HP Data Explorer 4 Series manuals

Hp Data Explorer 4 Series User Manual (447 pages)

Brand: Hp | Category: Software | Size: 3.67 MB |

English

Table of contents

Data Explorer

1

Software

1

Data Explorer

5

Software User’s Guide v

5

Software User’s Guide vii

7

Chapter 9 Troubleshooting

8

(Visual Basic Macros)

9

Table of Contents

10

How to Use This Guide

11

Notes, Cautions

13

Warnings, and

13

Send us your

14

1 Data Explorer

15

1.1 Overview

16

Starting and

17

1-4 Applied Biosystems

18

1.2 File Formats and Types

19

1-6 Applied Biosystems

20

File Formats and Types

21

Software User’s Guide 1-7

21

Additional files

22

Software User’s Guide 1-9

23

1-10 Applied Biosystems

24

1.3 Parts of the

25

Data Explorer Window

25

Software User’s Guide 1-13

27

Context-sensitive

28

Output window

29

1.4 Customizing the

31

1-18 Applied Biosystems

32

Software User’s Guide 1-19

33

Opening

34

Applying a .SET

34

1.4.3 Customizing Toolbars

35

Undocking

36

1.5 Setting Graphic Options

37

Accessing

38

Setting Graphic Options

39

Software User’s Guide 1-25

39

Setting line

40

Setting data

41

Setting traces in

42

Line or Vertical

42

Bar mode

42

Setting graphic

42

Software User’s Guide 1-29

43

1.6 Managing Files

44

Managing Files

45

Software User’s Guide 1-31

45

Viewing file

46

Searching file

46

1.6.2 Converting Data from

47

1.6.3 Converting to and

48

Exporting ASCII Data

48

Importing a Trace

49

Exporting .BIC

50

.MSM, and .CAL

50

Software User’s Guide 1-37

51

Saving .LBS

52

Copy displayed

53

1-40 Applied Biosystems

54

Software User’s Guide 1-41

55

1-42 Applied Biosystems

56

2 Using Chromatogram

57

2.1.1 Opening Data Files

58

2-4 Applied Biosystems

60

Software User’s Guide 2-5

61

Software User’s Guide 2-7

63

Using Activate

64

Software User’s Guide 2-9

65

2.1.6 Closing Data Files

66

Adjusting the Display Range

67

Software User’s Guide 2-11

67

2-12 Applied Biosystems

68

2.3 Organizing Windows

69

2.4 Manipulating Traces

70

2.4.2 Duplicating a Trace

71

2.4.4 Adding Traces from

72

Setting the

73

Replace mode

73

2-18 Applied Biosystems

74

Manipulating Traces

75

Software User’s Guide 2-19

75

2-20 Applied Biosystems

76

2.4.5 Removing Traces

77

(Processing History)

78

History options

79

2.4.8 Overlaying Traces

80

Overlaying traces

81

2-26 Applied Biosystems

82

Software User’s Guide 2-27

83

2.4.9 Annotating Traces

84

Annotating the

85

2.4.10 Viewing Trace Labels

86

Spectrum trace

87

2-32 Applied Biosystems

88

2.4.11 Printing Traces

89

2-34 Applied Biosystems

90

Dedicating a

91

2-36 Applied Biosystems

92

2.5.2 Copying Traces from

93

2.6 Saving, Opening, and

94

Deleting .DAT Results

94

2.7 Exporting, Opening, and

95

Files (Mariner Data Only)

95

.SPC Results Files

96

Deleting results

97

2-42 Applied Biosystems

98

3 Peak Detection

99

3.1 Overview

100

3.1.2 The Resolution-Based

101

Peak Detection Routine

101

3-4 Applied Biosystems

102

Voyager data

103

Overlapping peak

103

PSD peak

103

3.2 Peak Detection

104

Peak Detection

105

Software User’s Guide 3-7

105

3-8 Applied Biosystems

106

Software User’s Guide 3-9

107

3-10 Applied Biosystems

108

Software User’s Guide 3-11

109

3-12 Applied Biosystems

110

Setting Basic

111

Settings

111

(spectrum data)

