Table 3 The list of novel proteins identified using proteogenomics approach. These proteins/sequences were either not present in TAIR10 or incomplete, but present in the latest TAIR11 proteome database.

1

Atchr1@19256097@19256652

AT1G51850.2

Leucine-rich repeat protein kinase family protein

New isoform/entry in Tair11

2

2

AtChr5@18590218@18590728

AT5G45830.4

Delay of gemination 1

New isoform/entry in Tair11

3

31

3

AtChr3@1743539@1745543

AT3G05850.1

MuDR family transposase

New entry in Tair11

7

1

2

1

14

13

15

6

29

1

4

AtChr3@1745505@1745964

AT3G05850.1

MuDR family transposase

New entry in Tair11

1

2

1

2

5

AtChr5@20952547@20953303

AT5G51585.1

Transmembrane protein

New entry in Tair11

2

6

AtChr3@6174451@6174928

AT3G18040.4

MAP kinase 9

New entry in Tair11

1

1

1

7

AtChr4@9187917@9188217

AT4G16233.1

GDSL-like lipase/acylhydrolase superfamily protein

New entry in Tair11

4

4

8

AtChr3@3252605@3253004

AT3G10455.1

Plant self-incompatibility protein S1 family protein

New entry in Tair11

3

6

9

AtChr5@4376549@4378589

AT5G13590.1

Unknown protein

Point correction

2

1

2

1

1

10

AtChr4@15093731@15095657

AT4G30990.3

ARM repeat superfamily protein

Sequence addition in Tair11

2

11

AtChr4@13558438@13559653

AT4G27010.2

Ribosome 60S biogenesis amino-terminal protein

Sequence addition in Tair11

2

12

AtChr4@7455224@7455494

AT4G12610.1

Transcription initiation factor IIF subunit alpha RAP74

Sequence addition in Tair11

1

2

5

4

3

6

4

13

AtChr4@1344112@1344550

AT4G03050.1

2-oxoglutarate-dependent dioxygenase

Sequence addition in Tair11

40

19

14

AtChr5@15331919@15332135

AT5G38360.1

Alpha/beta-Hydrolases superfamily protein

Sequence addition in Tair11

3

1

3

1

1

1