Exercise: Data Analysis PXD070899
Plan
read data and log2 transform intensity values
aggregate peptide intensities to protein intensities
format data from long to wide format
remove contaminant proteins
check for missing values
Clustermap of sample and proteins
differential analysis (Volcano Plots)
Enrichment Analysis
check for maltose update pathway (Fig. 3 in paper)
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Note: you may need to restart the kernel to use updated packages.
Paramters
file_in: input file with the quantified peptide data in MSstats format
as provided by quantms
out_dir: output directory for the results of the data analysis,
which will be used later for the report generation with VueGen.
The file will be loaded from the online repository if it is not present.
Create output directory if it does not exist
Output directory: data/PXD070899/report
We have the following columns in the data:
|
Protein.Names |
Genes |
First.Protein.Description |
N.Sequences |
N.Proteotypic.Sequences |
SB_4_64_SH_AYa2022_R1.raw |
SB_4_64_SH_AYa2022_R2.raw |
SB_4_64_SH_AYa2022_R3.raw |
SB_4_64_SH_WT_R1.raw |
SB_4_64_SH_WT_R2.raw |
SB_4_64_SH_WT_R3.raw |
SB_4_64_SH_AY_R1.raw |
SB_4_64_SH_AY_R2.raw |
SB_4_64_SH_AY_R3.raw |
SB_4_64_SH_AYa18_R1.raw |
SB_4_64_SH_AYa18_R2.raw |
SB_4_64_SH_AYa18_R3.raw |
| Protein.Group |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| A5Z2X5 |
YP010_YEAST |
YPR010C-A |
NaN |
4 |
4 |
196,213,000.000 |
201,658,000.000 |
224,749,000.000 |
220,341,000.000 |
210,709,000.000 |
269,670,000.000 |
163,279,000.000 |
137,780,000.000 |
225,286,000.000 |
197,233,000.000 |
150,317,000.000 |
193,584,000.000 |
| D6VTK4 |
STE2_YEAST |
STE2 |
NaN |
6 |
6 |
8,340,980.000 |
5,193,640.000 |
2,078,550.000 |
9,899,680.000 |
4,052,790.000 |
NaN |
20,108,400.000 |
8,787,580.000 |
2,464,330.000 |
8,628,820.000 |
11,099,400.000 |
2,842,180.000 |
| O13329 |
FOB1_YEAST |
FOB1 |
NaN |
1 |
1 |
NaN |
58,997.800 |
NaN |
NaN |
NaN |
NaN |
NaN |
45,124.500 |
NaN |
NaN |
NaN |
NaN |
| O13516 |
RS9A_YEAST |
RPS9A |
NaN |
17 |
1 |
194,925,000.000 |
142,185,000.000 |
170,798,000.000 |
210,142,000.000 |
124,835,000.000 |
157,529,000.000 |
305,432,000.000 |
113,893,000.000 |
127,791,000.000 |
188,020,000.000 |
150,662,000.000 |
85,463,000.000 |
| O13525 |
COQ4_YEAST |
COQ4 |
NaN |
17 |
17 |
50,320,900.000 |
58,710,400.000 |
61,916,400.000 |
64,847,800.000 |
70,983,700.000 |
66,808,300.000 |
66,351,200.000 |
60,963,000.000 |
51,681,200.000 |
57,557,100.000 |
64,895,400.000 |
41,240,700.000 |
Potentiall clean filepath names in DIANN output
|
Protein.Names |
Genes |
First.Protein.Description |
N.Sequences |
N.Proteotypic.Sequences |
