raw.pd

Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.

Bundled with MSstatsTMT · exported, loads via data()

Class

data.table

data.table/data.frame

Dimensions

2,858 × 50

Missing

7,201

Format

rda · xz

version 2 · 349 KB

File

data/raw.pd.rda

Fingerprint

6997d667

Format documented

Yes

Source

Source not stated

About this object

A data.frame with a sort-order key for fast joins and lookups. After loading from an .rda file, the internal self-reference needs refreshing via setalloccol(). R object catalogue

Declared attributes

Other attributes

Read by name, kind and length, with the value where it is short enough to show. No rule here knows what any of them means.

Attribute	Holds	Length
.internal.selfref	NULL	0

Columns

Column

Type

Distinct

Missing

Summary

Checked

logical

0 true·2,858 false

Confidence

character

4 characters

Identifying.Node

character

11 characters

PSM.Ambiguity

character

8 – 11 characters

Annotated.Sequence

character

228

15 – 49 characters

Modifications

character

145

16 – 90 characters

Marked.as

logical

2,858

0 true·0 false

Longest missing run

2,858

Leading

2,858

Trailing

2,858

X..Protein.Groups

integer

X..Proteins

integer

Master.Protein.Accessions

character

6 characters

Master.Protein.Descriptions

character

43 – 83 characters

Protein.Accessions

character

6 characters

Protein.Descriptions

character

43 – 83 characters

X..Missed.Cleavages

integer

0 – 1mean 0.1361

Min.

1st Qu.

Median

Mean

0.1361

3rd Qu.

Max.

Std. dev

0.343

Skewness

2.121

Kurtosis

2.501

Zeros

2,469

Charge

integer

2 – 5mean 2.898

Min.

1st Qu.

Median

Mean

2.8985

3rd Qu.

Max.

Std. dev

0.6144

Skewness

0.1619

Kurtosis

-0.0131

DeltaScore

numeric

460

0 – 1mean 0.8968

Min.

1st Qu.

0.88

Median

Mean

0.8968

3rd Qu.

Max.

Std. dev

0.1937

Skewness

-2.444

Kurtosis

5.678

Zeros

Outliers

322322 low · 0 high

DeltaCn

numeric

0 – 0.05mean 0

Min.

1st Qu.

Median

Mean

3rd Qu.

Max.

0.05

Std. dev

0.0015

Skewness

31.12

Kurtosis

972.7

Zeros

2,855

Rank

integer

1 – 3mean 1.004

Min.

1st Qu.

Median

Mean

1.0042

3rd Qu.

Max.

Std. dev

0.0699

Skewness

18.28

Kurtosis

374.2

Search.Engine.Rank

integer

1 – 3mean 1.011

Min.

1st Qu.

Median

Mean

1.0112

3rd Qu.

Max.

Std. dev

0.1117

Skewness

10.75

Kurtosis

127.5

m.z..Da.

numeric

1,959

338.185 – 1318.69mean 765.2

Min.

338.185

1st Qu.

630.701

Median

772.445

Mean

765.229

3rd Qu.

915.132

Max.

1318.69

Std. dev

186.44

Skewness

-0.197

Kurtosis

-0.2942

MH...Da.

numeric

1,959

1012.54 – 4914.35mean 2209

Min.

1012.54

1st Qu.

1554.97

Median

2224.08

Mean

2208.97

3rd Qu.

2743.38

Max.

4914.35

Std. dev

716.776

Skewness

0.4972

Kurtosis

0.1281

Outliers

140 low · 14 high

Theo..MH...Da.

numeric

229

1012.54 – 4914.36mean 2209

Min.

1012.54

1st Qu.

1554.98

Median

2224.08

Mean

2208.97

3rd Qu.

2743.38

Max.

4914.36

Std. dev

716.775

Skewness

0.4972

Kurtosis

0.1281

Outliers

140 low · 14 high

DeltaM..ppm.

numeric

522

-9.55 – 9.88mean 0.8843

Min.

-9.55

1st Qu.

0.24

Median

0.86

Mean

0.8843

3rd Qu.

1.43

Max.

9.88

Std. dev

1.2067

Skewness

0.5797

Kurtosis

8.222

Zeros

Outliers

13243 low · 89 high

Deltam.z..Da.

numeric

459

-0.0072 – 0.0079mean 0.0007

Min.

