Table 3.
iTRAQ proteomics directed SRM candidate selection
| Gene | GI accession number | Protein | Gene ontology: molecular function | Gene ontology: cellular component | Peptide ID | Peptide sequence |
|---|---|---|---|---|---|---|
| IBSP | 167466187 | Bone sialoprotein 2 precursor [Homo sapiens] | Extracellular matrix [GO:0031012]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; membrane [GO:0016020]; membrane-bounded vesicle [GO:0031988] | SRM-1 SRM-2 SRM-3 |
HAYFYPHLK IEDSEENGVFK AYEDEYSYFK |
|
| BGLAP | 40316933 | Osteocalcin preproprotein [Homo sapiens] | Calcium ion binding [GO:0005509]; hydroxyapatite binding [GO:0046848]; structural constituent of bone [GO:0008147]; structural molecule activity [GO:0005198] | Cytoplasm [GO:0005737]; dendrite [GO:0030425]; endoplasmic reticulum lumen [GO:0005788]; extracellular space [GO:0005615]; Golgi lumen [GO:0005796]; membrane-bounded vesicle [GO:0031988]; perikaryon [GO:0043204]; rough endoplasmic reticulum [GO:0005791] | SRM-4 SRM-5 SRM-6 |
YLYQWLGAPVPYPDPLEPR GAAFVSK QEGSEVVK |
| OMD | 4826876 | Osteomodulin precursor [Homo sapiens] | Extracellular exosome [GO:0070062]; extracellular region [GO:0005576]; extracellular space [GO:0005615]; Golgi lumen [GO:0005796]; lysosomal lumen [GO:0043202]; proteinaceous extracellular matrix [GO:0005578] | SRM-7 SRM-8 SRM-9 |
IDYGVFAK LLLGYNEISK NLEHLYLQNNEIEK |
|
| COL1A2 | 48762934 | Collagen alpha-2(I) chain precursor [Homo sapiens] | Extracellular matrix structural constituent [GO:0005201]; heparin binding [GO:0008201]; integrin binding [GO:0005178]; metal ion binding [GO:0046872]; platelet-derived growth factor binding [GO:0048407]; proteoglycan binding [GO:0043394] | Basement membrane [GO:0005604]; collagen type V trimer [GO:0005588]; endoplasmic reticulum lumen [GO:0005788]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576] | SRM-10 SRM-11 SRM-12 |
GPAGPSGPAGK GEIGNPGR AQPENIPAK |
| COL5A1 | 495528154 | Collagen alpha-1(V) chain isoform 2 preproprotein [Homo sapiens] | Extracellular matrix structural constituent [GO:0005201]; heparin binding [GO:0008201]; integrin binding [GO:0005178]; metal ion binding [GO:0046872]; platelet-derived growth factor binding [GO:0048407]; proteoglycan binding [GO:0043394] | Basement membrane [GO:0005604]; collagen type V trimer [GO:0005588]; endoplasmic reticulum lumen [GO:0005788]; extracellular exosome [GO:0070062]; extracellular matrix [GO:0031012]; extracellular region [GO:0005576] | SRM-13 SRM-14 SRM-15 |
VLDFHNLPDGITK DAQLSAPTK QLYPASAFPEDFSILTTVK |
| ALPL | 530360994 | Predicted: alkaline phosphatase, tissue-nonspecific isozyme isoform X3 [Homo sapiens] | Alkaline phosphatase activity [GO:0004035]; metal ion binding [GO:0046872]; pyrophosphatase activity [GO:0016462] | Anchored component of membrane [GO:0031225]; extracellular exosome [GO:0070062]; extracellular membrane-bounded organelle [GO:0065010]; extracellular space [GO:0005615]; integral component of membrane [GO:0016021]; membrane [GO:0016020]; plasma membrane [GO:0005886]; proteinaceous extracellular matrix [GO:0005578] | SRM-16 SRM-17 SRM-18 |
GFFLLVEGGR ANEGTVGVSAATER LDGLDLVDTWK |
| LPIN2 | 530425009 | Predicted: phosphatidate phosphatase LPIN2 isoform X2 [Homo sapiens] | Phosphatidate phosphatase activity [GO:0008195]; transcription coactivator activity [GO:0003713] | Cytosol [GO:0005829]; endoplasmic reticulum membrane [GO:0005789]; nucleus [GO:0005634] | SRM-19 SRM-20 SRM-21 |
GLEPEVAALYFPK VDSPSK VIPSEDNLISEVEK |
| RRP12 | 547234776 | RRP12-like protein isoform 3 [Homo sapiens] | Poly(A) RNA binding [GO:0044822] | integral component of membrane [GO:0016021]; nuclear membrane [GO:0031965]; nucleolus [GO:0005730] | SRM-22 | FGFELVK |
| SRM-23 | AAQHGVCSVLK | |||||
| SRM-24 | AVEEGLTYK | |||||
| TRAF3 | 578804053 | Predicted: TRAF3-interacting protein 1 isoform X2 [Homo sapiens] | SRM-25 SRM-26 SRM-27 |
YLHDIITEVIR ISFLQK ITDCAVEPLK |
||
| PPM1J | 65506328 | Protein phosphatase 1J [Homo sapiens] | Protein serine/threonine phosphatase activity [GO:0004722] | SRM-28 SRM-29 SRM-30 |
AIIVR ASFSRPTFLQLSPGGLR SPDLPNAASAPPAAAPEAPR |
Ten proteins were chosen for selected monitoring reaction (SRM) MS analysis based on iTRAQ data. Three peptides per protein were synthesized for assay development, and the molecular function and cellular component gene ontologies for each SRM candidate were annotated