SB_4_64_SH_AYa2022_R1.raw |
SB_4_64_SH_AYa2022_R2.raw |
SB_4_64_SH_AYa2022_R3.raw |
SB_4_64_SH_WT_R1.raw |
SB_4_64_SH_WT_R2.raw |
SB_4_64_SH_WT_R3.raw |
SB_4_64_SH_AY_R1.raw |
SB_4_64_SH_AY_R2.raw |
SB_4_64_SH_AY_R3.raw |
SB_4_64_SH_AYa18_R1.raw |
SB_4_64_SH_AYa18_R2.raw |
SB_4_64_SH_AYa18_R3.raw |
| Protein.Group |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| A5Z2X5 |
YP010_YEAST |
YPR010C-A |
NaN |
4 |
4 |
196,213,000.000 |
201,658,000.000 |
224,749,000.000 |
220,341,000.000 |
210,709,000.000 |
269,670,000.000 |
163,279,000.000 |
137,780,000.000 |
225,286,000.000 |
197,233,000.000 |
150,317,000.000 |
193,584,000.000 |
| D6VTK4 |
STE2_YEAST |
STE2 |
NaN |
6 |
6 |
8,340,980.000 |
5,193,640.000 |
2,078,550.000 |
9,899,680.000 |
4,052,790.000 |
NaN |
20,108,400.000 |
8,787,580.000 |
2,464,330.000 |
8,628,820.000 |
11,099,400.000 |
2,842,180.000 |
| O13329 |
FOB1_YEAST |
FOB1 |
NaN |
1 |
1 |
NaN |
58,997.800 |
NaN |
NaN |
NaN |
NaN |
NaN |
45,124.500 |
NaN |
NaN |
NaN |
NaN |
| O13516 |
RS9A_YEAST |
RPS9A |
NaN |
17 |
1 |
194,925,000.000 |
142,185,000.000 |
170,798,000.000 |
210,142,000.000 |
124,835,000.000 |
157,529,000.000 |
305,432,000.000 |
113,893,000.000 |
127,791,000.000 |
188,020,000.000 |
150,662,000.000 |
85,463,000.000 |
| O13525 |
COQ4_YEAST |
COQ4 |
NaN |
17 |
17 |
50,320,900.000 |
58,710,400.000 |
61,916,400.000 |
64,847,800.000 |
70,983,700.000 |
66,808,300.000 |
66,351,200.000 |
60,963,000.000 |
51,681,200.000 |
57,557,100.000 |
64,895,400.000 |
41,240,700.000 |
The first 6 columns contain the meta information about the peptides,
while the remaining columns contain the intensities.
|
Protein.Names |
Genes |
First.Protein.Description |
N.Sequences |
N.Proteotypic.Sequences |
| Protein.Group |
|
|
|
|
|
| A5Z2X5 |
YP010_YEAST |
YPR010C-A |
NaN |
4 |
4 |
| D6VTK4 |
STE2_YEAST |
STE2 |
NaN |
6 |
6 |
| O13329 |
FOB1_YEAST |
FOB1 |
NaN |
1 |
1 |
| O13516 |
RS9A_YEAST |
RPS9A |
NaN |
17 |
1 |
| O13525 |
COQ4_YEAST |
COQ4 |
NaN |
17 |
17 |
| ... |
... |
... |
... |
... |
... |
| cRAP-P02769 |
cRAP-ALBU_BOVIN |
cRAP-ALB |
NaN |
44 |
44 |
| cRAP-P04264 |
cRAP-K2C1_HUMAN |
cRAP-KRT1 |
NaN |
16 |
16 |
| cRAP-P13645 |
cRAP-K1C10_HUMAN |
cRAP-KRT10 |
NaN |
18 |
16 |
| cRAP-P35527 |
cRAP-K1C9_HUMAN |
cRAP-KRT9 |
NaN |
14 |
14 |
| cRAP-P35908 |
cRAP-K22E_HUMAN |
cRAP-KRT2 |
NaN |
12 |
11 |
3586 rows × 5 columns
| ProteinName |
A5Z2X5 |
D6VTK4 |
O13329 |
O13516 |
O13525 |
O13563 |
O13585 |
O14455 |
O14467 |
O14468 |
... |
cRAP-P02662 |
cRAP-P02663 |
cRAP-P02666 |
cRAP-P02668 |
cRAP-P02768 |
cRAP-P02769 |
cRAP-P04264 |
cRAP-P13645 |
cRAP-P35527 |
cRAP-P35908 |
