ArticleBioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference)2024
SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics.
Article in Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Metaproteomics, utilizing high-throughput LC-MS, offers a profound understanding of microbial communities. Quantitative metaproteomics further enriches this understanding by measuring relative protein abundance and revealing dynamic changes under different conditions. However, the challenge of missing peptide quantification persists in metaproteomics analysis, particularly in data-dependent acquisition mode, where high-intensity precursors for MS2 scans are selected. To tackle this issue, the match-between-runs (MBR) technique is used to transfer peptides between LC-MS runs. Inspired by the benefits of MBR and the need for streamlined metaproteomics data analysis, we developed SEMQuant, an end-to-end software integrating Sipros-Ensemble's robust peptide identifications with IonQuant's MBR function. The experiments show that SEMQuant consistently obtains the highest or second highest number of quantified proteins with notable precision and accuracy. This demonstrates SEMQuant's effectiveness in conducting comprehensive and accurate quantitative metaproteomics analyses across diverse datasets and highlights its potential to propel advancements in microbial community studies. SEMQuant is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/SEMQuant.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.