Improved mass defect model for theoretical tryptic peptides

Indranil Mitra, Alexey V. Nefedov, Allan R. Brasier, Rovshan Sadygov

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of 20 natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well-defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, and peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95% of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the 20 natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the 20 natural amino acids, oxidized Met, and phosphorylated Ser, Thr, and Tyr. We found that extension of the amino acid set by modifications increases the 95% peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.

Original languageEnglish (US)
Pages (from-to)3026-3032
Number of pages7
JournalAnalytical Chemistry
Volume84
Issue number6
DOIs
StatePublished - Mar 20 2012

Fingerprint

Defects
Peptides
Amino Acids
Mass spectrometers
Bioinformatics
Protein Sorting Signals
Mass spectrometry

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Improved mass defect model for theoretical tryptic peptides. / Mitra, Indranil; Nefedov, Alexey V.; Brasier, Allan R.; Sadygov, Rovshan.

In: Analytical Chemistry, Vol. 84, No. 6, 20.03.2012, p. 3026-3032.

Research output: Contribution to journalArticle

Mitra, Indranil ; Nefedov, Alexey V. ; Brasier, Allan R. ; Sadygov, Rovshan. / Improved mass defect model for theoretical tryptic peptides. In: Analytical Chemistry. 2012 ; Vol. 84, No. 6. pp. 3026-3032.
@article{8a249220fe6c460e8f5eee0291bf7840,
title = "Improved mass defect model for theoretical tryptic peptides",
abstract = "Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of 20 natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well-defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, and peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95{\%} of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the 20 natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the 20 natural amino acids, oxidized Met, and phosphorylated Ser, Thr, and Tyr. We found that extension of the amino acid set by modifications increases the 95{\%} peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.",
author = "Indranil Mitra and Nefedov, {Alexey V.} and Brasier, {Allan R.} and Rovshan Sadygov",
year = "2012",
month = "3",
day = "20",
doi = "10.1021/ac203255e",
language = "English (US)",
volume = "84",
pages = "3026--3032",
journal = "Analytical Chemistry",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "6",

}

TY - JOUR

T1 - Improved mass defect model for theoretical tryptic peptides

AU - Mitra, Indranil

AU - Nefedov, Alexey V.

AU - Brasier, Allan R.

AU - Sadygov, Rovshan

PY - 2012/3/20

Y1 - 2012/3/20

N2 - Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of 20 natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well-defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, and peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95% of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the 20 natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the 20 natural amino acids, oxidized Met, and phosphorylated Ser, Thr, and Tyr. We found that extension of the amino acid set by modifications increases the 95% peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.

AB - Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of 20 natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well-defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, and peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95% of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the 20 natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the 20 natural amino acids, oxidized Met, and phosphorylated Ser, Thr, and Tyr. We found that extension of the amino acid set by modifications increases the 95% peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.

UR - http://www.scopus.com/inward/record.url?scp=84858712313&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84858712313&partnerID=8YFLogxK

U2 - 10.1021/ac203255e

DO - 10.1021/ac203255e

M3 - Article

VL - 84

SP - 3026

EP - 3032

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

IS - 6

ER -