PTM Viewer

For each protein all PTMs are highlighted by default in the respective protein sequence (right-hand side). One can adjust a selection of PTMs in the PTM table on the left-hand side. In addition, functional protein domains and sites can be underlined if desired.

In the PTM table per PTM the PTM position and type is indicated, as well as the plain peptide sequence that was identified by mass spectrometry. The respective proteomics study is indicated by a number, providing a link to consult the experimental details. Additional PTM meta-data includes various confidence measures such as peptide score provided by search algorithms, posterior error probability (PEP), precursor mass deviation (in ppm) and modification site probability. The available confidence meta-data can be consulted in the extended PTM table by clicking SHOW CONFIDENCE. However, in the default PTM table, a color-coding of confidence is provided with green indicating high confidence, olive medium confidence, grey low confidence, and no color an unassigned confidence. More details regarding this confidence assignment can be consulted in the tutorial or the Plant PTM Viewer manuscript.

Besides confidence measures, log2 fold changes between two conditions with significance values (P- or Q-values) are shown if provided in the respective publication. Log2 fold changes are colored in heatmap-like gradient (green = induced, red = repressed) and significant values are highlighted in green. To determine significance, we employed the threshold used in the respective publication. For more details on the quantitative measurements we refer to the experimental details and respective publication, as methodologies can differ.

On the bottom of the page one can send the whole protein or a part of the protein (i.e. a functional domain) to PTM Blast. This will display aligned protein sequences that potentially report aligned PTMs.

