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ProteomicsUPS2 Orbitrap data from Dicker, Lin and Ivanov (PMID: 20823122)
These raw data were first introduced in "Increased Power for the Analysis of Label-free LC-MS/MS Proteomics Data by Combining Spectral Counts and Peptide Peak Attributes" by Lee Dicker, Xihong Lin, and Alexander R. Ivanov (PubMed ID 20823122) (doi 10.1074/mcp.M110.002774). They represent the Sigma ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2014-01-10 | MSV000078520 | MassIVE
ProteomicsOn-capillary cell lysis enables top-down proteomic analysis of single HeLa cells by CE-MS/MS
Proteomic analysis of limited samples and single cells requires specialized methods that prioritize high sensitivity and minimize sample loss. Consequently, sample preparation is one of the most important steps in limited sample analysis workflows to prevent sample loss. In this work, we have elimin...
ORGANISM(S): Homo sapiens (Human) 
2022-10-26 | PXD035339 | Pride
Top-down proteomics Single-cell top-down proteomics Tandem mass spectrometry Single-cell proteomics Capillary electrophoresis Ce-ms/ms 
ProteomicsCapillary electrophoresis coupled to electrospray ionization tandem mass spectrometry (CE-MS/MS) for ultra-sensitive proteomic analysis of limited sample
In this work, we developed an ultra-sensitive CE-MS/MS method for bottom-up proteomics analysis of limited samples, down to sub-nanogram levels of total protein. Analysis of 880 pg and 88 pg of HeLa protein digest standard by CE-MS/MS yielded ~1,100±46 and ~160±59 proteins, respectively, demonstrati...
ORGANISM(S): Homo sapiens (Human) 
2022-02-17 | PXD027226 | Pride
Ultra-low flow liquid phase separation Ce-ms Ultra-sensitive proteomics Monolithic columns Capillary electrophoresis Rp-nlc-ms 
ProteomicsNew mixture models for decoy-free false discovery rate estimation in mass-spectrometry proteomics
We introduce a new decoy-free framework for false discovery rate (FDR) estimation that generalizes present decoy-free approaches (DFAs) while exploiting more search data in a manner similar to target-decoy approaches (TDAs).
ORGANISM(S): Homo sapiens (Human) 
2020-01-10 | PXD020322 | Pride
Proteomics Decoy-free framework False discovery rate Bioinformatics 
ProteomicsImproved sensitivity of ultra-low flow LC-MS-based proteomic profiling of limited samples using monolithic capillary columns and FAIMS technology
In this work, we pioneered a combination of ultra-low flow (ULF) high-efficiency ultra-narrow bore monolithic LC columns coupled to MS via a high-field asymmetric waveform ion mobility spectrometry (FAIMS) interface to evaluate the potential applicability for high sensitivity, robust and reproducibl...
ORGANISM(S): Homo sapiens (Human) 
2021-01-10 | PXD020669 | Pride
Faims Lc-ms Proteomic analysis Ultra-low flow lc Monolithic column 
ProteomicsSimple and efficient micro-SPE tip-based sample preparation workflow to enable sensitive proteomic profiling of limited samples
In-depth LC-MS-based proteomic profiling of limited samples has been problematic due, in large part, to the inefficiency of sample preparation and attendant sample losses. To address this issue, we developed On-Micro Solid-phase Extraction Tip-based (OmSET) sample preparation for limited biological...
ORGANISM(S): Homo sapiens (Human) 
2021-02-23 | PXD022313 | Pride
Micro-spe tip Omset Limited sample On-micro solid-phase extraction tip Sample preparation Stagetip 
ProteomicsHigh throughput microfluidic 3D biomimetic model enabling quantitative description of human breast tumor microenvironment
Cancer is driven by genetic aberrations in the tumor cells and fundamental changes in the tumor microenvironment (TME). These changes offer potential targets for novel therapeutics, yet lack of in vitro 3D models recapitulating this complex microenvironment impedes such progress. Here, we generated ...
ORGANISM(S): Homo sapiens (Human) 
2022-10-13 | PXD021509 | Pride
Breast cancer Microfluidics Tumor microenvironment Proteomic profiling Alginate 
ProteomicsCoupling high-field asymmetric ion mobility spectrometry with capillary electrophoresis-electrospray ionization-tandem mass spectrometry improves protein identifications in bottom-up proteomic analysis of low nanogram samples
In this work, we pioneered the assessment of coupling high-field asymmetric waveform ion mobility spectrometry (FAIMS) with ultra-sensitive capillary electrophoresis hyphenated with tandem mass spectrometry (CE-MS/MS) to achieve deeper proteome coverage of low nanogram amounts of digested cell lysa...
ORGANISM(S): Homo sapiens (Human) 
2023-05-10 | PXD034255 | Pride
Faims Ultra-sensitive proteomics Tandem mass spectrometry Bottom-up proteomics Capillary electrophoresis Ce-ms/ms 
ProteomicsExperimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays
Mass spectrometry (MS)-based thermal stability assays have recently emerged as one of the most promising solutions for the identification of protein-ligand interactions. Here, we have investigated eight combinations of several recently introduced MS-based advancements, including the Phase-Constraine...
ORGANISM(S): Homo sapiens (Human) 
2023-05-10 | PXD040284 | Pride
Cetsa Mass spectrometry Tpp Target identification Thermal stability assays Drug-protein interactions 
ProteomicsExperimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays
In this study, we developed a model system for the assessment of small molecule-protein interactions using intact cells treated with a commercially available highly specific mitogen-activated protein kinase (MEK) 1/2 inhibitor to prepare a set of unfractionated test samples labeled with tandem mass ...
ORGANISM(S): Homo sapiens (Human) 
2023-05-10 | PXD034087 | Pride
Cetsa Mass spectrometry Tpp Target identification Thermal stability assays Drug-protein interactions 
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