Pivotal Role of Computers and Software in Mass Spectrometry – <i>SEQUEST</i> and 20 Years of Tandem MS Database Searching

Yates, John R.

doi:10.1007/s13361-015-1220-0

Cited by 27 publications

(22 citation statements)

References 91 publications

(84 reference statements)

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“…Acquired MS/MS spectra were searched against and mapped on the expected 1918 H1 HA sequence. Spectra were searched against three constructed proteome databases: (i) influenza virus, (ii) Sf9 cells, and (iii) baculovirus using the program SEQUEST and Fixed Value Peptide Spectrum Match (PSM) validator algorithms in the Proteome Discoverer 1.4 software (Thermo Scientific, CA) 61 . The total numbers of PSMs from searches were 174 from the influenza database, 23 from the Sf9 cell database, and 1 from the baculovirus database.…”

Section: Methodsmentioning

confidence: 99%

Structural analysis of influenza vaccine virus-like particles reveals a multicomponent organization

McCraw

Gallagher

Torian

et al. 2018

Sci Rep

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Influenza virus continues to be a major health problem due to the continually changing immunodominant head regions of the major surface glycoprotein, hemagglutinin (HA). However, some emerging vaccine platforms designed by biotechnology efforts, such as recombinant influenza virus-like particles (VLPs) have been shown to elicit protective antibodies to antigenically different influenza viruses. Here, using biochemical analyses and cryo-electron microscopy methods coupled to image analysis, we report the composition and 3D structural organization of influenza VLPs of the 1918 pandemic influenza virus. HA molecules were uniformly distributed on the VLP surfaces and the conformation of HA was in a prefusion state. Moreover, HA could be bound by antibody targeting conserved epitopes in the stem region of HA. Taken together, our analysis suggests structural parameters that may be important for VLP biotechnology such as a multi-component organization with (i) an outer component consisting of prefusion HA spikes on the surfaces, (ii) a VLP membrane with HA distribution permitting stem epitope display, and (iii) internal structural components.

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Section: Methodsmentioning

confidence: 99%

Structural analysis of influenza vaccine virus-like particles reveals a multicomponent organization

McCraw

Gallagher

Torian

et al. 2018

Sci Rep

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“…This review discusses MS/MS databases and software approaches for small molecules less than 2000 Da. Proteomics and glycomics MS/MS search strategies as well as multiple stage tandem mass spectrometry (MS n ) are discussed elsewhere.…”

Section: Introductionmentioning

confidence: 99%

Identification of small molecules using accurate mass MS/MS search

Kind

Tsugawa

Čajka

et al. 2017

Mass Spectrometry Reviews

356

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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“…Data bank search has long been in use, especially for electron impact spectra [1][2][3]. Comparison to expected (theoretical) tandem mass spectra is the basis of proteomics [4], even if comparisons use predominantly fragment ion masses only, with no or limited use of ion abundance.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

Bazsó

Ozohanics

Schlosser

et al. 2016

J. Am. Soc. Mass Spectrom.

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Abstract. The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D Bheat map^, indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

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Pivotal Role of Computers and Software in Mass Spectrometry – SEQUEST and 20 Years of Tandem MS Database Searching

Cited by 27 publications

References 91 publications

Structural analysis of influenza vaccine virus-like particles reveals a multicomponent organization

Structural analysis of influenza vaccine virus-like particles reveals a multicomponent organization

Identification of small molecules using accurate mass MS/MS search

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

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