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MetabolomicsMetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Standard mixture assay)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-05 | MTBLS1311 | MetaboLights
MetabolomicsMetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Mouse liver assays)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-02 | MTBLS1266 | MetaboLights
ProteomicsLarge scale intact glycopeptide identification by Mascot database search
We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) pr...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-07-02 | MSV000082567 | MassIVE
ProteomicsA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide datas...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-06-19 | MSV000079841 | MassIVE
OtherJUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy.
Data from authors [[http://stjuderesearch.org/site/lab/peng web site]]. Experiment: dataset3, file: pl08.mzXML. Published as part of Mol Cell Proteomics. 2014 Sep 8 . From the Abstract: {{i}} ... Here we present JUMP, a new hybrid database search program that generates amino acid tags and ranks pep...
ORGANISM(S): Homo_sapiens_viruses, Human 
GPM32320003491 | GPMDB
TranscriptomicsA search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation.
Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumu...
ORGANISM(S): Staphylococcus aureus 
2010-05-18 | E-GEOD-17135 | biostudies-arrayexpress
ProteomicsHuman skull base chordoma LC-MSMS
The prognostic factors of skull base chordoma associated with outcomes of patients after surgical resection remain poorly defined. This project aimed to identify a novel prognostic factor for patients with skull base chordoma. Using a proteomics approach, we screened tumor biomarkersthat upregulated...
ORGANISM(S): Homo sapiens (Human) 
2021-11-03 | PXD025894 | Pride
Human Lc-msms Skull base chordoma 
ProteomicsA systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines
Background: Liquid chromatography- tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventio...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2021-03-11 | MSV000087034 | MassIVE
ProteomicsMS Annika: A new Cross-Linking Search Engine
A cross linking mass spectrometry search engine was developed and implemented into Thermo Proteome Discoverer. The search engine is capable to handle several linker types as well as data input formats. To demonstrate its ability processing Bruker -ion mobility data, synthetic peptides (Beveridge, et...
ORGANISM(S): Streptococcus pyogenes ABC020006030 
2021-05-27 | PXD022772 | Pride
Xl-ms Proteome-discoverer Ion-mobility Search-engine 
ProteomicsHuman Fecal Gut Microbiome proteomics
5 human fecal gut samples, collected and prepared for standard MudPIT data collection from healthy volunteers, searched with the ComPIL database. x3 replicates each
ORGANISM(S): Human Metagenome (ncbitaxon:646099) 
2017-10-18 | MSV000081622 | MassIVE
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