Abstract
The high mass accuracy and resolution of modern mass spectrometers provides new opportunities to employ theoretical peptide distributions in large-scale proteomic studies. We used theoretical distributions to study noise filtering and mass measurement errors and to examine mass-based differentiation of phosphorylated and nonphosphorylated peptides. Only the monoisotopic mass of the experimental precursor ion was necessary for this analysis. We found that peak deviations can be used to characterize the modification states of peptides in a sample. When applied to large-scale proteomic data sets, the peak deviation distribution can be used to filter chemical/electronic noise for singly charged species. Using peak deviation distributions, it is possible to separate the phosphorylated peptides from the nonphosphorylated peptides, enabling evaluation of the phosphoproteome content of a sample. Because this approach is simple, with light computational requirements, the analysis of theoretical peptide distributions has a significant potential for application to phosphoproteome analyses. For our studies we used publicly available data sets from three large-scale proteomic studies.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 3207-3214 |
| Number of pages | 8 |
| Journal | Journal of Proteome Research |
| Volume | 12 |
| Issue number | 7 |
| DOIs | |
| State | Published - Jul 5 2013 |
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Keywords
- high mass accuracy informatics
- mass defect
- noise filtering
- peak deviation
- phosphopeptides
- tandem mass spectrometry
- theoretical peptides
- theoretical phosphopeptide enrichment
ASJC Scopus subject areas
- Biochemistry
- Chemistry(all)
Cite this
Use of theoretical peptide distributions in phosphoproteome analysis. / Kalita, Mridul; Kasumov, Takhar; Brasier, Allan R.; Sadygov, Rovshan.
In: Journal of Proteome Research, Vol. 12, No. 7, 05.07.2013, p. 3207-3214.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Use of theoretical peptide distributions in phosphoproteome analysis
AU - Kalita, Mridul
AU - Kasumov, Takhar
AU - Brasier, Allan R.
AU - Sadygov, Rovshan
PY - 2013/7/5
Y1 - 2013/7/5
N2 - The high mass accuracy and resolution of modern mass spectrometers provides new opportunities to employ theoretical peptide distributions in large-scale proteomic studies. We used theoretical distributions to study noise filtering and mass measurement errors and to examine mass-based differentiation of phosphorylated and nonphosphorylated peptides. Only the monoisotopic mass of the experimental precursor ion was necessary for this analysis. We found that peak deviations can be used to characterize the modification states of peptides in a sample. When applied to large-scale proteomic data sets, the peak deviation distribution can be used to filter chemical/electronic noise for singly charged species. Using peak deviation distributions, it is possible to separate the phosphorylated peptides from the nonphosphorylated peptides, enabling evaluation of the phosphoproteome content of a sample. Because this approach is simple, with light computational requirements, the analysis of theoretical peptide distributions has a significant potential for application to phosphoproteome analyses. For our studies we used publicly available data sets from three large-scale proteomic studies.
AB - The high mass accuracy and resolution of modern mass spectrometers provides new opportunities to employ theoretical peptide distributions in large-scale proteomic studies. We used theoretical distributions to study noise filtering and mass measurement errors and to examine mass-based differentiation of phosphorylated and nonphosphorylated peptides. Only the monoisotopic mass of the experimental precursor ion was necessary for this analysis. We found that peak deviations can be used to characterize the modification states of peptides in a sample. When applied to large-scale proteomic data sets, the peak deviation distribution can be used to filter chemical/electronic noise for singly charged species. Using peak deviation distributions, it is possible to separate the phosphorylated peptides from the nonphosphorylated peptides, enabling evaluation of the phosphoproteome content of a sample. Because this approach is simple, with light computational requirements, the analysis of theoretical peptide distributions has a significant potential for application to phosphoproteome analyses. For our studies we used publicly available data sets from three large-scale proteomic studies.
KW - high mass accuracy informatics
KW - mass defect
KW - noise filtering
KW - peak deviation
KW - phosphopeptides
KW - tandem mass spectrometry
KW - theoretical peptides
KW - theoretical phosphopeptide enrichment
UR - http://www.scopus.com/inward/record.url?scp=84879941322&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84879941322&partnerID=8YFLogxK
U2 - 10.1021/pr4003382
DO - 10.1021/pr4003382
M3 - Article
C2 - 23731183
AN - SCOPUS:84879941322
VL - 12
SP - 3207
EP - 3214
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 7
ER -