PTMs

Export
Results

PTM Type	Mod AA	Pos	Peptide	Exp ID	Log2 FC	P/Q val	Score Type	Ident Score	Loc Prob	PEP	Mass Error (ppm)
nt	S	2	SSSPFPVLDNR	99			MASCOT Score	54.860		2.868e-2	-0.929
nta	S	2	SSSPFPVLDNRPIDKW	80			MASCOT Score	42.850		1.898e-3
			SSSPFPVLDNR	99			MASCOT Score	54.860		2.868e-2	-0.929
			SSSPFPVLDN	119			MaxQuant score	164.960
ph	S	2	SSSPFPVLDNRPIDK	114			MaxQuant score	159.180	0.982	5.222e-13
ph	S	4	SSSPFPVLDNRPIDK	88			MASCOT Score	38.000	0.869		-0.290
ph	S	4	SSSPFPVLDNRPIDK	114			MaxQuant score	261.610	0.997	0.000e+0
ph	T	20	WKVTELKEELK	114			MaxQuant score	137.730	1.000	8.972e-7
ph	T	20	WKVTELK	100			XCorr	2.679	1.000	1.808e-2
nt	G	35	GLKEELVR	51c			MASCOT Score	56.000			0.000
ph	S	60	INSATVAAAEK	114			MaxQuant score	164.560	1.000	4.466e-11
ph	T	90	NQTTPVTPVEAAFSTETTPVTAEK	85			XCorr	2.566	0.993	4.014e-4
				100			XCorr	5.139	1.000	6.950e-6
				106			MASCOT Score	56.000
				114			MaxQuant score	64.720	0.963	4.530e-7
ph	T	108	NQTTPVTPVEAAFSTETTPVTAEKTPEPTQTK	114			MaxQuant score	230.260	0.961	0.000e+0
ph	S	144	ITTEASAGVETTPAPVFSEPEVNAVPFASDEDEKEKVDDVR	109					0.999
			ITTEASAGVETTPAPVFSEPEVNAVPFASDEDEKEKVDDVR	114			MaxQuant score	320.110	1.000	0.000e+0
			ITTEASAGVETTPAPVFSEPEVNAVPFASDEDEKEK	85			XCorr	5.854	0.999	4.749e-16
			ITTEASAGVETTPAPVFSEPEVNAVPFASDEDEK	100			XCorr	5.219	1.000	1.589e-7
nt	D	157	DIAGLDSSVVAR	51c	3.444		MASCOT Score	92.000			-0.315
ph	S	163	DIAGLDSSVVAR	114			MaxQuant score	134.610	0.921	2.615e-5
ph	S	164	DIAGLDSSVVAR	114			MaxQuant score	147.730	0.958	9.273e-7
ph	S	177	DAAVVQVASSEHKSENNEPFSGLDGGDSK	85			XCorr	2.932	0.811	4.340e-13
				111a	0.445	0.000		32.560			0.621
				111b	0.445	0.000		32.560			0.621
				111c	1.557	0.000		32.560			0.621
				111d	1.557	0.000		32.560			0.621
			DAAVVQVASSEHK	60			MASCOT Score	33.630			-0.635
				85			XCorr	3.687	0.953	6.329e-4
				88			MASCOT Score	74.000	0.954		-0.060
				100			XCorr	4.375	0.936	8.183e-7
				106			MASCOT Score	63.000
				114			MaxQuant score	233.620	1.000	0.000e+0
ph	S	178	DAAVVQVASSEHK	83			MASCOT Score	23.000			0.000
				88			MASCOT Score	49.000	0.962		0.000
				106			MASCOT Score	54.000
				111a	-2.276	0.000		26.850			-0.104
				111b	-2.276	0.000		26.850			-0.104
				111c	-0.153	0.000		26.850			-0.104
				111d	-0.153	0.000		26.850			-0.104
				114			MaxQuant score	240.460	1.000	0.000e+0
ph	S	182	DAAVVQVASSEHKSENNEPFSGLDGGDSK	114			MaxQuant score	186.500	0.936	0.000e+0
ph	S	189	SENNEPFSGLDGGDSK	88			MASCOT Score	53.000	1.000		-1.510
ph	S	189	SENNEPFSGLDGGDSK	114			MaxQuant score	150.110	1.000	3.290e-10
ph	S	196	SENNEPFSGLDGGDSK	114			MaxQuant score	162.060	1.000	2.195e-21
ph	S	231	SDCISTDSVSNNEK	44			XCorr	2.963
				88			MASCOT Score	60.000	0.948		0.170
				114			MaxQuant score	190.060	0.992	2.334e-31
ph	S	234	SDCISTDSVSNNEK	44			XCorr	3.204
				88			MASCOT Score	60.000	1.000		0.170
				114			MaxQuant score	127.050	0.993	3.013e-5
ph	S	236	SDCISTDSVSNNEK	114			MaxQuant score	151.030	0.998	3.938e-12
ph	S	285	TSVGGGDDSNAANADMIK	88			MASCOT Score	51.000	0.955		-0.610
ph	S	285	TSVGGGDDSNAANADMIK	114			MaxQuant score	222.110	0.935	0.000e+0
ph	S	292	TSVGGGDDSNAANADMIKENNIIDAGDSEK	114			MaxQuant score	247.790	1.000	0.000e+0
			TSVGGGDDSNAANADMIK	59			MASCOT Score	60.000			-0.111
				61a			MASCOT Score	60.000	1.000
				88			MASCOT Score	45.000	1.000		-0.040
				100			XCorr	5.368	1.000	3.310e-7
				106			MASCOT Score	32.000
				109					1.000
ph	S	311	ENNIIDAGDSEKLNLDR	114			MaxQuant score	186.600	1.000	6.763e-30
