Fig 1.
The applied workflow for sample preparation and data analysis for LFQ and iTRAQ quantification is graphically depicted.
Table 1.
Overview of the number of peptides and the corresponding proteins as being identified in the individual MS-runs.
Fig 2.
Comparison of peptide and protein identifications in iTRAQ and LFQ experiments.
Venn diagrams representing the comparison of all identified peptides, without considering fixed/variable modifications (A), and proteins (B) from LFQ, fractionated/ unfractionated iTRAQ analysis.
Fig 3.
Evaluation of protein sequence coverage for LFQ and iTRAQ.
Average protein sequence coverage was compared for all identified proteins per technique as well as for the overlapping identifications (A). The total number of identified proteins based on the particular number of peptides (B) and the average number of peptides per protein are also presented (C).
Fig 4.
Comparison of differentially expressed proteins identified in both iTRAQ experiments and LFQ.
Venn diagrams representing differentially expressed proteins found among the identified proteins after exclusion of single peptide hits.
Table 2.
Comparison of number of differentially expressed proteins identified by LFQ and iTRAQ approaches.
Table 3.
Evaluation of the proteins with the altered abundance found as a unique based on the results obtained for three methods.
Fig 5.
Immunohistochemical staining of Annexin A6.
Quantification results obtained from non-cancerous tissue and bladder cancer tissues (pTa, pT1 and pT2+) along with the representative images of stained sections are presented. Quantification of the immunoreactivity was conducted by using Image J software followed by color deconvolution and background subtraction.
Table 4.
List of proteins with conflicting expression trend.
Table 5.
Comparison of the quantification results at the peptide and protein level for identifications with conflicting expression trends between fractionated iTRAQ and LFQ.
Table 6.
Assessment of the validity of the differentially expressed proteins identified in proteomics experiments.