111

3-14 Applied Biosystems

112

Software User’s Guide 3-15

113

Setting Peak

114

Processing

114

(spectrum data

114

Setting Advanced

115

Resetting Basic

116

3.2.4 Peak Detection

117

Parameter Descriptions

117

Continued

118

Software User’s Guide 3-21

119

Software User’s Guide 3-25

123

Software User’s Guide 3-27

125

Software User’s Guide 3-31

129

3.2.5 Charge State

130

Determination and Examples

130

Max Charge State

131

3-34 Applied Biosystems

132

Max Isotope #

133

Effect of Minimum

134

Intensity

134

Charge state

134

3.3 Peak List

135

Contents

136

Chromatogram

136

Procedure To insert peaks:

137

3.3.3 Saving the Peak List

138

Importing and

139

3.3.4 Sorting, Filtering

140

Peak List

141

Software User’s Guide 3-43

141

Printing

142

Deleting items

142

3.4 Deisotoping a Spectrum

143

3-46 Applied Biosystems

144

Deisotoping a Spectrum

145

Software User’s Guide 3-47

145

Using the

146

Deisotope

146

Software User’s Guide 3-49

147

3-50 Applied Biosystems

148

Returning to the

149

3.5 Peak Labeling

150

3.5.1 Charge State Labels

151

3.5.2 Setting Chromatogram

152

Peak Labeling

153

Software User’s Guide 3-55

153

3-56 Applied Biosystems

154

Software User’s Guide 3-57

155

3-58 Applied Biosystems

156

Labels not

157

Charge state

158

Software User’s Guide 3-61

159

3-62 Applied Biosystems

160

Software User’s Guide 3-63

161

3-64 Applied Biosystems

162

Applying user

163

Displaying user

163

User labels not

164

3.6 Process that Occurs

165

During Peak Detection

165

Centroiding, and Integration

165

3-68 Applied Biosystems

166

After peak

167

3-70 Applied Biosystems

168

Default .SET files

169

3-72 Applied Biosystems

170

Additional

171

Voyager .SET files

171

3-74 Applied Biosystems

172

Chromatogram Data

173

4 Examining

173

4.1 Overview

174

Types of

175

4-4 Applied Biosystems

176

4.2 Creating an

177

Extracted Ion Chromatogram

177

4-6 Applied Biosystems

178

Software User’s Guide 4-7

179

From the

180

Spectrum window

180

4.2.2 Creating a Constant

181

4-10 Applied Biosystems

182

Software User’s Guide 4-11

183

4-12 Applied Biosystems

184

4.3 Creating an Extracted

185

Absorbance Chromatogram

185

(XAC) (Mariner Data Only)

185

4-14 Applied Biosystems

186

4-16 Applied Biosystems

188

Noise Filtering/Smoothing

189

Software User’s Guide 4-17

189

4-18 Applied Biosystems

190

Software User’s Guide 4-19

191

4.5 Adding and Subtracting

192

Software User’s Guide 4-21

193

4-22 Applied Biosystems

194

(Mariner Data Only)

