Clustering and filtering tandem mass spectra

tribecagamosisAI and Robotics

Nov 8, 2013 (3 years and 9 months ago)

105 views

S
-
1


Clustering and filtering tandem mass spectra
acquired in data
-
independent mode

Huisong Pak
1
; Frederic Nikitin
2
; Florent Gluck
1, 3
; Frederique Lisacek
2
; Alexander Scherl
1, 3
;
Markus Muller
1,2
*

1
University of Geneva, Geneva, Switzerland

2
SIB

Swiss
institute of Bioinformatics, Geneva, Switzerland

3
Swiss Centre for Applied Human Toxicology, Switzerland




S
-
2




Figure S
-
1
. Dependency of the number of MS/MS spectra and peptides identifications as a function of
the similarity cut
-
off. A) Number of unique
peptides identified at FDR = 5% f. B) Number of submitted
MS/SM spectra.


0
200
400
600
800
1000
1200
0
0.2
0.4
0.6
0.8
1
1.2
# unique peptides
similarity cut
-
off
a
0
5000
10000
15000
20000
25000
0
0.2
0.4
0.6
0.8
1
1.2
# MS/MS spectra
similarity cut
-
off
b
S
-
3









Equation S
-
1
. Normalized dot product score.



































2
1
1
2
2
2
1
1
1
1
1
2
1
2
1
2
1
1
2
2
2
2
1
2
2
2
2
2
2
1
1
2
1
1
1
1
1
1
1
1
cos
,..,
,
1
;
,

Spectrum
,..,
,
1
;
,

Spectrum
min
min

















































N
i
i
i
N
i
i
i
N
i
i
i
j
m
m
j
m
k
i
k
j
N
binning
i
i
i
N
binning
i
i
i
s
s
s
s
s
s
S
S
S
S
score
I
s
s
s
s
S
n
i
I
m
P
S
s
s
s
S
n
i
I
m
P
S
k
i









S
-
4


S = s
i

... s
n




# spectra in the file

M
pch





precursor channel of a given MS/MS spectrum


Y = y
i

... y
k




fragment
y
-
ions with y
i

> M
pch

of a given

spectrum


bc
i

...
bc
k




complementary
fragment
b
-
ions


b_window




window around bc
i

bf
j

... bf
l




b
-
ion fragments with
in

a given window

Δbm
j

... Δbm
l




deviation from the center of bc
i

precursors




list of calculated precursors with associated Δbm and






intensities



z






charge state ( 2+)





begin

for (s
i

... s
n
)




for ( y
i

... y
k
)





bc
i

=
(M
pch

-

H)z + 2H
-

y
i




Find_b_peaks
(bc
i

± b_window)


//find all peaks within the window



for (
bf
j

... bf
l
)




Δ
bm
j

= bc
i

-

bf
j





precursor
calc

= M
pch

+
Δ
bm
j


//new calculated precursor




I
j

= bf
j

+ y
i


//intensity of
precursor
calc





precursor
s
.add(
Δ
bm
i
, precursor
calc
, I
j
)


Histogram

(precursors)


//plot 2D histogram

precursors


Local_maxima

(precursors)

//select two precursors from histogram data


Write_spectra

(s
i
)


//write MS/MS spectra
with new calculated precursors

end

Figure S
-
2
. Precursor ions
m/z

calculation is described here as pseudocode. Details are given in the
materials and
methods.

S
-
5




Figure S
-
3
. Histogram of the differences between measured and theoretical precursor ion
m/z
. (A)
Distribution without data clustering and precursor ion correction. (B) Distribution with data clustering and
precursor ion correction. As s
hown in B), the distribution is more centered around 0 after data clustering
and precursor ion correction.










a

b

S
-
6




Figure S
-
4
. A time
window
of precursor ion chromatogram of 822 m/z (
TIC
MS2). All spectra from scan
8800 to 8950

(A
-

E)

are identified by type II spectra while only
2
spectra

(
A

and
B
)

are identified by non
-
processed spectra. Additionally 1 type
II

spectrum are formed from 2 spectra

and matched 1 unique
peptide s
p
e
cific to type II (
C
).







