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Discovery Division
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MS Cleaner Version 2.0
Experimental data used to test the Version 2.0 

 


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0) Abbreviations:

SL - sequence ladder length (in residues)
Int - intensity threshold (percentage of the most intense peaks from the total number of peaks)
MB - megabytes
fmol - femtomole

1) Experimental data from:

Data before cleaning

Data after cleaning

Cleaned spectra ready for interpretation

Number of non-interpretable spectra not sent to Mascot

Dataset

Name of protein

Number of spectra

File size [MB]

SL Length

Intensity

Cleaned spectra

Number of spectra

File size [MB]

100fmol_BSA_run1

BSA

2679

6324

3

100

100fmol_BSA_run1_c_SL3_Int100

1664

3607

1015

3

15

100fmol_BSA_run1_c_SL3_Int15

390

2040

2289

3

20

100fmol_BSA_run1_c_SL3_Int20

490

2362

2189

3

25

100fmol_BSA_run1_c_SL3_Int25

601

2667

2078

3

30

100fmol_BSA_run1_c_SL3_Int30

688

2890

1991

4

100

100fmol_BSA_run1_c_SL4_Int100

940

2756

1739

4

15

100fmol_BSA_run1_c_SL4_Int15

260

1537

2419

4

20

100fmol_BSA_run1_c_SL4_Int20

321

1792

2358

4

25

100fmol_BSA_run1_c_SL4_Int25

380

2005

2299

4

30

100fmol_BSA_run1_c_SL4_Int30

441

2226

2238

5

100

100fmol_BSA_run1_c_SL5_Int100

593

2155

2086

5

15

100fmol_BSA_run1_c_SL5_Int15

174

1122

2505

5

20

100fmol_BSA_run1_c_SL5_Int20

232

1409

2447

5

25

100fmol_BSA_run1_c_SL5_Int25

281

1618

2398

5

30

100fmol_BSA_run1_c_SL5_Int30

313

1755

2366

100fmol_Alkoholdeh_run3

ADH

2325

4177

3

100

100fmol_Alkoholdeh_run3_c_SL3_Int100

1446

2321

879

3

15

100fmol_Alkoholdeh_run3_c_SL3_Int15

269

896

2056

3

20

100fmol_Alkoholdeh_run3_c_SL3_Int20

347

1123

1978

3

25

100fmol_Alkoholdeh_run3_c_SL3_Int25

440

1339

1885

3

30

100fmol_Alkoholdeh_run3_c_SL3_Int30

697

1532

1628

4

100

100fmol_Alkoholdeh_run3_c_SL4_Int100

902

1781

1423

4

15

100fmol_Alkoholdeh_run3_c_SL4_Int15

173

602

2152

4

20

100fmol_Alkoholdeh_run3_c_SL4_Int20

216

744

2109

4

25

100fmol_Alkoholdeh_run3_c_SL4_Int25

271

901

2054

4

30

100fmol_Alkoholdeh_run3_c_SL4_Int30

325

1064

2000

5

100

100fmol_Alkoholdeh_run3_c_SL5_Int100

594

1359

1731

5

15

100fmol_Alkoholdeh_run3_c_SL5_Int15

94

336

2231

5

20

100fmol_Alkoholdeh_run3_c_SL5_Int20

125

464

2200

5

25

100fmol_Alkoholdeh_run3_c_SL5_Int25

145

533

2180

5

30

100fmol_Alkoholdeh_run3_c_SL5_Int30

186

699

2139

100fmol_Apo_trans_run1

Transferin

2608

5728

3

100

100fmol_Apo_trans_run1_c_SL3_Int100

1587

3200

1021

3

15

100fmol_Apo_trans_run1_c_SL3_Int15

373

1752

2235

3

20

100fmol_Apo_trans_run1_c_SL3_Int20

485

2103

2123

3

25

100fmol_Apo_trans_run1_c_SL3_Int25

568

2341

2040

3

30

100fmol_Apo_trans_run1_c_SL3_Int30

639

2517

1969

4

100

100fmol_Apo_trans_run1_c_SL4_Int100

864

2391

1744

4

15

100fmol_Apo_trans_run1_c_SL4_Int15

231

1224

2377

4

20

100fmol_Apo_trans_run1_c_SL4_Int20

298

1500

2310

4

25

100fmol_Apo_trans_run1_c_SL4_Int25

360

1728

2248

4

30

100fmol_Apo_trans_run1_c_SL4_Int30

414

1907

2194

5

100

100fmol_Apo_trans_run1_c_SL5_Int100

540

1844

2068

5

15

100fmol_Apo_trans_run1_c_SL5_Int15

164

951

2444

5

20

100fmol_Apo_trans_run1_c_SL5_Int20

194

1070

2414

5

25

100fmol_Apo_trans_run1_c_SL5_Int25

245

1316

2363

5

30

100fmol_Apo_trans_run1_c_SL5_Int30

286

1491

2322

 

Data before cleaning

Data after cleaning with Sequence Ladder length 4, and Intensity 20%

Cleaned spectra ready for interpretation

Bad spectra not sent to Mascot

Dataset

Name of protein

Number of spectra

File size [MB]

Cleaned data file

Number of spectra

File size [MB]

alphaAmyl_col1

α-amylase

10108

51020

alphaAmyl_col1_c

4036

24491

6072

alphaAmyl_col2

10184

54712

alphaAmyl_col2_c

5070

30106

5114

AmylGlu_col1

Amylogucosidase

10030

40453

AmylGlu_col1_c

2082

13278

7948

AmylGlu_col2

9870

44653

AmylGlu_col2_c

2702

17353

7168

apo_col1

Apo-transferrin

10032

47833

apo_col1_c

3702

22637

6330

apo_col2

10090

52363

apo_col2_c

4730

28688

5360

betaGal_col1

β-galactidase

10324

70869

betaGal_col1_c

5362

43513

4962

betaGal_col2

10368

74268

betaGal_col2_c

5920

47035

4448

CarAnly_col1

Carbonic anhydrase

9946

32553

CarAnly_col1_c

964

4376

8982

CarAnly_col2

9534

33781

CarAnly_col2_c

1328

5987

8206

Cat_col1

Catalase

10098

48447

Cat_col1_c

3306

21188

6792

Cat_col2

10034

51879

Cat_col2_c

4064

25812

5970

phosB_col1

Phosphorylase B

10118

49440

phosB_col1_c

3694

22965

6424

phosB_col2

10096

53536

phosB_col2_c

4648

28879

5448

GluDey_col1

Glutamic dehydrogenase

10006

38166

GluDey_col1_c

2046

11160

7960

GluDey_col2

9886

41582

GluDey_col2_c

2718

14430

7168

GluTra_col1

Glutathione transferase

10022

43787

GluTra_col1_c

2842

15589

7180

GluTra_col2

10156

50330

GluTra_col2_c

3946

22328

6210

Immo_col1

Immunoglobulin γ

10330

72607

Immo_col1_c

5960

48107

4370

Immo_col2

10334

75633

Immo_col2_c

6504

52060

3830

LacDe_col1

Lactic dehydrogenase

10286

60131

LacDe_col1_c

4814

34522

5472

LacDe_col2

10250

66981

LacDe_col2_c

6134

43738

4116

LactoPee_col1

Lactoperoxidase

10242

55687

LactoPee_col1_c

3880

27021

6362

LactoPee_col2

10402

65984

LactoPee_col2_c

5024

36709

5378

Myo_col1

Myoglobin

9958

36697

Myo_col1_c

1452

7645

8506

Myo_col2

9744

37140

Myo_col2_c

1868

9068

7876


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