195

Filtering

196

Software User’s Guide 4-25

197

Evaluating

198

Displaying

198

4.7 Adjusting the Baseline

199

4-28 Applied Biosystems

200

Adjusting the Baseline

201

Software User’s Guide 4-29

201

4.8 Using UV Trace Offset

202

Software User’s Guide 4-31

203

4-32 Applied Biosystems

204

5 Examining

205

Spectrum Data

205

5.1 Overview

206

5-4 Applied Biosystems

208

5.3 Manual Calibration

209

5-6 Applied Biosystems

210

5.3.2 Manually Calibrating

211

Manually

212

Manual Calibration

213

Software User’s Guide 5-9

213

Manually matching

214

Software User’s Guide 5-11

215

Eliminating data

216

Software User’s Guide 5-13

217

Automatically

218

Applying new

219

5-16 Applied Biosystems

220

Software User’s Guide 5-17

221

5-18 Applied Biosystems

222

Software User’s Guide 5-19

223

Modifying a

224

Specifying mass

225

5-22 Applied Biosystems

226

Software User’s Guide 5-23

227

Ensuring that

228

Importing a

229

5.4 Automatic Calibration

230

Automatic

231

Mariner data

231

Importing

233

5-30 Applied Biosystems

234

Automatic Calibration

235

Software User’s Guide 5-31

235

5-32 Applied Biosystems

236

Saving the .SET

237

Software User’s Guide 5-35

239

5.5 Centroiding

240

5.6 Mass Deconvolution

241

5-38 Applied Biosystems

242

Software User’s Guide 5-39

243

Converting to

244

Software User’s Guide 5-41

245

5-42 Applied Biosystems

246

Software User’s Guide 5-43

247

5-44 Applied Biosystems

248

5.8 Adjusting the Baseline

249

5-46 Applied Biosystems

250

Software User’s Guide 5-47

251

5-48 Applied Biosystems

252

Correcting the

253

(continued)

254

Software User’s Guide 5-53

257

5-54 Applied Biosystems

258

5.9 Truncating a Spectrum

260

Truncating a Spectrum

261

Software User’s Guide 5-57

261

5-58 Applied Biosystems

262

Spectrum (Mariner Data Only)

263

5-60 Applied Biosystems

264

Software User’s Guide 5-61

265

Effect on Mariner

267

.RST files

267

Processed Spectra from the

268

Same or Different Data Files

268

Software User’s Guide 5-65

269

5-66 Applied Biosystems

270

6 Using Tools and

271

Applications

271

6.1 Using the Elemental

272

Composition Calculator

272

Software User’s Guide 6-3

273

6-4 Applied Biosystems

274

Electron state for

275

If no results are

276

6.1.2 Setting Limits

277

6-8 Applied Biosystems

278

Adding new

279

Figure 6-6 Periodic Table

280

Software User’s Guide 6-11

281

Setting limits for

282

Using the Isotope

283

Calculator

283

6-14 Applied Biosystems

284

Using the Isotope Calculator

285

Software User’s Guide 6-15

285

Add and subtract

286

Software User’s Guide 6-17

287

If results are not

289

6.3 Using the

290

Mass Resolution Calculator

290

Software User’s Guide 6-21

291

6-22 Applied Biosystems

292

6-24 Applied Biosystems

294

6.5 Using the

295

Ion Fragmentation Calculator

295

6-26 Applied Biosystems

296

Software User’s Guide 6-27

297

Calculating the

298

Software User’s Guide 6-29

299

Creating a

300

6.6 Using the Elemental

301

Targeting Application

301

6-32 Applied Biosystems

302

Displaying the

303

6.7 Using the Macro Recorder

304

6-36 Applied Biosystems

306

6.7.2 Recording a Macro

307

Assigning a

308

6.7.4 Running a Macro

309

If the macro

310

6.7.5 Deleting a Macro

311

6.7.6 Advanced Macro Editing

312

Importing when

313

Exporting To export macros:

