Data files for Various HMGB1 proteases
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Ian
PROVIDER: MSV000083882 | MassIVE | Mon Jun 03 09:33:00 BST 2019
SECONDARY ACCESSION(S): PXD014106
REPOSITORIES: MassIVE
Similar Datasets
Project description:Ancient skeletal proteomes are increasingly utilised for phylogenetic and evolutionary analysis. These proteomes are, however, often small and with low sequence coverage. We expand on previous observations which have shown that parallel digestion of Pleistocene skeletal proteomes increases proteome size and protein sequence coverage. Furthermore, we demonstrate that the consecutive digestion of a skeletal proteome using two proteases, particularly Glu-C or chymotrypsin followed by trypsin digestion, enables the recovery of alternative proteome components not reachable through trypsin digestion alone. The sequential utilisation of several proteases is a promising avenue for the study of highly degraded ancient proteomes for phylogenetic purposes.
2024-03-06 | PXD047069 | Pride
Project description:Stable expression of tRNA-Glu(UUC) and tRNA-Arg(CCG) followed by transcriptomic profiling to measure transcripts.
2016-06-07 | GSE77285 | GEO
Project description:High specificity and ease of use make trypsin the most used enzyme in proteomics. Proteases with complementary cleavage specificity to trypsin have been applied to obtain additional data. However, use of proteases with broad specificity proved especially challenging. In this work, we analyzed the characteristics of five protease alternatives to trypsin for protein identification and sequence coverage when applied to S. pombe whole cell lysates. The specificity of the protease heavily impacted on the number of proteins identified. Proteases with higher specificity let to the identification of more proteins than proteases with lower specificity. However, AspN, GluC, chymotrypsin and proteinase K largely benefited from being paired with trypsin in sequential digestion, as had been shown by us for elastase before. In the most extreme case, the addition of trypsin to a proteinase K digest increased the number of identified proteins by 524 %. Also, AspN (82 %) and GluC (74 %) protein identifications largely improved following the additional digestion with trypsin. In general, protein identifications improved most over the use of the single protease when the enzymes followed on an initial digestion with trypsin. In the most extreme case, the sequential digest with trypsin and AspN yielded even higher number of protein identifications than digesting with trypsin alone.
2021-06-07 | PXD017321 | Pride
Project description:Stable expression of tRNA-Glu(UUC) and tRNA-Arg(CCG) followed by whole-genome transcript stability measurements using a-amanitin mediated inhibition of RNA Pol II.
2016-06-07 | GSE77349 | GEO
Project description:The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments, but due to the additional sample preparation and analysis time required, it has not been widely adapted in routine proteomic workflows. While data-independent acquisition (DIA) has been primarily optimized for fragmenting tryptic peptides with beam type (bt)-CID, it has the potential to analyze multiplexed samples from different protease digests. Here we evaluate a DIA multiplexing method that combines three proteolytic digests (Trypsin, AspN, and GluC) into a single sample. We first optimize DIA conditions for both resonance excitation (re-CID) and bt-CID to determine the optimal consensus fragmentation conditions for tryptic and non-tryptic peptides, and apply these methods to a human cell line. We demonstrate that using this multiplexed approach results in similar protein identifications and quantitative performance as compared to trypsin alone, but enables up to a 63% increase in peptide detections, resulting in up to a 8% increase in average sequence coverage. Importantly, this resulted in 100% sequence coverage for numerous proteins, suggesting the utility of this approach in applications where sequence coverage is critical, such as proteoform analysis.
