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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

Venn diagrams of the matching b/y ions of the three technical replicate HCD spectra (S1, S2, and S3) of myoglobin (A) and identified unique proteoforms of the three technical replicate RPLC-MSMS datasets (D1, D2, and D3) of the E. coli intact proteome (B).
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f6: Venn diagrams of the matching b/y ions of the three technical replicate HCD spectra (S1, S2, and S3) of myoglobin (A) and identified unique proteoforms of the three technical replicate RPLC-MSMS datasets (D1, D2, and D3) of the E. coli intact proteome (B).

Mentions: The protein-level reproducibility was characterized with matching b and y ions, which are the two ion series used for protein identification scoring and PTM localization. The results are shown in Fig. 6(A). The shared matching b and y ions among all three replicates are more than 60%. The proteome-level reproducibility was characterized using identified unique proteoforms, and those shared among the three technical replicates of the RPLC-MS/MS analysis of the E. coli intact proteome were more than 80% (Fig. 6(B)). Better reproducibility at the proteome level would be possible with additional dimension(s) of separation to increase the dynamic detection range.


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)

Venn diagrams of the matching b/y ions of the three technical replicate HCD spectra (S1, S2, and S3) of myoglobin (A) and identified unique proteoforms of the three technical replicate RPLC-MSMS datasets (D1, D2, and D3) of the E. coli intact proteome (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Venn diagrams of the matching b/y ions of the three technical replicate HCD spectra (S1, S2, and S3) of myoglobin (A) and identified unique proteoforms of the three technical replicate RPLC-MSMS datasets (D1, D2, and D3) of the E. coli intact proteome (B).
Mentions: The protein-level reproducibility was characterized with matching b and y ions, which are the two ion series used for protein identification scoring and PTM localization. The results are shown in Fig. 6(A). The shared matching b and y ions among all three replicates are more than 60%. The proteome-level reproducibility was characterized using identified unique proteoforms, and those shared among the three technical replicates of the RPLC-MS/MS analysis of the E. coli intact proteome were more than 80% (Fig. 6(B)). Better reproducibility at the proteome level would be possible with additional dimension(s) of separation to increase the dynamic detection range.

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