-0.0072

1st Qu.

0.0002

Median

0.0006

Mean

0.0007

3rd Qu.

0.0012

Max.

0.0079

Std. dev

0.0011

Skewness

0.9318

Kurtosis

8.602

Zeros

Outliers

14437 low · 107 high

Activation.Type

character

3 characters

MS.Order

character

3 characters

Isolation.Interference....

numeric

2,403

0 – 100mean 21.91

Min.

1st Qu.

6.4733

Median

16.869

Mean

21.9103

3rd Qu.

31.8766

Max.

100

Std. dev

20.1997

Skewness

1.327

Kurtosis

2.019

Zeros

398

Outliers

790 low · 79 high

Average.Reporter.S.N

numeric

782

0.1 – 215.8mean 28.2

Min.

0.1

1st Qu.

10.5

Median

19.65

Mean

28.2004

3rd Qu.

35.7

Max.

215.8

Std. dev

28.7637

Skewness

2.543

Kurtosis

8.468

Outliers

1810 low · 181 high

Ion.Inject.Time..ms.

numeric

2,209

0.099 – 50mean 19.97

Min.

0.099

1st Qu.

4.8842

Median

12.1125

Mean

19.9715

3rd Qu.

35.1782

Max.

Std. dev

17.9917

Skewness

0.7108

Kurtosis

-1.077

RT..min.

numeric

2,832

14.7012 – 268.699mean 155.5

Min.

14.7012

1st Qu.

120.585

Median

162.221

Mean

155.524

3rd Qu.

199.042

Max.

268.699

Std. dev

60.553

Skewness

-0.5058

Kurtosis

-0.3998

First.Scan

integer

2,794

3184 – 140654mean 7.922e+4

Min.

3184

1st Qu.

59382.5

Median

83187.5

Mean

79217.1

3rd Qu.

105006

Max.

140654

Std. dev

33285.8

Skewness

-0.5437

Kurtosis

-0.469

Spectrum.File

character

44 characters

File.ID

character

2 – 3 characters

Abundance..126

numeric

2,682

153

459.317 – 1.20789e+7mean 1.336e+5

Min.

459.317

1st Qu.

7790.08

Median

27555.5

Mean

133610

3rd Qu.

94262.8

Max.

1.20789e+7

Std. dev

485778

Skewness

13.25

Kurtosis

250.6

Outliers

3180 low · 318 high

Longest gap

Abundance..127N

numeric

2,677

158

422.705 – 1.23751e+7mean 1.344e+5

Min.

422.705

1st Qu.

7941.71

Median

28371.1

Mean

134430

3rd Qu.

94710.9

Max.

1.23751e+7

Std. dev

494921

Skewness

13.06

Kurtosis

240

Outliers

3170 low · 317 high

Longest gap

Abundance..127C

numeric

2,697

138

350.751 – 1.14114e+7mean 1.326e+5

Min.

350.751

1st Qu.

7798.48

Median

27433.2

Mean

132573

3rd Qu.

94194.6

Max.

1.14114e+7

Std. dev

478260

Skewness

12.5

Kurtosis

218.6

Outliers

3210 low · 321 high

Longest gap

Abundance..128N

numeric

2,706

129

355.582 – 1.19604e+7mean 1.377e+5

Min.

355.582

1st Qu.

7953.11

Median

28215.4

Mean

137673

3rd Qu.

100749

Max.

1.19604e+7

Std. dev

500004

Skewness

13.02

Kurtosis

239

Outliers

3110 low · 311 high

Longest gap

Abundance..128C

numeric

2,703

133

340.307 – 1.18476e+7mean 1.331e+5

Min.

340.307

1st Qu.

8118.7

Median

28559.8

Mean

133085

3rd Qu.

96920.9

Max.

1.18476e+7

Std. dev

477283

Skewness

12.94

Kurtosis

236.1

Outliers

3130 low · 313 high

Longest gap

Abundance..129N

numeric

2,696

139

413.731 – 1.20105e+7mean 1.299e+5

Min.

413.731

1st Qu.

7908.95

Median

27688

Mean

129885

3rd Qu.

95094.8

Max.

1.20105e+7

Std. dev

471831

Skewness

13.32

Kurtosis

252

Outliers

3140 low · 314 high

Longest gap

Abundance..129C

numeric

2,705

130

422.444 – 1.38474e+7mean 1.414e+5

Min.

