Sample Data - MKN45, Phosphotyrosine Enrichment
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Instrument
ORGANISM(S): Homo_sapiens_viruses, Human_female
DISEASE(S): Not Available
SUBMITTER: 
Silva J, et al.
PROVIDER: GPM32320014125 | GPMDB |
REPOSITORIES: GPMDB
Similar Datasets
Project description:We have compared three different glycopeptide enrichment techniques (SAX-ERLIC, HILIC, and lectin affinity) and a C18 control to a tryptic digest of proteins from depleted human plasma.
2017-02-16 | PXD005655 | Pride
Project description:Purpose: To identify significantly different individual mRNA species or genetic pathways in the GCNAKO mutant sample when compared to the wildtype sample. GCNA is encoded by CG14814 (Flybase ID: FBgn0023515). Method: Total RNA was extracted using the Qiagen miRNEasy kit, followed by on column DNAse digest using the Qiagen DNAse digest kit. We used the miRNEasy kit to ensure collection of small RNA species as well as total RNA. RNA was collected from three independent bological replicates of freshly dissected Drosophila ovaries ( 100 ovaries per replicate), collected from 1-3 day old female Drosophila. Ovaries were flash frozen in liquid nitrogen after dissection to preserve the RNA species and prevent degradation. RNAse free conditions were maintained throughout the extraction protocol. RNA quality was tested by the sequencing core before sequencing the RNA.
2019-10-22 | GSE127220 | GEO
Project description:Proteome analysis of cerebrospinal fluid is associated with many of the same challenges that has to be faced when analyzing other biofluids like plasma or urine. Most importantly is the high dynamic range of protein concentrations, which makes it difficult to quantify more than a thousand proteins in a singleshot analysis of a tryptic digest of a raw sample. In addition, cerebrospinal fluid—especially when collected from children—is a much more scarce and precious sample as compare to urine and plasma. The aim of this work therefore was to find the optimal way to process and analyze cerebrospinal fluid from a minimal amount of sample and still obtain the deepest possible cerebrospinal fluid proteome. The work shows that enrichment of extracellular vesicles by ultracentrifugation increases the complexity of the cerebrospinal fluid proteome by two-fold or more. Thus, by following the enrichment protocol, more than two thousand proteins can routinely be quantified reproducibly by label-free quantification and data independent acquisition (DIA) in single-shot LC-MSMS runs of less than one hour. The project also present an optimized workflow for cerebrospinal fluid proteomics that enables a high-throughput method with a short chromatographic gradient (12 min) allowing analysis of hundred samples per day and still obtaining deep proteome coverage, especially when including a study-specific spectral library generated by repeated injection and gas-phase fractionation of pooled samples.
2024-10-16 | PXD052666 | Pride
Project description:We have compared three different glycopeptide enrichment techniques (SAX-ERLIC, HILIC, and lectin affinity) and a C18 control to a tryptic digest of proteins from depleted human plasma.
2018-07-02 | MSV000082565 | MassIVE
Project description:2 phosphopeptide enrichment methods (TiO2 and Ti-IMAC) were evaluated on synthetic libraries and HeLa cells digest. The resulting peptides were compared to the ones without enrichment with regards to the nature of the phosphorylation site (serine, threonine, tyrosine) and the characteristics of the peptide enriched. It was found that the enrichment methods are unbiased for these properties and that the result of the enrichment reflects the original condition of the sample.
2014-08-11 | PXD000759 | Pride
Project description:Total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- (KO) and Pou2f3+/+, Pou2f3+/- (heterozygous and homozygous WT mice together in WT sample) littermated mice were sorted for live cells on Moflo XDP cell sorter (singlets, FSCAxSSCA, DAPI-). Immediately post-sorting, cells were run on 10X Chromium (10X Genomics) and then through library preparation by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry). Libraries were run on the NovaSeq 6000 for Illumina sequencing. Post-processing and quality control were performed by the Genomics Core Facility at the Institute for Human Genetics at UCSF using the 10X Cell Ranger package (Cell Ranger Version 3.0.2, 10X Genomics). Primary assessment with this software for WT DC sample reported 2,441 cell-barcodes with 7,651 median unique molecular identifiers (UMIs, transcripts) per cell and 2,004 median genes per cell sequenced to 61.4% sequencing saturation with 48,559 mean reads per cell. Primary assessment with this software for MARCH1-/- DC sample reported 681 cell-barcodes with 6,309 median unique transcripts per cell and 1,774 median genes per cell sequenced to 73.1% sequencing saturation with 202,410 mean reads per cell.