			ENNIIDAGDSEK	59			MASCOT Score	53.000			-0.940
				83			MASCOT Score	50.000			-0.000
				100			XCorr	2.950	1.000	1.320e-4
ph	S	319	LNLDRSSGDESMEDEPETK	38			MASCOT Score	42.920
				44			XCorr	3.656
				59			MASCOT Score	49.000			-2.690
				60			MASCOT Score	40.910			-0.665
				83			MASCOT Score	48.000			0.004
				84a			XCorr	3.530	0.845	5.094e-3
				85			XCorr	3.877	1.000	1.922e-3
				88			MASCOT Score	37.000	1.000		-0.230
				94			MaxQuant Score	204.350	1.000	0.000e+0	1.683
				100			XCorr	6.131	1.000	8.268e-5
				109					1.000
			SSGDESMEDEPETK	84b			XCorr	3.990	0.941	6.189e-3
				88			MASCOT Score	56.000	1.000		-2.120
				114			MaxQuant score	264.340	1.000	0.000e+0
ph	S	320	LNLDRSSGDESMEDEPETK	44			XCorr	4.851
				60			MASCOT Score	40.910			-0.665
				61a			MASCOT Score	49.000	1.000
				83			MASCOT Score	48.000			0.004
				85			XCorr	4.685	0.995	2.829e-3
				88			MASCOT Score	37.000	1.000		-0.230
				94			MaxQuant Score	204.350	1.000	0.000e+0	1.683
				100			XCorr	6.131	1.000	8.268e-5
			SSGDESMEDEPETK	114			MaxQuant score	264.340	1.000	0.000e+0
ph	S	324	LNLDRSSGDESMEDEPETK	60			MASCOT Score	40.910			-0.665
				83			MASCOT Score	48.000			0.004
				84a			XCorr	3.530	0.845	5.094e-3
				85			XCorr	4.685	1.000	2.829e-3
				88			MASCOT Score	37.000	1.000		-0.230
				94			MaxQuant Score	204.350	1.000	0.000e+0	1.683
				100			XCorr	6.131	1.000	8.268e-5
			SSGDESMEDEPETK	84b			XCorr	3.990	1.000	6.189e-3
				85			XCorr	3.641	1.000	7.656e-3
				88			MASCOT Score	63.000	1.000		-0.110
				100			XCorr	4.718	1.000	3.857e-7
				106	0.003	0.934	MASCOT Score	31.000
				114			MaxQuant score	300.900	1.000	0.000e+0
ph	T	331	LNLDRSSGDESMEDEPETK	83			MASCOT Score	27.000			-0.001
ph	S	336	QSESITSDDKSAK	114			MaxQuant score	171.930	1.000	2.850e-15
ph	S	336	QSESITSDDK	88			MASCOT Score	51.000	0.997		-0.750
ph	T	338	QSESITSDDKSAK	114			MaxQuant score	231.320	0.964	0.000e+0
ph	S	339	QSESITSDDKSAK	88			MASCOT Score	24.000	1.000		1.650
			QSESITSDDKSAK	114			MaxQuant score	193.970	0.981	4.047e-30
			QSESITSDDK	88			MASCOT Score	30.000	1.000		-0.710
ph	S	343	QSESITSDDKSAK	114			MaxQuant score	85.742	0.986	9.856e-4
ph	S	354	IEMLSKEESRADMDAGK	114			MaxQuant score	93.729	0.990	5.512e-6
ph	S	365	ADMDAGKGKSPENK	114			MaxQuant score	59.372	1.000	1.992e-3
ac	K	378	SHPLVASDKR	101
ac	K	396	KLPANDQEAVGNNEPAKR	101
ph	S	402	RWNSNSIK	114			MaxQuant score	155.830	0.999	0.000e+0
ph	S	404	WNSNSIKVPEAQITNSATPTTTPR	114			MaxQuant score	204.500	0.928	0.000e+0
ph	S	404	WNSNSIK	100			XCorr	2.646	0.995	3.637e-3
ph	T	413	VPEAQITNSATPTTTPR	83			MASCOT Score	74.000			-0.002
				88			MASCOT Score	30.000	1.000		-0.860
				106	0.153	0.585	MASCOT Score	45.000
ph	S	415	VPEAQITNSATPTTTPR	61a			MASCOT Score	57.000	1.000
				83			MASCOT Score	74.000			-0.000
				84a			XCorr	4.720	0.925	3.720e-8
				84b			XCorr	4.500	0.942	3.900e-5
				85			XCorr	4.705	0.960	8.755e-5
				94			MaxQuant Score	191.220	0.858	6.713e-30	0.030
				100			XCorr	5.514	0.999	8.452e-9
				106	0.660	0.008	MASCOT Score	65.000
				114			MaxQuant score	222.930	1.000	0.000e+0
ph	T	417	WNSNSIKVPEAQITNSATPTTTPR	18a			MaxQuant Score	98.210	0.839	6.975e-12	-0.251
				45			MaxQuant Score	107.060
				111a	0.834	0.000		52.140			0.659
				111b	0.834	0.000		52.140			0.659
				111c	1.283	0.000		52.140			0.659
				111d	1.283	0.000		52.140			0.659
			VPEAQITNSATPTTTPR	83			MASCOT Score	84.000			-0.000
				88			MASCOT Score	62.000	1.000		0.620
				94			MaxQuant Score	205.680	1.000	0.000e+0	1.281
				100			XCorr	5.514	0.862	8.452e-9