2022-03-18 | PXD027242 | Pride
Project description:Accurate characterization of the amino acid sequence and post-translational modifications (PTMs) of monoclonal antibodies (mAbs) is essential for evaluating product quality. Peptide mapping through bottom-up LC/MS analysis is a key methodology for this purpose. While trypsin is commonly the first choice for mAb digestion, it typically yields high but incomplete sequence coverage. As a result, supplementary endoproteases such as Asp-N, chymotrypsin, Glu-C or Lys-C are often employed to enhance coverage. In this report, we evaluated another endoprotease, Tryp-N, which serves as an effective alternative to trypsin for mAb analysis. The sequence coverages achieved for bevacizumab, cetuximab, NISTmAb, and trastuzumab with Tryp-N were comparable to that of trypsin, and the combination of both enzymes slightly improved overall sequence coverage. Notably, both trypsin and Tryp-N generated identical peptides beside the N- and C-terminal ends. The presence of a basic amino acid at opposite ends of the peptide often resulted in complementary sequence coverage of the MS2 of the same peptide sequences. These complementary ion series can be leveraged for precise localization of PTMs, as demonstrated in detail for deamidation, and oxidation sites as well as single amino acid variations (SAVs).
2026-04-15 | PXD072803 | JPOST Repository
Project description:Histone post-translational modifications (PTMs) alter chromatin dynamics and contribute to the regulation of gene expression in health and disease. Mass spectrometry-based analysis is the gold-standard for histone PTM analysis, but it remains constrained by inefficient sample preparation workflows requiring multiple days. Here, we develop RIPUP (Rapid Identification of histone PTMs in Underivatized Peptides), a streamlined multi-protease workflow that reduces sample preparation from days to hours while improving PTM coverage and quantitative accuracy. Through systematic evaluation of Arg-C Ultra and a prototype recombinant (r)-Chymotrypsin proteases from Promega™ under varied conditions, with or without chemical derivatization using propionic anhydride and tandem mass tags (TMT), we demonstrate that Arg-C Ultra with TMT labeling achieves comparable total PTM detection to conventional Trypsin-based approaches. Using the HiP-Frag computational framework for unrestrictive PTM identification, we discover that TMT's tertiary amine provides charge compensation that rescues ionization of negatively charged acylation marks, revealing 50 succinylation and 27 glutarylation sites—a 'dark epigenome' largely undetected by propionylation-based methods. We demonstrate that complementary digestion with Arg-C Ultra and r-Chymotrypsin provides orthogonal sequence coverage, enabling detection of PTMs in H2A variants, linker histones, and regions poorly represented by arginine-specific cleavage alone. Application of RIPUP to frozen-thawed rat hippocampal sections within a 3-hour workflow identifies >200 PTMs including biologically critical PTM sites H3 K27/K36/K37 methylation, H4 N-terminal acetylation patterns, and H2A ubiquitination at K118/K119. This rapid, high-efficiency platform enables timely discovery of epigenetic mechanisms and accelerates the path from PTM identification to therapeutic target validation.
2026-06-20 | PXD073683 | Pride
Project description:LC-MS/MS raw files for Jurkat cell lysate aliquots digested with either Arg-C, Asp-N, Chymotrypsin, Glu-C, Lys-C or Trypsin and fractionated offline to produce 11 fractions (Trypsin only has 10 fractions).
2019-01-08 | MSV000083304 | MassIVE
Project description:Characterization of WN NS3 protease and characterization of AspN protease with double digestion protocol
2021-02-04 | PXD022973 | Pride
Project description:L-Arginine (L-Arg) is the substrate for both inducible nitric oxide synthase and arginase, which are upregulated in human IBD and in mouse colitis models. We have found that L-Arg supplementation enhances wound restitution in vitro, and improves the clinical parameters of weight loss, survival, and colon weight/length, in dextran sulfate sodium (DSS) induced murine colitis. Our aim was to further identify the potential mechanisms underlying the clinical benefit of L-Arg supplementation. 12 Total samples were analyzed, 3 samples from each of 4 groups. We generated the following pairwise comparisons: Ctrl vs Ctrl + L-Arg; Ctrl vs DSS; DSS vs DSS + L-Arg; Ctrl + L-Arg vs DSS, Ctrl + L-Arg vs DSS + L-Arg. Genes with a p-value < 0.01 and a fold-change ≥2 were selected. To identify genes that were altered in response to L-Arg, we performed the following multiple sample comparisons using a p-value < 0.01 and a fold-change ≥2: Ctrl vs DSS vs DSS + L-Arg
2012-06-26 | E-GEOD-34874 | biostudies-arrayexpress