UND NIDA Brain Proteome Individual (peptide-level) log2z+8 (Mar21)

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Summary

Brain proteome data. Deep proteome data were generated using whole brain tissue from both parents and 29 members of the HXB family, one male and one female per strain. Proteins in these samples were identified and quantified using the tandem-mass-tag (TMT) labeling strategy coupled with two-dimensional liquid chromatography-tandem mass spectrometry (LC/LC-MS/MS).

This rat whole brain proteome data provide protein expression of 31 HXB/BXH strains, including 29 RI strains, and two parental strains, SHR/OlaIpcv and BN-Lx/Cub. A total of 8,124 proteins were quantified across all 31 strains.

About cases

Index

Strain

Sex

TMT Batch

TMT Channel

1

SHR

M

1

sig127C

2

SHR

F

1

sig128N

3

BN.Lx

M

1

sig129C

4

BN.Lx

F

1

sig131N

5

HXB18

F

1

sig126

6

HXB18

M

1

sig127N

7

BXH3

M

1

sig131C

8

BXH3

F

1

sig132N

9

BXH12

M

1

sig132C

10

BXH12

F

1

sig133N

11

BXH13

M

1

sig133C

12

BXH13

F

1

sig134N

13

BXH6

M

2

sig127N

14

BXH6

F

2

sig127C

15

BXH8

M

2

sig128N

16

BXH8

F

2

sig128C

17

HXB1

M

2

sig129N

18

HXB1

F

2

sig129C

19

HXB10

M

2

sig130N

20

HXB10

F

2

sig130C

21

HXB13

M

2

sig131N

22

HXB13

F

2

sig131C

23

HXB15

M

2

sig132N

24

HXB15

F

2

sig132C

25

HXB17

M

2

sig133N

26

HXB17

F

2

sig133C

27

HXB4

M

2

sig134N

28

HXB4

F

3

sig127N

29

HXB2

M

3

sig127C

30

HXB2

F

3

sig128N

31

HXB20

M

3

sig128C

32

HXB20

F

3

sig129N

33

HXB22

M

3

sig129C

34

HXB22

F

3

sig130N

35

HXB29

M

3

sig130C

36

HXB29

F

3

sig131N

37

HXB3

M

3

sig131C

38

HXB3

F

3

sig132N

39

HXB31

M

3

sig132C

40

HXB31

F

3

sig133N

41

HXB7

M

3

sig133C

42

HXB7

F

3

sig134N

43

BXH5

F

4

sig126

44

BXH5

M

4

sig127N

45

BXH9

F

4

sig127C

46

BXH9

M

4

sig128N

47

BXH10

F

4

sig128C

48

BXH10

M

4

sig129N

49

BXH11

F

4

sig129C

50

BXH11

M

4

sig130N

51

HXB5

F

4

sig130C

52

HXB5

M

4

sig131N

53

HXB21

F

5

sig126

54

HXB21

M

5

sig127N

55

HXB23

F

5

sig127C

56

HXB23

M

5

sig128N

57

HXB24

F

5

sig128C

58

HXB24

M

5

sig129N

59

HXB25

F

5

sig129C

60

HXB25

M

5

sig130N

61

HXB27

F

5

sig130C

62

HXB27

M

5

sig131N

About data processing

Sample processing protocol: The proteomic data were generated with 3 batches of 16-plex and 2 batches of 11-plex TMT experiments. The rat brain samples from 31 HXB/BXH strains with replicates (i.e., male and female) were lysed, digested, and labeled with either 11 or 16 different TMT tags. The TMT-labeled peptides were pooled with an equal amount of each and fractionated into 42 fractions in a concatenated fashion on an RP-HPLC column (4.6 mm x 250 mm) under basic pH conditions. each fraction was run sequentially on a column (75 μm x 20 cm for the whole proteome, 50 μm x ∼30 cm for phosphoproteome, 1.9 μm C18 resin from Dr. Maisch GmbH, 65°C to reduce backpressure) interfaced with a Q Exactive HF Orbitrap or Fusion MS (Thermo Fisher). Peptides were eluted by a 2-3 hr gradient (buffer A: 0.2% formic acid, 5% DMSO; buffer B: buffer A plus 65% acetonitrile). MS settings included the MS1 scan (410-1600 m/z, 60,000 or 120,000 resolution, 1 × 106 AGC and 50 ms maximal ion time) and 20 data-dependent MS2 scans (fixed first mass of 120 m/z, 60,000 resolution, 1 × 105 AGC, 100-150 ms maximal ion time, HCD, 35%–38% normalized collision energy, ∼1.0 m/z isolation window). 

Data processing protocol: The MS/MS raw files are processed using the JUMP searching engine against the UniProt mouse database.  Searches were performed using 8 ppm mass tolerance for precursor ions due to JUMP’s auto mass correction function and 15 ppm for fragment ions, allowing up to two missed trypsin cleavage sites. TMT tags on lysine residues and peptide N termini (+229.162932 Da) were used for static modifications and the dynamic modifications include oxidation of methionine residues (+15.99492 Da). The assigned peptides are filtered by minimal peptide length, maximum miscleavages, mass-to-charge accuracy and matching scores. The peptides are then divided into groups according to peptide length, trypticity, modification, miscleavage, and charge and then further filtered by matching scores to reduce protein or phosphopeptide FDR to below 1%. Proteins or phosphopeptides were quantified by summing reporter ion counts across all matched PSMs using our in-house software.

Protein quantification: We first extracted the TMT reporter ion intensities of each PSM and corrected the raw intensities based on the isotopic distribution of each labeling reagent. We discarded PSMs with low intensities (i.e., the minimum intensity of 1,000 and the median intensity of 5,000). After normalizing abundance with the trimmed median intensity of all PSMs, we calculated the mean-centered intensities across samples (e.g., relative intensities between each sample and the mean) and summarized protein relative intensities by averaging related PSMs. Finally, we derived protein absolute intensities by multiplying the relative intensities by the grand mean of the three most highly abundant PSMs. We first used the internal standard to normalize 3 batches of 16-plex experiments and 2 batches of 11-plex experiments. We then used the LIMMA batch removal function to normalize all five batches of TMT experiments.  

Specifics of this data set

UND NIDA Brain Proteome Individual (peptide-level) log2z+8 (Mar21)