Instrument database system and application to mass spectrometry/mass spectrometry

Crawford, R.W.; Brand, Hal R.; Wong, Carla M.; Gregg, Hugh R.; Hoffman, Phillip A.; Enke, Christie G.

doi:10.1021/ac00271a015

Cited by 11 publications

(4 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Spectral searching of tandem mass spectral data (MS/MS) against reference databases has been developed with the broader availability of tandem mass spectrometers since the early 1980s . In fact, searching MS/MS databases is currently the fastest approach for confident compound annotations in small molecule analysis including metabolomics, lipidomics, food, and environmental sciences .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Identification of small molecules using accurate mass MS/MS search

Kind

Tsugawa

Čajka

et al. 2017

Mass Spectrometry Reviews

371

325

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

“…This may lead to a lower number of acquired Data were obtained from public sources and might vary slightly. Some instruments allow collecting data at different mass resolving power in MS 1 and MS/MS in order to increase the sensitivity or duty cycle.…”

mentioning

confidence: 99%

Identification of small molecules using accurate mass MS/MS search

Kind

Tsugawa

Čajka

et al. 2017

Mass Spectrometry Reviews

371

325

View full text Add to dashboard Cite

show abstract

“…The need to standardize acquisition of electron impact mass spectra necessitated the definition of both a quality index and a set of standard conditions. Attempts at creating reference libraries of CID tandem mass spectra quickly recognized the need to define and standardize operating conditions. , The appearance of CID spectra is sensitive to conditions such as collisional cross sections and collision energies. These conditions have been difficult to standardize to achieve uniform spectra suitable for searching reference databases.…”

mentioning

confidence: 99%

Method To Compare Collision-Induced Dissociation Spectra of Peptides: Potential for Library Searching and Subtractive Analysis

et al. 1998

View full text Add to dashboard Cite

We report the development of a method to compare collision-induced dissociation (CID) spectra of peptides. This method employs a cross-correlation analysis of a CID spectrum to a reference spectrum and normalizes the cross-correlation score to the autocorrelation of the CID spectra. The query spectrum is compared by using both mass information and fragmentation patterns. Fragmentation patterns are compared to each other using a correlation function. To evaluate the specificity of the approach, a set of 2180 tandem mass spectra obtained from both triple-quadrupole tandem mass spectrometers (TSQ) and quadrupole ion trap mass spectrometers (LCQ) was created. Comparisons are performed between tandem mass spectra obtained on the same instrument type as well as between different instrument types. Accurate and reliable comparisons are demonstrated in both types of analyses. The scores obtained in the cross-comparison of TSQ and LCQ tandem mass spectra of the same peptide are found to be slightly lower than comparisons performed with spectra obtained on the same instrument type. The method appears insensitive to variations in day-to-day performance of the instrument, minor variations in fragment ion abundance, and instrumental differences inherent in the same instrument model. The use of this method of comparison is demonstrated for library searching and subtractive analysis of tandem mass spectra obtained during LC/MS/MS experiments.

show abstract

“…In an historical perspective, Heller (LS14) discussed the development and status of the spectral databases presently available in the Chemical Information Service (CIS). Groups at the Lawrence Livermore National Laboratory and Michigan State University have collaborated in establishing a protocol for an instrument database system for MS/MS applications (LS6). They discuss file structures and format of the user interface.…”

Section: Library Searchingmentioning

confidence: 99%