a
b
c
e
e
S
-
7



Table S
-
1
. Summary of uniq
ue peptide identifications per spectrum and fraction. up = unique peptides, g1
= nb of
spectra with 1
identification per scan (group 1), up_g1 = nb unique peptides among group 1, r_g1
= nb redundant spectra among group 1, g2 = nb of
spectra with
2 identifi
cation
s

per scan (group 2),
up_g2 = nb of unique peptides in group 2, r_g2 = nb redundant spectra among group 2, g3 = nb of
up
g1
up_g1
r_g1
g2
up_g2
r_g2
g3
up_g3
r_g3
F9
29
55
23
32
5
3
7
1
2
1
F9_cl
13
18
10
8
2
2
2
0
0
0
F10
128
263
119
144
10
7
13
1
1
2
F10_cl
155
251
146
105
10
8
12
0
0
0
F11
346
797
309
488
64
45
83
15
13
32
F11_cl
333
566
305
261
36
27
45
4
6
6
F12
454
1054
424
630
63
39
87
4
9
3
F12_cl
465
883
442
441
38
26
50
2
6
0
F13
657
1735
614
1121
88
84
92
13
9
30
F13_cl
623
1251
575
676
57
76
38
8
10
14
F14
824
2347
763
1584
116
115
117
22
66
60
F14_cl
848
1825
794
1031
94
84
104
6
4
14
F15
834
2263
769
1494
123
92
154
19
27
30
F15_cl
843
1807
790
1017
105
82
128
10
14
16
F16
792
2198
748
1450
83
106
60
8
8
16
F16_cl
834
1865
793
1072
63
72
54
2
5
1
F17
775
2097
716
1381
171
121
221
16
14
34
F17_cl
820
1773
761
1012
127
87
167
11
11
22
F18
875
2590
830
1760
117
110
124
4
10
2
F18_cl
943
2242
889
1353
92
109
75
3
8
1
F19
652
2505
617
1888
88
65
111
4
10
2
F19_cl
740
1836
703
1133
361
68
654
22
13
53
F20
566
1854
540
1314
67
66
68
8
2
22
F20_cl
609
1615
586
1029
47
44
50
6
2
16
F21
635
2849
608
2241
100
57
143
5
3
12
F21_cl
669
2523
637
1886
59
58
60
12
1
35
F22
512
1454
498
956
59
27
91
1
3
0
F22_cl
564
1300
549
751
33
30
36
1
3
0
F23
381
1184
374
810
15
14
16
2
4
2
F23_cl
409
1048
397
651
14
17
11
2
3
3
F24
414
1585
407
1178
68
15
121
2
3
3
F24_cl
482
1481
472
1009
82
17
147
3
6
3
F25
208
755
202
553
10
5
15
0
0
0
F25_cl
230
623
225
398
9
5
13
0
0
0
F26
113
492
110
382
3
2
4
0
0
0
F26_cl
123
370
120
250
3
4
2
0
0
0
F27
96
304
95
209
0
0
0
0
0
0
F27_cl
113
242
112
130
0
0
0
0
0
0
F28
91
462
90
372
0
0
0
0
0
0
F28_cl
108
435
105
330
1
2
0
0
0
0
F29
46
92
45
47
0
0
0
0
0
0
F29_cl
46
68
45
23
0
0
0
0
0
0
F30
52
118
49
69
2
2
2
0
0
0
F30_cl
42
81
41
40
0
0
0
0
0
0
S
-
8


spectra with
3 identification
s

per scan (group 3), up_g3 = nb of unique peptides in group 3, r_g3 = nb
redundant spectra among group

3.



Figure S
-
5
.

P
eptide identification per spectrum. One peptide per spectrum (
A
), 2 peptides per spectrum
(
B
) and 3 peptides per spectrum

(C)
.


0
100
200
300
400
500
600
700
800
900
1000
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
# MS/MS spectra
Fractions
One peptide identification per spectrum
raw_up_g1
cl_up_g1
0
20
40
60
80
100
120
140
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
# MS/MS spectra
Fractions
2 peptide identifications per spectrum
raw_up_g2
cl_up_g2
0
10
20
30
40
50
60
70
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
# MS/MS spectra
Fractions
3 peptide identifications per spectrum
raw_up_g3
cl_up_g3
A
B
C
a
b
c