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ProteomicsUltraPlex: Expanding isobaric hyperplexing via orthogonal protease cleavage
Sample preparation was conducted using an adaptation of our SimPLIT workflow10. Four cell pellets corresponding to four different colorectal cancer cell lines were lysed in a buffer containing 1% sodium deoxycholate (SDC, Merck, Cat. No. 30970), 100 mM triethylammonium bicarbonate (TEAB, Merck, Cat....
ORGANISM(S): Homo sapiens (Human) 
2026-01-30 | PXD070352 | Pride
ProteomicsAssessing Interference in Isobaric Tag-based Sample Multiplexing using an 18-plex Interference Standard
Reporter ion interference remains a limitation of isobaric tag-based sample multiplexing. Advances in instrumentation and data acquisition modes, such as the recently developed real-time database search (RTS), can reduce interference. However, interference persists as does the need to benchmark upst...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-01-06 | PXD029458 | Pride
Faims Eclipse Ifi Sps-ms3 Rts Tmtpro18 
UnknownAssessing interference in isobaric tag-based sample multiplexing using an 18-plex interference standard.
Not available
S-EPMC9231818 | biostudies-literature
ProteomicsProteoMixture: A Cell Deconvolution Tool for Bulk Tissue Proteomics Data
Numerous multi-omic investigations of cancer tissue have documented varying and poor pairwise transcript:protein quantitative correlations and most deconvolution tools aiming to predict cell type proportions (cell admixture) have been developed and credentialed using transcript-level data alone. To ...
ORGANISM(S): Homo sapiens (Human) 
2024-01-12 | PXD044157 | Pride
Laser microdissection High grade serous ovarian cancer Proteomics Stroma signature Immune signature Cellular admixture Tumor signature 
UnknownEnhancing Proteome Coverage by Using Strong Anion-Exchange in Tandem with Basic-pH Reversed-Phase Chromatography for Sample Multiplexing-Based Proteomics.
Not available
S-EPMC11090996 | biostudies-literature
ProteomicsComparative proteomic profiling of human cell lines using capillary and micro-pillar array column
Chromatographic column selection can impact proteomic profiling, yet comparative studies remain limited. Here, we evaluate the performance of a conventional flame-pulled Accucore resin-packed capillary column and a microfabricated pillar array column (μPAC) in a sample multiplexed global proteome pr...
ORGANISM(S): Homo sapiens (Human) 
2025-11-24 | PXD063964 | Pride
Accucore Chromatography Tmt Μpac Ascend 
ProteomicsA programmed decline in ribosome levels governs human early neurodevelopment
How reductions in ribosome biogenesis can result in tissue- and developmental-specific defects remain a mystery. Here we describe allelic variants in the ribosome biogenesis factor AIRIM/C1orf109 that are primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combi...
ORGANISM(S): Homo sapiens (Human) 
2025-04-30 | PXD063298 | Pride
Tmtpro 18plex Ribosome Mtor 
ProteomicsEnhancing proteome coverage by using strong anion exchange in tandem with basic-pH reversed-phase chromatography for sample multiplexing-based proteomics
Sample multiplexing-based proteomic strategies rely on fractionation to improve proteome coverage. Tandem mass tag (TMT) experiments, for example, can currently accommodate up to 18 samples with proteins spanning several orders of magnitude, thus necessitating fractionation to achieve reasonable pro...
ORGANISM(S): Homo sapiens (Human) 
2023-12-28 | PXD044393 | Pride
Faims Tmtpro Eclipse Sax Sps-ms3 Rts 
ProteomicsInhibition of mTOR attenuates the initiation and progression of BRCA1-associated mammary tumors
We conducted global proteome and phosphoproteome profiling of vehicle- and everolimus-treated tumors from 17 mice that were allografted with spontaneously developed mammary tumors from Brca1co/coMMTV-Cre mice using LC-MS/MS. The Proteome Discoverer analysis identified 9,625 proteins having two uniqu...
ORGANISM(S): Mus musculus (Mouse) 
2025-01-24 | PXD054301 | Pride
Everolimus Brca1 Lc-ms/ms 
ProteomicsEnhanced sample multiplexing-based targeted proteomics with intelligent data acquisition
Targeted proteomics has been playing an increasingly important role in hypothesis-driven protein research and clinical bi-omarker discovery. We have previously created a workflow, Tomahto, to enable real-time targeted pathway proteomics assays using two-dimensional multiplexing technology. Coupled w...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-08-14 | MSV000095604 | MassIVE
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