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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

Graphical fragmentation map of the identified proteoform RL7_ECOLI (P0A7K2) with S1 acetylation and K81 methylation.
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f2: Graphical fragmentation map of the identified proteoform RL7_ECOLI (P0A7K2) with S1 acetylation and K81 methylation.

Mentions: Among the 128 unique proteoforms that were identified from 3 technical replicates, 13 were modified with acetylation, biotinylation, monomethylation, trimethylation, O-(pantetheine 4′-phosphoryl), or a combination thereof. PTMs on 12 of these modified proteoforms were uniquely localized with high PTM scores. For example, in protein RL7_ECOLI (accession number P0A7K2), S1 acetylation and K81 methylation were identified with PTM scores of 25 and 4, respectively. These scores imply that 25 and 4 matching b or y ions independently defined the unique locations of these two modifications (Fig. 2).


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)

Graphical fragmentation map of the identified proteoform RL7_ECOLI (P0A7K2) with S1 acetylation and K81 methylation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Graphical fragmentation map of the identified proteoform RL7_ECOLI (P0A7K2) with S1 acetylation and K81 methylation.
Mentions: Among the 128 unique proteoforms that were identified from 3 technical replicates, 13 were modified with acetylation, biotinylation, monomethylation, trimethylation, O-(pantetheine 4′-phosphoryl), or a combination thereof. PTMs on 12 of these modified proteoforms were uniquely localized with high PTM scores. For example, in protein RL7_ECOLI (accession number P0A7K2), S1 acetylation and K81 methylation were identified with PTM scores of 25 and 4, respectively. These scores imply that 25 and 4 matching b or y ions independently defined the unique locations of these two modifications (Fig. 2).

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