				106	0.219	0.413	MASCOT Score	47.000
				109					0.997
				111a	0.113	0.000		85.130			1.127
				111b	0.113	0.000		85.130			1.127
				111c	-0.003	0.000		85.130			1.127
				111d	-0.003	0.000		85.130			1.127
				114			MaxQuant score	378.010	1.000	0.000e+0
ph	T	419	WNSNSIKVPEAQITNSATPTTTPR	45			MaxQuant Score	55.208
				111a	0.849	0.000		30.680			1.213
				111b	0.849	0.000		30.680			1.213
				111c	0.721	0.000		30.680			1.213
				111d	0.721	0.000		30.680			1.213
			VPEAQITNSATPTTTPR	83			MASCOT Score	50.000			0.000
				94			MaxQuant Score	205.680	0.996	0.000e+0	-1.510
				106	0.272	0.298	MASCOT Score	46.000
ph	T	420	WNSNSIKVPEAQITNSATPTTTPR	45			MaxQuant Score	99.407
			VPEAQITNSATPTTTPR	83			MASCOT Score	41.000			-0.000
				94			MaxQuant Score	191.220	0.844	2.654e-41	-0.908
				106			MASCOT Score	61.000
				111a	0.029	0.000		42.350			0.551
				111b	0.029	0.000		42.350			0.551
				111c	-0.574	0.000		42.350			0.551
				111d	-0.574	0.000		42.350			0.551
				114			MaxQuant score	370.350	0.914	0.000e+0
ph	T	421	WNSNSIKVPEAQITNSATPTTTPR	45			MaxQuant Score	107.060
				85			XCorr	3.095	0.842	1.489e-4
				111a	0.564	0.000		53.290			0.115
				111b	0.564	0.000		53.290			0.115
				111c	0.075	0.000		53.290			0.115
				111d	0.075	0.000		53.290			0.115
			VPEAQITNSATPTTTPR	18a			MaxQuant Score	98.210	0.841	6.975e-12	0.280
				28
				61a			MASCOT Score	57.000	1.000
				83			MASCOT Score	84.000			-0.000
				84a			XCorr	4.720	0.993	3.720e-8
				84b			XCorr	4.500	0.942	3.900e-5
				85			XCorr	4.705	0.998	8.755e-5
				88			MASCOT Score	62.000	0.950		0.620
				94			MaxQuant Score	191.220	0.895	6.713e-30	0.030
				100			XCorr	5.887	0.940	2.686e-8
				106	0.660	0.008	MASCOT Score	65.000
				109					0.998
				111a	0.119	0.000		73.840			1.271
				111b	0.119	0.000		73.840			1.271
				111c	-0.345	0.000		73.840			1.271
				111d	-0.345	0.000		73.840			1.271
				114			MaxQuant score	430.760	1.000	0.000e+0
ph	S	432	RDFSRSDSSVSEDGPK	83			MASCOT Score	34.000			-0.001
ph	S	434	RDFSRSDSSVSEDGPK	83			MASCOT Score	23.000			-0.002
ph	S	436	RDFSRSDSSVSEDGPK	83			MASCOT Score	38.000			-0.000
			RDFSRSDSSVSEDGPK	94			MaxQuant Score	118.360	0.961	4.000e-3	-4.647
			SDSSVSEDGPKER	38			MASCOT Score	45.380			0.376
				60			MASCOT Score	39.100			-0.153
				85			XCorr	3.491	0.884	1.501e-2
				88			MASCOT Score	34.000	1.000		-1.130
			SDSSVSEDGPK	38			MASCOT Score	41.130			0.963
				84a			XCorr	2.960	0.974	3.884e-4
				84b			XCorr	2.650	0.934	2.121e-4
				85			XCorr	3.176	0.996	2.578e-6
				88			MASCOT Score	67.000	0.941		-0.410
				97
				100			XCorr	3.150	0.913	8.056e-4
				109					0.988
				114			MaxQuant score	217.680	1.000	0.000e+0
ph	S	437	SDSSVSEDGPKER	109					0.931
			SDSSVSEDGPKER	114			MaxQuant score	214.230	0.947	1.032e-38
			SDSSVSEDGPK	88			MASCOT Score	23.000	0.993		-1.350
ph	S	439	RDFSRSDSSVSEDGPK	83			MASCOT Score	38.000			-0.000
			RDFSRSDSSVSEDGPK	94			MaxQuant Score	118.360	0.998	4.000e-3	0.271
			SDSSVSEDGPKER	88			MASCOT Score	44.000	0.829		0.190
				109					0.935
				114			MaxQuant score	243.490	1.000	0.000e+0
			SDSSVSEDGPK	88			MASCOT Score	67.000	0.940		0.170
			SDSSVSEDGPK	106			MASCOT Score	26.000
ph	S	451	VVPPSPKEPTNSLR	88			MASCOT Score	22.000	1.000		-1.000
			VVPPSPK	109					1.000
			VVPPSPK	114			MaxQuant score	149.300	1.000	5.925e-7
ub	K	453	VVPPSPKEPTNSLR	40			MaxQuant Score	86.944	1.000	1.322e-6	-0.077
so	C	495	THCYVSYPSVEEAAATR	108			pFind PSM Score	0.004			-0.114
nt	Y	496	YVSYPSVE	99	-0.310	0.136	MASCOT Score	39.410		2.113e-2	-1.143

