Features-Based Deisotoping Method for Tandem Mass Spectra

Yuan, Zheng; Shi, Jinhong; Lin, Wenjun; Chen, Bolin; Wu, Fang‐Xiang

doi:10.1155/2011/210805

Cited by 10 publications

(15 citation statements)

References 35 publications

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“…However, the relatively high increase in the number of proteins reported by both Zhang et al . and Yuan et al . may reflect the fact that large‐scale MS/MS data sets were not used.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, both Zhang et al . and Yuan et al . described approaches that use a combination of non‐template and template‐based approaches for deisotoping MS/MS spectra.…”

Section: Discussionmentioning

confidence: 99%

“…They do this using a feature‐based method to distinguish between isotopic clusters of peptide fragments and noise, thereby allowing monoisotopic peaks to be identified and isotopic peaks to be removed. By using MS/MS spectra of proteins from Rhodopseudomonas palustris , Yuan et al . demonstrated that their approach can increase the number of identifications by 35.9%.…”

Section: Discussionmentioning

confidence: 99%

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MS2‐Deisotoper: A Tool for Deisotoping High‐Resolution MS/MS Spectra in Normal and Heavy Isotope‐Labelled Samples

et al. 2019

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High‐resolution MS/MS spectra of peptides can be deisotoped to identify monoisotopic masses of peptide fragments. The use of such masses should improve protein identification rates. However, deisotoping is not universally used and its benefits have not been fully explored. Here, MS2‐Deisotoper, a tool for use prior to database search, is used to identify monoisotopic peaks in centroided MS/MS spectra. MS2‐Deisotoper works by comparing the mass and relative intensity of each peptide fragment peak to every other peak of greater mass, and by applying a set of rules concerning mass and intensity differences. After comprehensive parameter optimization, it is shown that MS2‐Deisotoper can improve the number of peptide spectrum matches (PSMs) identified by up to 8.2% and proteins by up to 2.8%. It is effective with SILAC and non‐SILAC MS/MS data. The identification of unique peptide sequences is also improved, increasing the number of human proteoforms by 3.7%. Detailed investigation of results shows that deisotoping increases Mascot ion scores, improves FDR estimation for PSMs, and leads to greater protein sequence coverage. At a peptide level, it is found that the efficacy of deisotoping is affected by peptide mass and charge. MS2‐Deisotoper can be used via a user interface or as a command‐line tool.

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“…However, the relatively high increase in the number of proteins reported by both Zhang et al . and Yuan et al . may reflect the fact that large‐scale MS/MS data sets were not used.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, both Zhang et al . and Yuan et al . described approaches that use a combination of non‐template and template‐based approaches for deisotoping MS/MS spectra.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

MS2‐Deisotoper: A Tool for Deisotoping High‐Resolution MS/MS Spectra in Normal and Heavy Isotope‐Labelled Samples

et al. 2019

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“…Although this technique can be quite useful for structural elucidation, it has two major drawbacks. Firstly, the resulting fragment ions having very low intensity can be accidentally removed as they might be considered as part of the noise peaks, and secondly, there are many cases in which it is extremely difficult to interpret the fragment ion spectra especially if the parent ion results from a mixture of structural isomers . As a consequence, the correct interpretation of the spectrum as well as the matching of the fragment ions to the corresponding parent ion is almost impossible.…”

Section: Introductionmentioning

confidence: 99%

High‐resolution GC/MS studies of a light crude oil fraction

Kondyli

Schräder

2018

J Mass Spectrom

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The continuous development in analytical instrumentation has brought the newly developed Orbitrap‐based gas chromatography / mass spectrometry (GC/MS) instrument into the forefront for the analysis of complex mixtures such as crude oil. Traditional instrumentation usually requires a choice to be made between mass resolving power or an efficient chromatographic separation, which ideally enables the distinction of structural isomers that is not possible by mass spectrometry alone. Now, these features can be combined, thus enabling a deeper understanding of the constituents of volatile samples on a molecular level. Although electron ionization is the most popular ionization method employed in GC/MS analysis, the need for softer ionization methods has led to the utilization of atmospheric pressure ionization sources. The last arrival to this family is the atmospheric pressure photoionization (APPI), which was originally developed for liquid chromatography / mass spectrometry (LC/MS). With a newly developed commercial GC‐APPI interface, it is possible to extend the characterization of unknown compounds. Here, first results about the capabilities of the GC/MS instrument under high or low energy EI or APPI are reported on a volatile gas condensate. The use of different ionization energies helps matching the low abundant molecular ions to the structurally important fragment ions. A broad range of compounds from polar to medium polar were successfully detected and complementary information regarding the analyte was obtained.

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“…While the top‐down methods Z score and THRASH were tested on MS1 spectra from peptide digests, we are unaware of any mention in the literature of an attempt to deconvolute bottom‐up MS/MS spectra with a top‐down method or vice versa, except for an unsuccessful application of MS‐Deconv to high‐resolution bottom‐up MS/MS spectra that led to poor results reported in …”

Section: Introductionmentioning

confidence: 99%

De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods

Vyatkina

Dekker

et al. 2017

Proteomics

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Despite high-resolution mass spectrometers are becoming accessible for more and more laboratories, tandem (MS/MS) mass spectra are still often collected at a low resolution. And even if acquired at a high resolution, software tools used for their processing do not tend to benefit from that in full, and an ability to specify a relative mass tolerance in this case often remains the only feature the respective algorithms take advantage of. We argue that a more efficient way to analyze high-resolution MS/MS spectra should be with methods more explicitly accounting for the precision level, and sustain this claim through demonstrating that a de novo sequencing framework originally developed for (high-resolution) top-down MS/MS data is perfectly suitable for processing high-resolution bottom-up datasets, even though a top-down like deconvolution performed as the first step will leave in many spectra at most a few peaks.

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Features-Based Deisotoping Method for Tandem Mass Spectra

Cited by 10 publications

References 35 publications

MS2‐Deisotoper: A Tool for Deisotoping High‐Resolution MS/MS Spectra in Normal and Heavy Isotope‐Labelled Samples

MS2‐Deisotoper: A Tool for Deisotoping High‐Resolution MS/MS Spectra in Normal and Heavy Isotope‐Labelled Samples

High‐resolution GC/MS studies of a light crude oil fraction

De Novo Sequencing of Peptides from High‐Resolution Bottom‐Up Tandem Mass Spectra using Top‐Down Intended Methods

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