2022-03-01 | GSE196546 | GEO
Project description:We established a spectral library for data-independent analysis of human plasma samples, using a pooled plasma sample from Danish adults. The samples were prepared for proteome analysis using an in-house developed protocol consuming one microliter of plasma per sample, and the tryptic digest and subsequent C18 purification was performed in 96-well plates. The spectral library consists of plasma which was analyzed neat (i.e. non-treated), and top 14 depleted. The samples were subjected to high pH reversed-phase peptide fractionated using C18 tips (8 fraction) and a HPLC system (20 fraction). The resulting peptides were analyzed on a Q Exactive with a capflow reversed-phase C18 LC-MS/MS setup in data-dependent mode. The final spectral library contains 21788 precursors and 1000 proteins (both at FDR<0.01).
2018-04-20 | PXD008163 | Pride
Project description:This work reports highly selective phosphopeptide enrichment using amorphous TiO2 nanotubes (TiO2NTs) and the same material decorated with superparamagnetic Fe3O4 nanoparticles (TiO2NTs@Fe3O4NPs). TiO2NTs and TiO2NTs@Fe3O4NPs materials were applied for phosphopeptide enrichment both from a simple peptide mixture (tryptic digest of bovine serum albumin and α-casein) as well as from a complex peptide mixture (tryptic digest of Jurkat T cell lysate). The obtained enrichment efficiency and selectivi-ty for phosphopeptides of TiO2NTs and TiO2NTs@Fe3O4NPs was excellent compared to those of the well-established TiO2 micro-spheres. The enrichment protocol was extended for a second elution step facilitating the identification of additional phosphopep-tides. It further turned out that both types of amorphous TiO2 nanotubes provide qualitatively new physico-chemical features that are clearly advantageous for highly selective phosphopeptide enrichment. This has been confirmed experimentally resulting in substantial reduction of non-phosphorylated peptides in the enriched samples. In addition, TiO2NTs@Fe3O4NPs combine a high selectivity with ease of handling due to the superparamagnetic character of the material. The presented materials and performances are further promising for applications towards a whole range of other types of biomolecules to be treated in similar fashion.
2019-06-26 | PXD012749 | Pride
Project description:A detailed description of the sample processing is published (Grün et al., 2014 Cell Rep). Briefly, a super Silac Mix using Lys8 was generated and spiked into all samples as an internal reference. Total Lysate was fractionated using SDS-PAGES. Up to 16 fractions were collected per sample. Proteins were in gel digest using LysC only.
2015-07-09 | PXD002482 | Pride
Project description:Targeted mass spectrometry-based assays typically rely on previously acquired large datasets for peptide target selection. Such repositories are widely available for unlabeled peptides. However, they are less common for isobaric tagged peptides. Here we have assembled two series of six datasets originating from a mouse embryonic fibroblast cell line (NIH/3T3). One series is of peptides derived from a tryptic digest of a whole cell proteome and a second from enriched phosphopeptides. These datasets encompass three labeling approaches (unlabeled, TMT11-labeled and TMTpro16-labeled) and two data acquisition strategies (ion trap MS2 with and without FAIMS-based gas phase separation). We identified a total of 1,509,526 peptide-spectrum matches which covered 11,482 proteins from the whole cell proteome tryptic digest, and 188,849 phosphopeptides from the phosphopeptide enrichment. For each series, the datasets were of similar depth, but peptide overlap across datasets was modest. We then examined differences in characteristics and physicochemical properties of dataset-unique peptide sequences. These datasets provide a rich resource of peptides which may be used as starting points for targeted assays. Future datasets may be compiled for any genome-sequenced organism using the technologies and strategies highlighted herein.
2021-06-03 | PXD024298 | Pride