422.444

1st Qu.

8155.46

Median

29193.5

Mean

141373

3rd Qu.

101349

Max.

1.38474e+7

Std. dev

523574

Skewness

13.64

Kurtosis

269.4

Outliers

3150 low · 315 high

Longest gap

Abundance..130N

numeric

2,696

140

388.378 – 1.05947e+7mean 1.356e+5

Min.

388.378

1st Qu.

8189.04

Median

28335.9

Mean

135623

3rd Qu.

99277.5

Max.

1.05947e+7

Std. dev

474761

Skewness

12.01

Kurtosis

203.7

Outliers

3090 low · 309 high

Longest gap

Abundance..130C

numeric

2,691

144

415.81 – 1.1376e+7mean 1.336e+5

Min.

415.81

1st Qu.

8199.5

Median

28569.7

Mean

133615

3rd Qu.

94586

Max.

1.1376e+7

Std. dev

480186

Skewness

12.81

Kurtosis

231.2

Outliers

3210 low · 321 high

Longest gap

Abundance..131

numeric

2,676

159

400.792 – 1.26074e+7mean 1.333e+5

Min.

400.792

1st Qu.

8502.97

Median

29371.4

Mean

133342

3rd Qu.

96335.1

Max.

1.26074e+7

Std. dev

483521

Skewness

13.34

Kurtosis

255

Outliers

3180 low · 318 high

Longest gap

Quan.Info

logical

2,858

0 true·0 false

Longest missing run

2,858

Leading

2,858

Trailing

2,858

Ions.Score

integer

110

0 – 123mean 32.99

Min.

1st Qu.

Median

Mean

32.9881

3rd Qu.

Max.

123

Std. dev

20.0748

Skewness

0.86

Kurtosis

0.625

Zeros

Outliers

590 low · 59 high

Identity.Strict

integer

18 – 32mean 27.26

Min.

1st Qu.

Median

Mean

27.2624

3rd Qu.

Max.

Std. dev

2.2807

Skewness

-1.387

Kurtosis

2.306

Outliers

195195 low · 0 high

Identity.Relaxed

integer

13 – 25mean 20.28

Min.

1st Qu.

Median

Mean

20.281

3rd Qu.

Max.

Std. dev

2.2286

Skewness

-1.255

Kurtosis

1.606

Outliers

195195 low · 0 high

Expectation.Value

numeric

2,850

1.7557e-12 – 9.8893mean 0.2705

Min.

1.7557e-12

1st Qu.

0.0002

Median

0.0065

Mean

0.2705

3rd Qu.

0.0966

Max.

9.8893

Std. dev

0.8612

Skewness

5.548

Kurtosis

37.59

Outliers

4990 low · 499 high

Percolator.q.Value

numeric

615

0 – 0.01mean 0.0006

Min.

1st Qu.

Median

Mean

0.0006

3rd Qu.

0.0003

Max.

0.01

Std. dev

0.0014

Skewness

3.493

Kurtosis

13.39

Zeros

1,397

Outliers

5090 low · 509 high

Order

ascending

Percolator.PEP

numeric

2,754

4.257e-14 – 0.222mean 0.008

Min.

4.257e-14

1st Qu.

4.4325e-6

Median

0.0002

Mean

0.008

3rd Qu.

0.003

Max.

0.222

Std. dev

0.0238

Skewness

4.57

Kurtosis

23.57

Outliers

5010 low · 501 high

The same data in 1 other package

This data is identical to the data these packages carry, down to the byte.

MSstatsShiny

The structure fingerprint found nothing beyond this list.

Version history

Version	Released	Size	Change	Stored as	Confidence
3.23	2026-04-28	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.22	2025-10-29	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.21	2025-04-15	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.20	2025-03-05	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.19	2024-05-20	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.18	2023-10-24	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.17	2023-04-25	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.16	2023-02-26	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.15	2022-09-12	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.14	2022-02-18	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.13	2021-06-14	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.12	2020-12-20	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.11	2020-10-13	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.10	2020-04-14	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.9	2019-05-04	2,858 × 50	Unchanged	rda · xz version 2 · 349 KB	exact
3.8	2019-02-25	2,858 × 50	–	rda · xz version 2 · 349 KB	exact