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|  An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinases | Homo sapiens | Q Exactive Plus | No | 2 | | Urisman A, Levin RS, Gordan JD, Webber JT, Hern... | |
| Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanoma | Homo sapiens | Q Exactive Plus | Yes | 5 | | Morales-Betanzos CA, Lee H, Gonzalez-Ericsson P... | |
| Stoichiometric surface density model | Streptococcus pyogenes | TSQ Quantiva | Yes | 2 | | Kristoffer Sjöholm, Ola Kilsgård, Johan Teleman... | |
| Inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 induces unique iron-dependent protein-level responses | Synechocystis sp. PCC 6803 | TSQ Vantage | No | 1 | | Linda Vuorijoki, Arjun Tiwari, Pauli Kallio, Ev... | |
| Spatially and temporally resolved protein interaction networks in living cells. | Homo sapiens | TSQ Quantiva | No | 2 | | Lobingier BT, Hüttenhain R, Eichel K, Miller KB... | |
| Role of type 2 NAD(P)H dehydrogenase NdbC in redox regulation of carbon allocation in Synechocystis sp. PCC 68031 | Synechocystis sp. PCC 6803 | TSQ Vantage | No | 1 | | Huokko T, Muth-Pawlak D, Battchikova N, Allahve... | |
| Quantitative Proteomics Method Comparison | Homo sapiens | TSQ Quantiva,Q Exactive Plus | No | 2 | | Hoffman MA, Fang B, Haura EB, Rix U, Koomen JM.... | |
| Multiplexed MRM-based Protein Quantitation Using Two Different Stable Isotope Labeled Peptides for Calibration | | | No | 16 | | André LeBlanc, Sarah A. Michaud, Andrew J. Perc... | |
| Proteomic assay development for reproductive maturation state determination in Geoduck: towards a non-invasive proteomic assay for improving aquaculture | Panopea generosa | TSQ Vantage | No | 2 | | Emma B. Timmins-Schiffman, Grace A Crandall, Br... | |
| Proteomics analysis identifies orthologs of human chitinase-like proteins as inducers of tube-morphogenesis defects in Drosophila | Drosophila melanogaster | TSQ Vantage | No | 2 | | Sandra G. Zimmerman, Gennifer E. Merrihew, Mich... | |
| PSB33 sustains Photosystem II D1 protein under fluctuating light conditions | Arabidopsis thaliana | TSQ Vantage | No | 1 | | | |
| Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer | Homo sapiens | TSQ Vantage,nanoACQUITY UPLC | No | 70 | | | |
| Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues | Homo sapiens | TSQ Vantage,nanoACQUITY UPLC | No | 8 | | Nie S, Shi T, Fillmore TL, Schepmoes AA, Brewer... | |
| Quantification of Mutant SPOP Proteins in Prostate Cancer | Homo sapiens | TSQ Vantage,nanoACQUITY UPLC | Yes | 16 | | | |
| An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics | Bartonella henselae str. Houston-1 | Orbitrap Fusion | No | 2 | | Ulrich Omasits, Adithi R. Varadarajan, Michael ... | |
| MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments | Homo sapiens, Bos taurus | 4000 QTRAP,QTRAP 5500,TSQ Vantage,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ MS | No | 8 | | Dogu, E, Mohammad-Taheri, S, Abbatiello, SE et ... | |
| A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain | Mus musculus | LTQ Orbitrap Elite,TSQ Quantiva | No | 3 | | Scott P. Goulding, Karen K. Szumlinski, Candice... | |
| Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagarTMSTEC media. | Escherichia coli | Q Exactive | No | 2 | | Kalule JB, Fortuin S, Calder B, Robberts L, Ked... | |
| A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide | Salmonella typhimurium | Bruker Amazon SL ion trap and Shimadzu 8050 QQQ,LCMS-8050 | No | 3 | | Karash S, Liyanage R, Qassab A, Lay JO Jr, Kwon... | |
| Quantification of Plasma proteins using PlasmaDive kit on nanoflow LC-MS system and standard flow LC-MS system | Homo sapiens | TSQ Vantage,6495A Triple Quadrupole LC/MS | Yes | 2 | | Yin X, Baig F, Haudebourg E, Blankley RT, Gandh... | |
| Cellular signaling underlying GSIS in pancreatic β-cells | Rattus norvegicus | Q Exactive HF | No | 1 | | Kang T, Jensen P, Huang H, Lund Christensen G, ... | |
| Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeS | Homo sapiens, Streptococcus pyogenes | TSQ Vantage,TSQ Quantiva | No | 2 | | Christofer A. Q. Karlsson, Sofia Järnum, Lena W... | |
| The conservation of sirtuin lipoamidase activity in bacteria as a regulator of metabolic enzyme complexes | Escherichia coli | Q Exactive,LTQ Orbitrap Velos | No | 5 | | Rowland EA, Greco TM, Snowden CK, McCabe AL, Si... | |
| MEERCAT: MULTIPLEXED EFFICIENT CELL FREE EXPRESSION OF RECOMBINANT QconCATS FOR LARGE SCALE ABSOLUTE PROTEOME QUANTIFICATION | | QTRAP 5500 | Yes | 6 | | | |
| DDR panel radiation response | Homo sapiens | QTRAP 6500 | No | 3 | | Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, S... | |
| Targeted proteomics in triple negative breast cancer on FFPE samples | Homo sapiens | Orbitrap Fusion Lumos | Yes | 2 | | Gámez-Pozo, A. et al. Prediction of adjuvant ch... | |
| SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803 | Synechocystis sp. PCC 6803 | TSQ Vantage | No | 1 | | Angeleri M, Zorina A, Aro EM, Battchikova N. In... | |
| Nitric oxide prevents Aft1 activation and metabolic remodeling in Frataxin-deficient yeast | Saccharomyces cerevisiae | 6420 Triple Quadrupole LC/MS | Yes | 1 | | Alsina D, Ros J, Tamarit J. Redox Biology.
Vo... | |
| Quantification of Site-Specific Protein Lysine Acetylation and Succinylation Stoichiometry using Data-Independent Acquisitions (DIA) Mass Spectrometry --Protocol Example | Bos taurus | TripleTOF 5600 | No | 1 | | Wei L, Meyer JG, Schilling B. Quantification of... | |
| Measurement by a Novel LC-MS/MS Methodology of Vitamin D–Binding Protein | Homo sapiens | Q Exactive Plus | Yes | 1 | | Henderson CM, Lutsey PL, Misialek JR, Laha TJ, ... | |
| Curated DIA assay for consistent ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus) | Gasterosteus aculeatus | ImpactHD UHR-QTOF | No | 4 | | J. Li, B.B. Levitan, S. Gomez-Jimenez and D. Kü... | |