Table 3. Selected studies of protein conformation, protein-protein interaction, and cellular components.
| Topic | Species (specimen) | MS scan | Proteins (peptides) | PTMs | Isotopic labeling (absolute quantification) | Ref. |
|---|---|---|---|---|---|---|
| 60S pre-ribosome | Saccharomyces cerevisiae | SRM | 51 (149) | None | None | [176] |
| Adenovirus | Adenovirus particles | SRM | 13 (33) | None | SPPS (stoichiometry) | [177] |
| ASK signalosome | Human (HEK293 cell line) | PRM | 99 (265) | None | None, SPPS (stoichiometry) | [178] |
| Blood-Streptococcus interactomics | Human (plasma) | SRM | 152 (406) | None | None | [179] |
| Blood-Streptococcus interactomics | Human (plasma), Streptococcus pyogenes | SRM | 56 (76) | None | SPPS (stoichiometry) | [89] |
| Centrosome | Human (5 cell lines) | SRM | 9 (18) | None | SPPS (copies/centrosome) | [180] |
| Cohesin complex | Human (MCF-7, HeLa cell lines) | MS1 | 11 (22) | None | QconCAT (stoichiometry) | [181] |
| Cullin-RING complex | Human (HEK293T cell line) | SRM | 25 (38) | None | SPPS (stoichiometry) | [182] |
| Focal adhesion complex | Human (breast cancer cells, tumor) | MS1, SRM | 17 (27) | None | None, SILAC | [183] |
| G protein subcellular localization | Mouse (4 brain tissues) | SRM | 12 (33) | None | None | [184] |
| GPCR proximity labeling | Human (HEK293 cell line) | SRM | 65 (187) | None | None | [90] |
| Hsp90-associated proteins | Human (HeLa cell line) | PRM | 4 (36) | None | SILAC | [185] |
| MP1-p14 complex | Mouse (recombinantly expressed) | MS1, SRM | 2 (10) | None | SPPS-mTRAQ (stoichiometry) | [186] |
| NFκB complex | Human (A549 lung epithelial cell line) | SRM | 3 (3) | None | SPPS (copies/cell) | [187] |
| NFκB complex | Human (SK-N-AS cell line) | SRM | 4 (11) | None | QconCAT (copies/cell) | [188] |
| Nuclear pore | Human (45 cells, tissues) | SRM | 47 (157) | None | SPPS (stoichiometry) | [83] |
| Nuclear pore | Human (HEK293 cell line) | SRM | 32 (76) | None | SPPS (stoichiometry) | [84] |
| Numb-associated endocytosis | Human (HEK293T cell line) | SRM | 14 (40) | None | None | [189] |
| NuRD complex | Human (HEK293, HeLa cell lines) | SRM | 10 (24) | None | SPPS | [85] |
| Podocyte slit diaphragm nephrin | Rat (renal glomeruli) | SRM | 1 (1) | None | SPPS (copies/cell) | [190] |
| Postsynaptic density | Rat (brain) | SRM | 112 (337) | None | None, SPPS | [191] |
| Postsynaptic density | Rat (brain) | SRM | 32 (32) | None | SPPS (pmol/mg protein) | [192] |
| Postsynaptic density | Rat (cerebral cortex) | SRM | 42 (89) | None | QconCAT (copies/postsynaptic density) | [193] |
| Protein complexes | Human (recombinantly expressed) | SRM | 6 (2) | None | SPPS (stoichiometry) | [194] |
| Protein conformation dynamics | Saccharomyces cerevisiae | SRM | 135 (697) | None | None | [86] |
| Protein phosphatase 2A complexes | Human (HEK293 cell line) | MS1 | 10 (n.i.) | None | SPPS (stoichiometry) | [195] |
| Ribosome | Escherichia coli | MS1 | 24 (41) | None | QconCAT (stoichiometry) | [196] |
| Ribosome | Mouse (ES-E14 embryonic stem cells) | SRM | 15 (28) | None | SPPS (stoichiometry) | [82] |
| RNA polymerase complex | Bacillus subtilis | SRM | 8 (16) | None | SPPS-mTRAQ (stoichiometry) | [197] |
| Rod photoreceptor outer segment | Rat (retinas) | SRM | 2 (2) | None | SPPS | [198] |
| Spliceosome | Human (HeLa cell line) | SRM | 5 (10) | None | SPPS (stoichiometry) | [199] |
| Transducin heterotrimeric G-protein | Bos taurus (retina) | MS1 | 3 (3) | None | QconCAT (stoichiometry) | [200] |
n.i., not indicated