Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases DOI
Muzaffer Arıkan,

Başak Atabay

Journal of Proteome Research, Год журнала: 2024, Номер unknown

Опубликована: Окт. 25, 2024

In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large critical for the peptide identification step. Therefore, availability of well-curated databases tools custom construction essential to enhance performance analyses. this review, we first provide an overview by presenting concise historical background, outlining typical experimental bioinformatics workflow, emphasizing crucial step metaproteomics. We then delve into current available building such databases, highlighting their individual approaches, utility, advantages limitations. Next, examine existing detailing scope relevance in research. Then, practical recommendations metaproteomics, along with challenges area. conclude discussion anticipated advancements, emerging trends, future directions

Язык: Английский

Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease DOI
M. Wolf,

Julian Lange,

Dirk Benndorf

и другие.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 3, 2024

Abstract Background The gut microbiome is an important contributor to the development and course of inflammatory bowel disease (IBD). While changes in composition were observed response IBD therapy using biologics, studies elucidating human microbial proteins pathways dependence on success are sparse. Methods Fecal samples a cohort patients collected before after 14 weeks treatment with three different biologics. Clinical activity scores used determine clinical remission. metaproteomes remitting (n=12) non-remitting compared within both groups assessed over sampling time identify functional potential biomarkers. Results abundance associated intestinal barrier, neutrophilic granulocytes, immunoglobulins significantly decreased patients. In contrast, increase those was There significant metabolism from remission therapy. This included, for example, increased butyrate fermentation. Finally, new biomarkers prediction monitoring could be identified, e.g. lysosome-associated membrane glycoprotein 1, cytotoxicity marker, or anthranilate synthase component 2, part tryptophan metabolism. Conclusions Distinct related inflammation showed whether achieved not. suggests that metaproteomics useful tool therapies.

Язык: Английский

Процитировано

0

Spectral entropy as a measure of the metaproteome complexity DOI
Haonan Duan, Zhibin Ning, Ailing Zhang

и другие.

PROTEOMICS, Год журнала: 2024, Номер 24(16)

Опубликована: Май 25, 2024

The diversity and complexity of the microbiome's genomic landscape are not always mirrored in its proteomic profile. Despite anticipated diversity, observed complexities microbiome samples often lower than expected. Two main factors contribute to this discrepancy: limitations mass spectrometry's detection sensitivity bioinformatics challenges metaproteomics identification. This study introduces a novel approach evaluating sample directly at full spectrum (MS1) level rather relying on peptide identifications. When analyzing under identical spectrometry conditions, displayed significantly higher complexity, as evidenced by spectral entropy candidate entropy, compared single-species samples. research provides solid evidence for proteomics indicating optimization potential workflow.

Язык: Английский

Процитировано

0

Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases DOI
Muzaffer Arıkan,

Başak Atabay

Journal of Proteome Research, Год журнала: 2024, Номер unknown

Опубликована: Окт. 25, 2024

In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large critical for the peptide identification step. Therefore, availability of well-curated databases tools custom construction essential to enhance performance analyses. this review, we first provide an overview by presenting concise historical background, outlining typical experimental bioinformatics workflow, emphasizing crucial step metaproteomics. We then delve into current available building such databases, highlighting their individual approaches, utility, advantages limitations. Next, examine existing detailing scope relevance in research. Then, practical recommendations metaproteomics, along with challenges area. conclude discussion anticipated advancements, emerging trends, future directions

Язык: Английский

Процитировано

0