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Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra.

Xiao K, Yu F, Fang H, Xue B, Liu Y, Tian Z - Sci Rep (2015)

Bottom Line: The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated.Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved.The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.

ABSTRACT
It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.

No MeSH data available.


Related in: MedlinePlus

The orthogonal plot of matching b and y ions with vs. without using the OIE_CARE method for the unique E. coli proteoforms.The orthogonal dotted line is added as a visual guide.
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f4: The orthogonal plot of matching b and y ions with vs. without using the OIE_CARE method for the unique E. coli proteoforms.The orthogonal dotted line is added as a visual guide.

Mentions: For E. coli protein identification at the proteome level, more matching b and y ions were found with the OIE_CARE resolving OIEs for most of the identified proteoforms (Fig. 4). For example, 3, 6, and 3 more matching b and y ions were found for GRCA_ECO45, IHFB_ECO24 and DBHB_ECO57, respectively. The corresponding labeled MS/MS spectra are provided in Supplemental Figure S3. With OIE_CARE and more matching b and y ions, four new proteins (ASR_ECOLU, C562_ECO57, YNFD_ECOLI, and RNFH_ECO7I) were also identified. The graphical fragmentation maps, along with matching b and y ions of these four new proteins, are provided in Supplemental Figure S4.


Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra.

Xiao K, Yu F, Fang H, Xue B, Liu Y, Tian Z - Sci Rep (2015)

The orthogonal plot of matching b and y ions with vs. without using the OIE_CARE method for the unique E. coli proteoforms.The orthogonal dotted line is added as a visual guide.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4593959&req=5

f4: The orthogonal plot of matching b and y ions with vs. without using the OIE_CARE method for the unique E. coli proteoforms.The orthogonal dotted line is added as a visual guide.
Mentions: For E. coli protein identification at the proteome level, more matching b and y ions were found with the OIE_CARE resolving OIEs for most of the identified proteoforms (Fig. 4). For example, 3, 6, and 3 more matching b and y ions were found for GRCA_ECO45, IHFB_ECO24 and DBHB_ECO57, respectively. The corresponding labeled MS/MS spectra are provided in Supplemental Figure S3. With OIE_CARE and more matching b and y ions, four new proteins (ASR_ECOLU, C562_ECO57, YNFD_ECOLI, and RNFH_ECO7I) were also identified. The graphical fragmentation maps, along with matching b and y ions of these four new proteins, are provided in Supplemental Figure S4.

Bottom Line: The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated.Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved.The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.

ABSTRACT
It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.

No MeSH data available.


Related in: MedlinePlus