Proteomic Biology Using LC‐MS: Large Scale Analysis of Cellular Dynamics and Function. Wiley‐Interscience Series on Mass Spectrometry. By Nobuhiro Takahashi and, Toshiaki Isobe. Hoboken (New Jersey): John Wiley & Sons. $74.95. x + 254 p. + 8 pl.; ill.; index. 978‐0‐471‐66258‐7. 2008.

Crosslinking mass spectrometry is widening its scope from structural analyzes of purified multi-protein complexes towards systems-wide analyzes of protein-protein interactions. Assessing the error in these large datasets is currently a challenge. Using a controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate a reliable false-discovery rate estimation procedure for protein-protein interactions identified by crosslinking mass spectrometry.

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Understanding platelets

Thrombosis and Haemostasis ◽

10.1160/th05-02-0121 ◽

2005 ◽

Vol 94 (11) ◽

pp. 916-925 ◽

Cited By ~ 31

Author(s):

Marcus Dittrich ◽

Ingvild Birschmann ◽

Christiane Stuhlfelder ◽

Albert Sickmann ◽

Sabine Herterich ◽

...

Keyword(s):

Mass Spectrometry ◽

Large Scale ◽

Building Blocks ◽

Clinical Implications ◽

Scale Analysis ◽

New Techniques ◽

Analysis Techniques ◽

Large Scale Analysis ◽

Sage Data ◽

New Framework

SummaryNew large-scale analysis techniques such as bioinformatics, mass spectrometry and SAGE data analysis will allow a new framework for understanding platelets. This review analyses some important options and tasks for these tools and examines an outline of the new, refined picture of the platelet outlined by these new techniques. Looking at the platelet-specific building blocks of genome, (active) transcriptome and proteome (notably secretome and phospho-proteome), we summarize current bioinformatical and biochemical approaches, tasks as well as their limitations. Understanding the surprisingly complex platelet regarding compartmentalization, key cascades, and pathways including clinical implications will remain an exciting and hopefully fruitful challenge for the future.

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High Accuracy Mass Spectrometry in Large-Scale Analysis of Protein Phosphorylation

Mass Spectrometry of Proteins and Peptides - Methods In Molecular Biology ◽

10.1007/978-1-59745-493-3_7 ◽

2009 ◽

pp. 131-142 ◽

Cited By ~ 36

Author(s):

Jesper V. Olsen ◽

Boris Macek

Keyword(s):

Mass Spectrometry ◽

Protein Phosphorylation ◽

Large Scale ◽

High Accuracy ◽

Scale Analysis ◽

Large Scale Analysis

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Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry

Current Protein and Peptide Science ◽

10.2174/1389203721666200426232531 ◽

2020 ◽

Vol 21 (7) ◽

pp. 725-739

Author(s):

Daniele Musiani ◽

Enrico Massignani ◽

Alessandro Cuomo ◽

Avinash Yadav ◽

Tiziana Bonaldi

Keyword(s):

Mass Spectrometry ◽

Large Scale ◽

High Resolution Mass Spectrometry ◽

Arginine Methylation ◽

Research Field ◽

Scale Analysis ◽

Post Translational Modification ◽

Large Scale Analysis ◽

Protein Arginine Methylation

: The absence of efficient mass spectrometry-based approaches for the large-scale analysis of protein arginine methylation has hindered the understanding of its biological role, beyond the transcriptional regulation occurring through histone modification. In the last decade, however, several technological advances of both the biochemical methods for methylated polypeptide enrichment and the computational pipelines for MS data analysis have considerably boosted this research field, generating novel insights about the extent and role of this post-translational modification. : Here, we offer an overview of state-of-the-art approaches for the high-confidence identification and accurate quantification of protein arginine methylation by high-resolution mass spectrometry methods, which comprise the development of both biochemical and bioinformatics methods. The further optimization and systematic application of these analytical solutions will lead to ground-breaking discoveries on the role of protein methylation in biological processes.

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MetaProClust-MS1: A tool for clustering metaproteomes using rapid MS1 profiling

10.1101/2021.03.31.437863 ◽

2021 ◽

Author(s):

Caitlin M. A. Simopoulos ◽

Zhibin Ning ◽

Leyuan Li ◽

Mona M Khamis ◽

Xu Zhang ◽

...

Keyword(s):

Mass Spectrometry ◽

Tandem Mass Spectrometry ◽

Large Scale ◽

Clinical Settings ◽

Tandem Mass ◽

Computational Framework ◽

Dynamics And Function ◽

Using Data ◽

Time Required ◽

And Function

Metaproteomics is used to explore the composition, dynamics and function of microbial communities. However, acquiring data by tandem mass spectrometry is time consuming and resource intensive. To mediate this challenge, we present MetaProClust-MS1, a computational framework for microbiome screening developed to reduce the time required for data acquisition by mass spectrometry. In this proof-of-concept study, we tested MetaProClust-MS1 on data acquired using short 15 minute MS1-only mass spectrometry gradients and compared the results to those produced using data acquired by a traditional tandem mass spectrometry approach. MetaProClust-MS1 identified robust microbiome shifts caused by xenobiotics in both datasets. Cluster topologies were also significantly correlated. We demonstrate that MetaProClust-MS1 is able to rapidly screen microbiomes using only short MS1 profiles. This approach can be used to prioritize samples for deep metaproteomic analysis and will be especially useful in large-scale metaproteomic screens or in clinical settings where rapid results are required.

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