LC-MS/MS-Based Proteomic Analysis of a Single Human-Derived Gel Band
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Hui Gu
LAB HEAD: Juan Chen
PROVIDER: PXD074137 | Pride | 2026-06-11
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| XB10683GI.zip | Other | |||
| XB10683GI_EGFR_3.raw | Raw | |||
| checksum.txt | Txt |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Proteomic Profiling of Protein Extracts from a Single Human-Derived Gel Band
2026-06-11 | PXD074141 | Pride
Project description:Protein identification from a gel band using our MSB-01 service. This includes in-gel digestion with trypsin, LC-MS/MS, database searching and reporting.
2019-06-19 | PXD012827 | Pride
Project description:LRRC8A protein in the OE-LRRC8A group was overexpressed by more than 2.5-fold compared with that noted in the control and LV-ctrl groups (P < 0.05); three clear bands were identified in the OE-LRRC8A sample by western blotting, and the uppermost band was not shown in the specification of LRRC8A antibody. Then the product was extracted from the SDS-PAGE gel of the uppermost band location and analyzed by mass spectroscopy to confirm whether this band contains LRRC8A; the specific peptides of LRRC8A were captured and detected successfully. This indicated that the uppermost band contains LRRC8A protein.
2024-02-02 | PXD049109 |
Project description:Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences now serving and promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences, and allows the characterization of TF binding determinants within and outside of core binding sites. Binding experiments were carried out with one of two input libraries; Lib1 (also referred to as “main lib”) includes designed sequence variants of length 150bp, and Lib2 (also referred to as “constant flanks lib”) includes designed sequence variants of length 200bp. The sequences of the variants of interest can be found in the second column of the processed data file (BunDLE-seq_data, see 3 excel sheets). EXP1, EXP2 and EXP3 were carried out using Lib1, and EXP4 was carried out using Lib2. Binding experiments were carried out with different proteins (in different concentrations) – DNA was extracted from bound bands that were formed on the gel and amplified with a primer with a unique 5bp upstream tail specifying the identity of the originating band (also referred to as “band barcode”). Data from the following bands was used in the analysis: EXP1_band1, no-protein band – with band barcode “AACGA”, EXP1_band2, single Gcn4 (conc 1:8) bound band* – with band barcode “TCGTA” , EXP1_band3, histones bound band – with band barcode “AGATA”, EXP2_band1, no-protein band – with band barcode “AACGA”, EXP2_band2, single Gcn4 (conc 1:8) bound band* – with band barcode “AGATA”, EXP2_band2, single Gcn4 (conc 1:7) bound band – with band barcode “CACTT”, EXP2_band2, single Gcn4 (conc 1:6) bound band – with band barcode “TCGTA”, EXP2_band2, single Gcn4 (conc 1:5) bound band – with band barcode “CATCA”, EXP2_band2, single Gcn4 (conc 1:4) bound band – with band barcode “TATTA”, EXP2_band2, single Gcn4 (conc 1:3) bound band – with band barcode “AGTCA”, EXP2_band2, single Gcn4 (conc 1:2) bound band – with band barcode “ACGAA”, EXP2_band2, single Gcn4 (conc 1:1) bound band – with band barcode “ACAGA”, EXP2_band2, two Gcn4 (conc 1:1) bound band – barcoded with “GTAGA”, EXP3_band1, no-protein band – with band barcode “GCATA”, EXP3_band2, single Gal4 (conc 1:1) bound band – with band barcode “GATGT”, EXP3_band3, single Gal4 (conc 3:1) bound band – with band barcode “GTTCA”, EXP3_band4, two Gal4 (conc 3:1) bound band – with band barcode “CTCAA”, EXP4_band1, no-protein band – with band barcode “GAGTA”, EXP4_band2, single Gcn4 (conc 1:3) bound band – “TACCA”, EXP4_band3, no-protein band – with band barcode “TCGTT”, EXP4_band3, single Gal4 (conc 3:1) bound band – with band barcode “ACATC”, *biological replicates
2015-03-04 | E-GEOD-66143 | biostudies-arrayexpress
Project description:Edible mealworms and crickets are high protein food sources, which have recently emerged on the European market. As the production of edible insects is more sustainable than conventional livestock proteins, they are a promising alternative protein source for human consumption. Protein compositions of mealworms and crickets that underwent different food processing and preparation steps were assessed by LC-MS analysis after tryptic in-gel digestion, and were compared to proteins from chicken breast.
2023-06-23 | PXD041521 | Pride
Project description:Recombinant H. volcanii Glycerol Kinase expressed in E.coli BL21 DE3 (HvGKEc) using the plasmid pET15b+glpK in LB Amp. The protein was initially eluted in 50mM HEPES buffer, 2M NaCl. The sample was resuspended in 2X laemmli sample buffer and run in the SDS gel using 1X SDS buffer. The sampled was fixed, the gel was stained with bio-safe commassie overnight, and the band was analyzed.
2025-05-20 | MSV000097933 | GNPS
Project description:Recombinant H. volcanii Glycerol Kinase expressed in E.coli BL21 DE3 (HvGKEc) using the plasmid pET15b+glpK in LB Amp. The protein was initially eluted in 50mM HEPES buffer, 2M NaCl. The sample was resuspended in 2X laemmli sample buffer and run in the SDS gel using 1X SDS buffer. The sampled was fixed, the gel was stained with bio-safe commassie overnight, and the band was analyzed.
2025-05-19 | MSV000097918 | GNPS
Project description:Identifying the intracellular and cell wall-ionically bound glycoside hydrolases (GHs) carbohydrate esterases (CEs) at the late growth stage of Arabidopsis stems is important for understanding the mechanisms regulating the cell wall integrity. The fact that whole plant stems are used as biomass feedstocks and the mixing of intracellular proteins with the cell wall proteome caused by an increasing proportion of broken cells of stems at the late growth stage pose a challenge in identifying these GHs and CEs. Here, we used a CaCl2-extraction procedure to isolate non-structural proteins from Arabidopsis whole stems, followed by protein solution method for direct identification of stem proteins, and by SDS-PAGE separation and protein gel band method for improving the identification of stem proteins, using Nano-LC-MS/MS analysis. Totally, 75 and 236 stem proteins were identified by using these two methods, respectively, confirming the later method (i.e. protein gel method) identified three time more stem proteins. Among these proteins, based on cell wall protein databases and data mining analyses, 6 and 22 proteins were identified as cell wall proteins from the late growth stage Arabidopsis stems, by using these two methods respectively.
2015-05-11 | PXD001852 | Pride
Project description:The objective of the present investigation was to consider the level of variation in the protein expression patterns of closely related Salmonella serovars, in order to search for protein factors with levels of expression or posttranslational modifications characteristic for each serovar. For the comparative expression analysis we have utilised classic 2D GE approach which revealed several proteins with serovar specific expression as well as proteins which do not alter their expression levels between serovars and strains. The proteins of interest were identified using LC/MS/MS. Keywords: 2D GE, MS/MS Analysis of 12 strains of S. enterica representing five different serovars.
2008-02-26 | E-GEOD-8931 | biostudies-arrayexpress
Project description:Presence of Psb27 was confirmed by single band LCMS of HPLC purified protein complexes
2023-06-06 | PXD034220 | Pride