Table 1. List of significantly enriched proteins in PTPRJ-His6 pull-down with respect of the control experiment.
| Uniprot Accession | Protein | Gene | Sequence Coverage | Unique Peptides | Peptides | MEAN M:L | p-value |
|---|---|---|---|---|---|---|---|
| P20020 | Plasma membrane calcium-transporting ATPase 1 | ATP2B1 | 4.85 | 4 | 4 | 8.13 | 0.00 |
| H7C5Q2 | Acyl-coenzyme A thioesterase 9, mitochondrial (Fragment) | ACOT9 | 13.26 | 2 | 2 | 8.13 | 0.00 |
| Q12913 | Receptor-type tyrosine-protein phosphatase eta | PTPRJ | 31.79 | 39 | 39 | 7.89 | 0.00 |
| A0A0A0MR02 | Voltage-dependent anion-selective channel protein 2 (Fragment) | VDAC2 | 12.77 | 3 | 3 | 7.74 | 0.00 |
| O95297 | Myelin protein zero-like protein 1 | MPZL1 | 14.13 | 3 | 3 | 7.43 | 0.00 |
| P67936 | Tropomyosin alpha-4 chain | TPM4 | 25.81 | 5 | 8 | 6.90 | 0.00 |
| Q9H330 | Transmembrane protein 245 | TMEM245 | 2.31 | 2 | 2 | 6.54 | 0.00 |
| P61019 | Ras-related protein Rab-2A | RAB2A | 19.34 | 3 | 3 | 6.53 | 0.00 |
| Q9UH99 | SUN domain-containing protein 2 | SUN2 | 3.77 | 2 | 2 | 5.86 | 0.01 |
| J3KNL5 | GRAM domain-containing protein 1B | GRAMD1B | 4.07 | 2 | 2 | 5.71 | 0.00 |
| O75306 | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | NDUFS2 | 7.56 | 3 | 3 | 5.62 | 0.00 |
| P42166 | Lamina-associated polypeptide 2, isoform alpha | TMPO | 2.88 | 2 | 2 | 5.40 | 0.01 |
| Q8NBU5 | ATPase family AAA domain-containing protein 1 | ATAD1 | 18.56 | 5 | 5 | 5.35 | 0.00 |
| J3KTA4 | Probable ATP-dependent RNA helicase DDX5 | DDX5 | 9.28 | 5 | 6 | 5.17 | 0.00 |
| F5H004 | Ras-related protein Rap-1b (Fragment) | RAP1B | 22.83 | 4 | 4 | 5.08 | 0.00 |
| D6RBN9 | RELT-like protein 1 (Fragment) | RELL1 | 25.51 | 3 | 3 | 4.79 | 0.00 |
| Q96ER9 | Coiled-coil domain-containing protein 51 | CCDC51 | 14.11 | 5 | 5 | 4.64 | 0.00 |
| Q8N766 | ER membrane protein complex subunit 1 | EMC1 | 5.34 | 4 | 4 | 4.21 | 0.01 |
| E9PB51 | RNA-binding protein 4 (Fragment) | RBM4 | 15 | 4 | 4 | 3.88 | 0.00 |
| P51148 | Ras-related protein Rab-5C | RAB5C | 21.3 | 4 | 4 | 3.73 | 0.01 |
| X6RFL8 | Ras-related protein Rab-14 (Fragment) | RAB14 | 24.86 | 5 | 5 | 3.62 | 0.00 |
| P35580 | Myosin-10 | MYH10 | 10.17 | 7 | 17 | 3.59 | 0.00 |
| P04083 | Annexin A1 | ANXA1 | 14.16 | 4 | 4 | 3.54 | 0.01 |
| Q92896 | Golgi apparatus protein 1 | GLG1 | 19.42 | 22 | 22 | 3.47 | 0.00 |
| P18031 | Tyrosine-protein phosphatase non-receptor type 1 | PTPN1 | 15.17 | 6 | 6 | 3.36 | 0.01 |
| P14618 | Pyruvate kinase PKM | PKM | 47.46 | 21 | 21 | 3.20 | 0.00 |
| O94826 | Mitochondrial import receptor subunit TOM70 | TOMM70A | 9.05 | 5 | 5 | 3.15 | 0.00 |
| P49257 | Protein ERGIC-53 | LMAN1 | 20.2 | 10 | 11 | 3.13 | 0.00 |
| P21980 | Protein-glutamine gamma-glutamyltransferase 2 | TGM2 | 8.3 | 6 | 6 | 2.95 | 0.00 |
| P61011 | Signal recognition particle 54 kDa protein | SRP54 | 17.86 | 7 | 7 | 2.94 | 0.00 |
| P46940 | Ras GTPase-activating-like protein IQGAP1 | IQGAP1 | 14.3 | 17 | 17 | 2.94 | 0.00 |
| P27105 | Erythrocyte band 7 integral membrane protein | STOM | 52.43 | 15 | 15 | 2.93 | 0.00 |
| P35579 | Myosin-9 | MYH9 | 37.24 | 62 | 73 | 2.89 | 0.00 |
| P14625 | Endoplasmin | HSP90B1 | 16.06 | 11 | 11 | 2.84 | 0.01 |
| F5GZS6 | 4F2 cell-surface antigen heavy chain (CD82hc) | SLC3A2 | 23.04 | 13 | 13 | 2.80 | 0.00 |
| A0A0A0MS51 | Gelsolin | GSN | 10.56 | 7 | 7 | 2.80 | 0.01 |
| P08107 | Heat shock 70 kDa protein 1A/1B | HSPA1A | 15.76 | 10 | 11 | 2.71 | 0.00 |
| P05026 | Sodium/potassium-transporting ATPase subunit beta-1 | ATP1B1 | 17.82 | 4 | 4 | 2.71 | 0.01 |
| P36542 | ATP synthase subunit gamma, mitochondrial | ATP5C1 | 25.17 | 8 | 8 | 2.65 | 0.00 |
| O94979 | Protein transport protein Sec31A | SEC31A | 7.05 | 8 | 8 | 2.64 | 0.00 |
| P27824 | Calnexin | CANX | 15.2 | 8 | 8 | 2.47 | 0.01 |
| Q13813 | Spectrin alpha chain, non-erythrocytic 1 | SPTAN1 | 4.94 | 9 | 9 | 2.47 | 0.00 |
| P08670 | Vimentin | VIM | 21.03 | 7 | 10 | 2.45 | 0.01 |
| P25705 | ATP synthase subunit alpha, mitochondrial | ATP5A1 | 21.7 | 11 | 11 | 2.40 | 0.00 |
| P19105 | Myosin regulatory light chain 12A | MYL12A | 34.5 | 5 | 5 | 2.39 | 0.00 |
| P31327 | Carbamoyl-phosphate synthase [ammonia], mitochondrial | CPS1 | 17.47 | 23 | 25 | 2.28 | 0.00 |
| H7C463 | MICOS complex subunit MIC60 (Fragment) | IMMT | 15.66 | 10 | 10 | 2.16 | 0.01 |
Section of potential PTPRJ-interacting protein list obtained by mass spectrometry analysis. Uniprot Accession numbers along with a brief description of protein functions were included in the table. “Sequence coverage” value corresponds to the total quantity of each protein present in the samples; “Unique Peptides” indicates the number of exclusive peptides found for each protein group while “Peptides” correlates with the total number of peptides assigned to each protein group. Medium/light ratio (Mean M:L) represents the fold change between eluted sample and eluted control. For more details see Supplementary Information 1.