Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics

Table 4 Two-sample t-test results

substring s	p-value	μ( $s_{A}^{-}$ )	μ( $s_{A}^{+}$ )	size( $s_{A}^{-}$ )	size( $s_{A}^{+}$ )
R	2.41e-15	2.76	3.73	171	244
K	2.85e-14	3.72	2.78	243	172
M	1.69e-06	3.44	2.53	366	49
H	2.25e-05	3.20	3.90	338	77
VKe	4.64e-05	3.36	2.31	403	12
VK	8.92e-05	3.36	2.39	402	13
VF	1.25e-04	3.29	4.65	403	12
Y	2.11e-04	3.18	3.71	296	119
F	2.99e-04	3.15	3.67	272	143
GF	5.83e-04	3.29	4.48	400	15
Q	8.97e-04	3.16	3.61	260	155
GKe	0.001	3.37	2.62	392	23
TKe	0.001	3.36	2.45	401	14
SV	0.001	3.28	4.15	393	22
TK	0.003	3.36	2.53	400	15
GK	0.009	3.37	2.76	390	25
PR	0.009	3.30	4.51	403	12
PRe	0.009	3.30	4.51	403	12
DS	0.009	3.29	4.10	395	20
substring s	p-value	μ( $s_{B}^{-}$ )	μ( $s_{B}^{+}$ )	size( $s_{B}^{-}$ )	size( $s_{B}^{+}$ )
R	4.12e-33	3.69	4.64	339	795
K	6.76e-31	4.65	3.74	770	364
M	3.72e-25	4.52	3.41	966	168
DK	3.80e-07	4.38	3.35	1112	22
DKe	1.18e-06	4.37	3.38	1113	21
GM	1.67e-05	4.38	3.23	1112	22
AKe	2.27e-05	4.39	3.64	1085	49
NKe	5.82e-05	4.38	3.42	1111	23
GRe	9.18e-05	4.31	4.93	1054	80
QRe	1.37e-04	4.33	5.10	1100	34
W	2.63e-04	4.40	3.93	1034	100
AK	2.75e-04	4.39	3.73	1083	51
NK	3.03e-04	4.37	3.51	1110	24
GR	6.16e-04	4.32	4.86	1051	83
QR	7.46e-04	4.34	5.01	1098	36
FRe	0.001	4.34	5.28	1111	23
IK	0.001	4.37	3.47	1113	21
IKe	0.001	4.37	3.47	1113	21
GKe	0.001	4.37	3.74	1104	30
GK	0.002	4.37	3.80	1101	33
DT	0.003	4.38	3.80	1083	51
AM	0.003	4.38	3.40	1108	26
S	0.004	4.47	4.25	538	596
P	0.006	4.25	4.46	579	555
TKe	0.008	4.37	3.76	1110	24
VRe	0.008	4.33	4.77	1069	65

Results of two-sample t-tests of set s⁺ (normalized intensities of peptides containing a substring s) against the set s^- of those not containing it in the corresponding dataset (A or B). Only substrings that occur in more than 10 (A)/20 (B) peptides and with a p-value ≤ 0.001 are shown. An "a" as a prefix denotes that the substring is located at the beginning of the string, "e" as suffix means it is located at the end of the string. Otherwise, the substring can occur anywhere in the peptide (including terminal positions). Rows in bold face mark substrings that are present in the lists of both datasets.

ISSN: 1471-2105