| SampleID |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| SB_4_64_SH_AYa2022_R1.raw |
196,213,000.000 |
8,340,980.000 |
NaN |
194,925,000.000 |
50,320,900.000 |
2,871,670.000 |
2,240,990.000 |
325,647,000.000 |
53,770,700.000 |
1,341,650.000 |
... |
1,293,560.000 |
8,061,300.000 |
NaN |
NaN |
5,591,100.000 |
2,954,770,000.000 |
10,837,100.000 |
4,622,900.000 |
9,769,450.000 |
3,494,090.000 |
| SB_4_64_SH_AYa2022_R2.raw |
201,658,000.000 |
5,193,640.000 |
58,997.800 |
142,185,000.000 |
58,710,400.000 |
2,695,290.000 |
1,323,580.000 |
224,329,000.000 |
49,659,900.000 |
1,710,070.000 |
... |
105,439,000.000 |
41,599,900.000 |
67,757,800.000 |
22,124,200.000 |
11,533,200.000 |
5,289,410,000.000 |
8,067,970.000 |
4,010,270.000 |
6,966,230.000 |
3,496,160.000 |
| SB_4_64_SH_AYa2022_R3.raw |
224,749,000.000 |
2,078,550.000 |
NaN |
170,798,000.000 |
61,916,400.000 |
1,364,950.000 |
NaN |
114,717,000.000 |
27,135,000.000 |
729,509.000 |
... |
2,417,300.000 |
NaN |
600,944.000 |
NaN |
3,634,230.000 |
2,255,610,000.000 |
5,640,980.000 |
1,964,420.000 |
6,998,510.000 |
2,408,860.000 |
| SB_4_64_SH_WT_R1.raw |
220,341,000.000 |
9,899,680.000 |
NaN |
210,142,000.000 |
64,847,800.000 |
3,740,660.000 |
1,978,800.000 |
377,715,000.000 |
82,570,700.000 |
2,985,240.000 |
... |
1,934,850.000 |
NaN |
NaN |
NaN |
10,806,300.000 |
3,734,340,000.000 |
19,107,400.000 |
10,082,500.000 |
9,497,230.000 |
7,434,660.000 |
| SB_4_64_SH_WT_R2.raw |
210,709,000.000 |
4,052,790.000 |
NaN |
124,835,000.000 |
70,983,700.000 |
2,623,000.000 |
931,863.000 |
197,967,000.000 |
42,563,700.000 |
803,845.000 |
... |
22,855,800.000 |
13,385,900.000 |
12,795,200.000 |
6,610,350.000 |
10,679,100.000 |
4,302,160,000.000 |
11,455,700.000 |
6,321,750.000 |
11,779,100.000 |
5,144,510.000 |
5 rows × 3586 columns
Log2 transform the intensity values and remove contaminant proteins
Index(['cRAP-P00698', 'cRAP-P00722', 'cRAP-P00761', 'cRAP-P02662',
'cRAP-P02663', 'cRAP-P02666', 'cRAP-P02668', 'cRAP-P02768',
'cRAP-P02769', 'cRAP-P04264', 'cRAP-P13645', 'cRAP-P35527',
'cRAP-P35908'],
dtype='object', name='ProteinName')
| ProteinName |
A5Z2X5 |
D6VTK4 |
O13329 |
O13516 |
O13525 |
O13563 |
O13585 |
O14455 |
O14467 |
O14468 |
... |
Q99325 |
Q99332 |
Q99369 |
Q99373 |
Q99382 |
Q99383 |
Q99385 |
Q99394 |
Q9P305 |
Q9URQ5 |
| SampleID |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| SB_4_64_SH_AYa2022_R1.raw |
27.548 |
22.992 |
NaN |
27.538 |
25.585 |
21.453 |
21.096 |
28.279 |
25.680 |
20.356 |
... |
22.768 |
22.297 |
21.419 |
19.735 |
24.338 |
22.629 |
26.505 |
19.170 |
21.049 |
21.062 |
| SB_4_64_SH_AYa2022_R2.raw |
27.587 |
22.308 |
15.848 |
27.083 |
25.807 |
21.362 |
20.336 |
27.741 |
25.566 |
20.706 |