Sequence

Length: 633

MSSSPFPVLDNRPIDKWKVTELKEELKRRRLTTRGLKEELVRRLDEALRAEQEESERINSATVAAAEKANQEPQMFPVTVGDRNQTTPVTPVEAAFSTETTPVTAEKTPEPTQTKITTEASAGVETTPAPVFSEPEVNAVPFASDEDEKEKVDDVRDIAGLDSSVVARDAAVVQVASSEHKSENNEPFSGLDGGDSKAQPSEAVLEKSAMYNQVSEVIPVTGFEVKSDCISTDSVSNNEKIELKDNKIADNVKLEQNVNKFQEPSTVVGESHPMDVEEPLEQKTSVGGGDDSNAANADMIKENNIIDAGDSEKLNLDRSSGDESMEDEPETKQSESITSDDKSAKIEMLSKEESRADMDAGKGKSPENKSHPLVASDKRKLPANDQEAVGNNEPAKRRRWNSNSIKVPEAQITNSATPTTTPRSTGLKRDFSRSDSSVSEDGPKERVVPPSPKEPTNSLRIDRFLRPFTLKAVQELLGKTGNVTSFWMDHIKTHCYVSYPSVEEAAATREAVYNLQWPPNGGRHLIAEFVRAEEVKEKLEAPLPPQPQHQPQAQTLSRPPPTALPPPPPLAKPPHVVERLPLPPPPPIAPEEQEPPIVTLDDLFKKTKAIPRIYYLPLSEEQVAAKLAANNNK

ID	PTM Type	Color
nt	N-terminus Proteolysis	X
nta	N-terminal Acetylation	X
ph	Phosphorylation	X
ac	Acetylation	X
ub	Ubiquitination	X
so	S-sulfenylation	X
	Multiple types	X

Domains & Sites

Clear highlighted range

**Interpro Domains**
Show	IPR ID	Description	From	To
	IPR003034	SAP domain	14	48
	IPR034257	Acinus, RNA recognition motif	456	540

AT4G39680.1

Arabidopsis thaliana [ath]

SAP domain-containing protein

53 PTM sites : 6 PTM types

PLAZA: AT4G39680

Gene Family: HOM05D001075

Other Names: NULL

Uniprot

A0A654FXJ3

O65655

Link out to other resources with this protein ID : TAIR | PeptideAtlas | ARAPORT | PhosPhAt

PTMs

Sequence

Length: 633

Domains & Sites

BLAST

Perform a BLAST search for this sequence, or a part of this sequence (minimum 50 characters)
A downloadable tutorial can be found here

AT4G39680.1

Arabidopsis thaliana [ath]

SAP domain-containing protein

53 PTM sites : 6 PTM types

PLAZA: AT4G39680

Gene Family: HOM05D001075

Other Names: NULL

Uniprot

A0A654FXJ3

O65655

Link out to other resources with this protein ID : TAIR | PeptideAtlas | ARAPORT | PhosPhAt

PTMs

Sequence

Length: 633

Domains & Sites

BLAST

Perform a BLAST search for this sequence, or a part of this sequence (minimum 50 characters)A downloadable tutorial can be found here

Perform a BLAST search for this sequence, or a part of this sequence (minimum 50 characters)
A downloadable tutorial can be found here