After Scan

414

Make Backup Copy

414

Hide Grid

414

Appendix E

416

E.1 GS-710 Acquisition Window

417

Appendix E. GS-710

418

E.3 Step II. Select Scan Area

422

E.5 Calibration

424

E.5.a Editing the Step Tablet

425

E.6 Acquire the Image

428

E.7 Other Options

429

Appendix F

432

F.1 GS-800 Acquisition Window

433

Appendix F. GS-800

434

F.3 Step II. Select Scan Area

438

F.5 Calibration

440

F.5.a Step Tablet Values

441

Reflective Step Tablet

443

F.6 Acquire the Image

444

F.7 Other Options

445

Appendix G

448

Appendix G. Fluor-S

450

Custom Applications

452

G.3 Step II. Position/Focus

453

Position

454

G.5 Acquire the Image

457

G.6 Options

458

G.6.a Dark Subtraction Type

459

Referenced

460

Reset Reference

460

G.6.b Live Exposure Mode

461

G.6.c Save

462

G.6.d Imaging Area Size

462

G.7 Other Features

463

Appendix H

466

Appendix H. Fluor-S MAX

468

Scan Dimension

471

H.3 Step II. Position/Focus

472

H.5 Acquire the Image

475

H.6 Options

476

H.6.a Dark Subtraction Type

477

Reset Reference Button

478

H.6.b Live Exposure Mode

479

H.6.c Save

480

H.6.d Imaging Area Size

480

H.7 Other Features

481

Appendix I

484

Appendix I. Personal FX

486

I.2 Step I. Select Scan Area

487

I.4 Acquire the Image

489

I.5 Options

490

Disable Default Filter

491

Warn on Saturated Pixels

491

Appendix J

492

Molecular Imager FX

492

Family (FX Pro, FX Pro

492

Plus and Molecular FX)

492

J.1 FX Acquisition Window

493

Appendix J. FX

494

J.2.a Selecting a Channel

495

Standard Applications

497

Standard FX Applications

497

Sample Intensity

499

J.3 Step II. Select Scan Area

502

J.5 Acquire the Image

504

J.6 Options

505

Appendix K

508

VersaDoc

508

Appendix K. VersaDoc

510

K.2.a. Selecting a Channel

510

K.3 Step II. Position/Focus

514

Setting an Exposure Time

515

K.5 Acquire the Image

517

Optimize Exposure

519

K.6 Options

521

Reference

522

K.6.b. Save

524

K.6.c. Imaging Area Size

524

K.7 Other Features

525

Appendix L

526

L.1.a Calibration Strip Data

527

Appendix L. Techniques

528

L.1.b Scan Information

529

Flip Calstrip (if necessary)

531

Box Segments in a Calstrip

532

Calibration Curve Problems

534

Why Merge Exposures?

535

Appendix M

538

Numerics

540




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