... |
22.218 |
21.849 |
22.326 |
20.254 |
24.351 |
21.473 |
26.856 |
19.296 |
21.207 |
21.121 |
| SB_4_64_SH_AYa2022_R3.raw |
27.744 |
20.987 |
NaN |
27.348 |
25.884 |
20.380 |
NaN |
26.774 |
24.694 |
19.477 |
... |
21.923 |
21.204 |
22.882 |
20.540 |
23.441 |
21.457 |
25.224 |
18.182 |
18.071 |
19.924 |
| SB_4_64_SH_WT_R1.raw |
27.715 |
23.239 |
NaN |
27.647 |
25.951 |
21.835 |
20.916 |
28.493 |
26.299 |
21.509 |
... |
23.027 |
22.554 |
21.419 |
19.827 |
24.763 |
22.968 |
26.934 |
18.237 |
21.557 |
22.068 |
| SB_4_64_SH_WT_R2.raw |
27.651 |
21.950 |
NaN |
26.895 |
26.081 |
21.323 |
19.830 |
27.561 |
25.343 |
19.617 |
... |
22.508 |
20.940 |
21.690 |
19.798 |
23.834 |
21.887 |
26.248 |
17.966 |
21.011 |
21.815 |
| SB_4_64_SH_WT_R3.raw |
28.007 |
NaN |
NaN |
27.231 |
25.994 |
NaN |
NaN |
26.694 |
23.840 |
NaN |
... |
20.278 |
NaN |
21.579 |
19.640 |
22.274 |
21.557 |
24.698 |
17.095 |
NaN |
NaN |
| SB_4_64_SH_AY_R1.raw |
27.283 |
24.261 |
NaN |
28.186 |
25.984 |
22.298 |
21.508 |
28.702 |
26.291 |
20.260 |
... |
22.419 |
23.165 |
23.174 |
19.862 |
24.227 |
23.309 |
27.179 |
18.961 |
21.864 |
21.818 |
| SB_4_64_SH_AY_R2.raw |
27.038 |
23.067 |
15.462 |
26.763 |
25.861 |
20.989 |
20.437 |
26.949 |
25.445 |
20.282 |
... |
22.981 |
22.215 |
22.402 |
20.017 |
24.341 |
21.198 |
27.059 |
17.872 |
20.540 |
19.814 |
| SB_4_64_SH_AY_R3.raw |
27.747 |
21.233 |
NaN |
26.929 |
25.623 |
NaN |
NaN |
26.262 |
24.292 |
19.950 |
... |
20.805 |
21.183 |
23.328 |
20.166 |
21.834 |
21.081 |
25.173 |
17.889 |
18.187 |
19.127 |
| SB_4_64_SH_AYa18_R1.raw |
27.555 |
23.041 |
NaN |
27.486 |
25.778 |
21.611 |
21.384 |
28.405 |
25.903 |
20.551 |
... |
22.940 |
22.038 |
22.308 |
19.885 |
24.329 |
22.955 |
26.574 |
19.529 |
21.309 |
22.649 |
| SB_4_64_SH_AYa18_R2.raw |
27.163 |
23.404 |
NaN |
27.167 |
25.952 |
21.216 |
20.952 |
27.579 |
25.254 |
NaN |
... |
22.893 |
22.278 |
22.526 |
19.705 |
24.568 |
21.738 |
26.625 |
19.872 |
21.077 |
18.024 |
| SB_4_64_SH_AYa18_R3.raw |
27.528 |
21.439 |
NaN |
26.349 |
25.298 |
NaN |
NaN |
25.744 |
23.759 |
NaN |
... |
21.374 |
NaN |
23.046 |
20.261 |
22.105 |
20.897 |
24.539 |
18.876 |
NaN |
NaN |
12 rows × 3573 columns
Add label encoding
SampleID
SB_4_64_SH_AYa2022_R1.raw AYa2022
SB_4_64_SH_AYa2022_R2.raw AYa2022
SB_4_64_SH_AYa2022_R3.raw AYa2022
SB_4_64_SH_WT_R1.raw WT
SB_4_64_SH_WT_R2.raw WT
SB_4_64_SH_WT_R3.raw WT
SB_4_64_SH_AY_R1.raw AY
SB_4_64_SH_AY_R2.raw AY
SB_4_64_SH_AY_R3.raw AY
SB_4_64_SH_AYa18_R1.raw AYa18
SB_4_64_SH_AYa18_R2.raw AYa18
SB_4_64_SH_AYa18_R3.raw AYa18
Name: condition, dtype: object
Homework
Repeat the analysis based on the tutorial from the course.
Small adjustments are needed.
