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|  Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma | Homo sapiens | 4000 QTRAP,QTRAP 5500,TSQ Vantage,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ MS,Xevo TQ-S | Yes | 54 | | Abbatiello SE, Schilling B, Mani DR, Zimmerman ... | |
| Protein acetylation in response to carbon overflow: detecting dynamic acetylation changes by mass spectrometry | Escherichia coli | TripleTOF 6600,TripleTOF 5600 | No | 4 | | Schilling B, Christensen D, Davis R, Sahu AK, H... | |
| Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptides | Mycobacterium tuberculosis | TripleTOF 5600 | Yes | 1 | | Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ... | |
| Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantification | Mycobacterium tuberculosis | TripleTOF 5600 | Yes | 1 | | Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ... | |
| Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using Skyline | Mycobacterium tuberculosis | TripleTOF 5600 | No | 1 | | Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ... | |
| Analytical protein standards | Homo sapiens | TSQ Vantage | No | 14 | | Searle BC, Egertson JD, Bollinger JG, Stergachi... | |
| Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomics | Homo sapiens | TSQ Vantage | Yes | 3 | | Dunkley T, Costa V, Friedlein A, Lugert S, Aign... | |
| Ariadne’s thread: a robust software solution leading to automated absolute and relative quantification of SRM data | synthetic peptides, Drosophila melanogaster | TSQ Quantum EMR | Yes | 3 | | Nasso et. al.; Ariadne's Thread: A Robust Softw... | |
| Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissues | Homo sapiens | TSQ Vantage | Yes | 13 | | Steiner C, Tille JC, Lamerz J, Kux van Geijtenb... | |
| MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments | Mus musculus | TripleTOF 5600 | No | 8 | | Rardin MJ, Schilling B, Cheng L, MacLean BX, So... | |
| Multiplexed, scheduled high resolution (sMRM-HR) acquisition on a full scan QqTOF instrument with integrated data-dependent and targeted mass spectrometric workflows. | Bos taurus, Saccharomyces cerevisiae, Escherichia coli | TripleTOF 5600 | No | 4 | | Schilling B, MacLean B, Held JM, Sahu AK, Rardi... | |
| Evaluation of multi-tRNA synthetase complex by multiple reaction monitoring mass spectrometry coupled with size exclusion chromatography | Homo sapiens | QTRAP 5500 | Yes | 4 | | Park SJ, Ahn HS, Kim JS, Lee C. Evaluation of M... | |
| Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks | Gasterosteus aculeatus | impact HD | No | 1 | | Proteomics Volume 15, Issue 23-24, December 201... | |
| Development of a quantitative SRM-based proteomics method to study iron metabolism of Synechocystis sp. PCC 6803 | Synechocystis sp. PCC 6803 | TSQ Vantage | No | 3 | | Development of a quantitative SRM-based proteom... | |
| Renal proteomes of marine and FW sticklebacks | Gasterosteus aculeatus | ImpactHD UHR-QTOF | No | 1 | | Journal of Proteomics. 2015 Sep;14(9):2331-40. ... | |
| Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. | Homo sapiens, Mus musculus, Saccharomyces cerevisiae | Orbitrap/HCD,TripleTOF 5600 | No | 1 | | Parker SJ, Rost H, Rosenberger G, Collins BC, M... | |
| Assembly dynamics and stoichiometry of the apoptosis signal-regulating kinase (ASK) signalosome in response to electrophile stress | Homo sapiens | Q Exactive Plus | No | 4 | | Joel D. Federspiel, Simona G. Codreanu, Amy M. ... | |
| A quantitative tagless co-purification method to validate and identify protein-protein interactions | Desulfovibrio vulgaris str. Hildenborough | 4800 Plus MALDI TOF/TOF,5800 TOF/TOF | No | 1 | | Maxim Shatsky, Ming Dong, Haichuan Liu, Lee Lis... | |
| Proteomic profile of deleted in breast cancer 1 (DBC1) protein-protein interactions | Homo sapiens | LTQ Orbitrap Velos | No | 1 | | Giguère SS, Guise AJ, Jean Beltran PM, Joshi PM... | |