314

Using the Macro Recorder

315

Software User’s Guide 6-45

315

6-46 Applied Biosystems

316

7 Data Explorer

317

Examples

317

7.1 Mariner Data Examples

318

Mariner Data Examples

319

Software User’s Guide 7-3

319

7.1.2 Deconvoluting and

320

Evaluating Unresolved

320

Chromatographic Peaks

320

Creating

321

Software User’s Guide 7-7

323

7.1.3 Determining if a Peak

324

Software User’s Guide 7-9

325

7.2 Voyager Data Examples

327

Adjusting peak

328

Voyager Data Examples

329

Software User’s Guide 7-13

329

Optimize Mass Accuracy

330

Software User’s Guide 7-15

331

7-16 Applied Biosystems

332

Software User’s Guide 7-17

333

7.2.3 Detecting Peaks

334

Setting detection

335

Basic Settings Tab

336

Software User’s Guide 7-21

337

Increasing

338

8 Viewing

339

Voyager PSD Data

339

8.1 Displaying PSD Data

340

Displaying PSD Data

341

Software User’s Guide 8-3

341

8-4 Applied Biosystems

342

Redisplaying the

343

8-6 Applied Biosystems

344

Region of

345

8.2 Applying Fragment Labels

346

Applying Fragment Labels

347

Software User’s Guide 8-9

347

When to use this

348

Overview of

348

.CAL file

348

Calibrating a PSD Spectrum

349

Software User’s Guide 8-11

349

8.3.2 Calibrating

350

Software User’s Guide 8-13

351

8-14 Applied Biosystems

352

Matching peaks

353

Selecting peaks

354

Software User’s Guide 8-17

355

Solving and

356

Selecting

357

Creating PSD

358

.CAL files

358

8.3.4 Creating PSD

359

8-22 Applied Biosystems

360

When to change

361

8-24 Applied Biosystems

362

9 Troubleshooting

363

9.1 Overview

364

9.2 General Troubleshooting

365

Chapter 9 Troubleshooting

366

9-4 Applied Biosystems

366

General Troubleshooting

367

Software User’s Guide 9-5

367

9.3 Processing, Tools, and

368

Applications Troubleshooting

368

Software User’s Guide 9-7

369

9-8 Applied Biosystems

370

Software User’s Guide 9-9

371

9-10 Applied Biosystems

372

Calibration Troubleshooting

373

Software User’s Guide 9-11

373

9-12 Applied Biosystems

374

Software User’s Guide 9-13

375

9.5 Printing Troubleshooting

376

9.6 Peak Detection and

377

Labeling Troubleshooting

377

9-16 Applied Biosystems

378

Software User’s Guide 9-17

379

9-18 Applied Biosystems

380

Software User’s Guide 9-19

381

9-20 Applied Biosystems

382

Software User’s Guide 9-21

383

9-22 Applied Biosystems

384

Appendix

385

Warranty period

386

Warranty

386

Warranties

387

Appendix A Warranty

388

A-4 Applied Biosystems

388

B.1 Isotopes

390

Isotopic pattern

391

Isotope-limited

392

Isotopes

393

Software User’s Guide B-5

393

B.2 Monoisotopic

394

Figure B-7 Average Mass

395

Average mass

395

B-8 Applied Biosystems

396

C.1 Overview

398

C.2 Preparing Data

399

Before Accessing Macros

399

C.3 Accessing the Macros

400

C.4 Using the

401

Ladder Sequencing Toolbox

401

C-6 Applied Biosystems

402

Software User’s Guide C-7

403

C.5 Using the Peptide

405

Fragmentation Toolbox

405

Pairs To list ion pairs:

406

Software User’s Guide C-11

407

C-12 Applied Biosystems

408

Software User’s Guide C-13

409

C.6 Using the

411

Polymer Analysis Toolbox

411

C-16 Applied Biosystems

412

Calculations

413

Preparing data

414

MS Fit/MS tag

414

Using MS Fit/MS Tag Toolbox

415

Software User’s Guide C-19

415

C-20 Applied Biosystems

416

Numerics and Symbols

417

Index-2 Applied Biosystems

418

Index-4 Applied Biosystems

420

Index-6 Applied Biosystems

422

Index-8 Applied Biosystems

424

Index-10 Applied Biosystems

426

Index-12 Applied Biosystems

428

Index-14 Applied Biosystems

430

Index-16 Applied Biosystems

432

Index-18 Applied Biosystems

434

Index-20 Applied Biosystems

436

Index-22 Applied Biosystems

438

Index-24 Applied Biosystems

440

Index-26 Applied Biosystems

442

Index-28 Applied Biosystems

444

Index-30 Applied Biosystems

446

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