SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries

Wu, Jemma X.; Song, Xiaomin; Pascovici, Dana; Zaw, Thiri; Care, Natasha; Krisp, Christoph; Molloy, Mark P.

doi:10.1074/mcp.m115.055558

Cited by 101 publications

(121 citation statements)

References 36 publications

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“…Immunopurified Kal7 samples were cleaved using in-gel tryptic digestion (V51111; Promega, Madison WI) and subjected to information-dependent acquisition and SWATH acquisition, as described 36, 84-86 . Skyline (v2.4) 87 was employed for precursor ion quantification using SWATH data for the various phosphorylation sites.…”

Section: Methodsmentioning

confidence: 99%

Brain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity

Miller¹,

Yan²,

Machida³

et al. 2017

ACS Chem. Neurosci.

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Kalirin7 (Kal7), a postsynaptic Rho GDP/GTP exchange factor (RhoGEF), plays a crucial role in long term potentiation and in the effects of cocaine on behavior and spine morphology. The KALRN gene has been linked to schizophrenia and other disorders of synaptic function. Mass spectrometry was used to quantify phosphorylation at 26 sites in Kal7 from individual adult rat nucleus accumbens and prefrontal cortex before and after exposure to acute or chronic cocaine. Region- and isoform-specific phosphorylation was observed along with region-specific effects of cocaine on Kal7 phosphorylation. Evaluation of the functional significance of multi-site phosphorylation in a complex protein like Kalirin is difficult. With the identification of five tyrosine phosphorylation (pY) sites, a panel of 71 SH2 domains was screened, identifying subsets that interacted with multiple pY sites in Kal7. In addition to this type of reversible interaction, endoproteolytic cleavage by calpain plays an essential role in long-term potentiation. Calpain cleaved Kal7 at two sites, separating the N-terminal domain, which affects spine length, and the PDZ binding motif from the GEF domain. Mutations preventing phosphorylation did not affect calpain sensitivity or GEF activity; phosphomimetic mutations at specific sites altered protein stability, increased calpain sensitivity and reduced GEF activity.

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Section: Methodsmentioning

confidence: 99%

Brain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity

Miller¹,

Yan²,

Machida³

et al. 2017

ACS Chem. Neurosci.

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“…There are a number of R‐language computational packages hosted on BioConductor (http://www.bioconductor.org/) that can be used to manipulate and process MS/MS spectra. That includes MSnID, MSnbase, msPurity, RMassBank, SwathXtend, and RAMClustR …”

Section: Creation Of Ms/ms Databasesmentioning

confidence: 99%

Identification of small molecules using accurate mass MS/MS search

Kind

Tsugawa

Čajka

et al. 2017

Mass Spectrometry Reviews

371

325

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Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in MS/MS-based annotation of chemical structures is impacted by instrumental settings and requirements, data acquisition modes including data-dependent and data-independent methods, library scoring algorithms, as well as post-curation steps. We critically discuss parameters that influence search results, such as mass accuracy, precursor ion isolation width, intensity thresholds, centroiding algorithms, and acquisition speed. A range of publicly and commercially available MS/MS databases such as NIST, MassBank, MoNA, LipidBlast, Wiley MSforID, and METLIN are surveyed. In addition, software tools including NIST MS Search, MS-DIAL, Mass Frontier, SmileMS, Mass++, and XCMS to perform fast MS/MS search are discussed. MS/MS scoring algorithms and challenges during compound annotation are reviewed. Advanced methods such as the in silico generation of tandem mass spectra using quantum chemistry and machine learning methods are covered. Community efforts for curation and sharing of tandem mass spectra that will allow for faster distribution of scientific discoveries are discussed.

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“…The first advantage of the approach is a more comprehensive fragmentation, including low abundance sub‐proteomes, such as citrullination. The second advantage is the reference assay library that should contain all the prior knowledge of the peptide components to be extracted from the SWATH data . Thus, assay library generation is one key challenge and limitation of this approach.…”

Section: Mass Spectrometry Applied To the Study Of Citrullination In mentioning

confidence: 99%

Insights into the study and origin of the citrullinome in rheumatoid arthritis

Fert-Bober

Darrah

Andrade

2019

Immunological Reviews

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The presence of autoantibodies and autoreactive T cells to citrullinated proteins and citrullinating enzymes in patients with rheumatoid arthritis (RA), together with the accumulation of citrullinated proteins in rheumatoid joints, provides substantial evidence that dysregulated citrullination is a hallmark feature of RA. However, understanding mechanisms that dysregulate citrullination in RA has important challenges. Citrullination is a normal process in immune and non‐immune cells, which is likely activated by different conditions (eg, inflammation) with no pathogenic consequences. In a complex inflammatory environment such as the RA joint, unique strategies are therefore required to dissect specific mechanisms involved in the abnormal production of citrullinated proteins. Here, we will review current models of citrullination in RA and discuss critical components that, in our view, are relevant to understanding the accumulation of citrullinated proteins in the RA joint, collectively referred to as the RA citrullinome. In particular, we will focus on potential caveats in the study of citrullination in RA and will highlight methods to precisely detect citrullinated proteins in complex biological samples, which is a confirmatory approach to mechanistically link the RA citrullinome with unique pathogenic pathways in RA.

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SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries

Cited by 101 publications

References 36 publications

Brain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity

Brain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity

Identification of small molecules using accurate mass MS/MS search

Insights into the study and origin of the citrullinome in rheumatoid arthritis

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