## 2 Results
### Proteome Analysis by Isotope Coded Protein Label (ICPL)  
The proteome analysis of the 2 \(\times\) 24 OFFGEL-fraction and the non-fractionated samples (50 samples in total) was performed via ICPL-ESI_Quant_ Software. Proteins were referred as quantifiedand identified with at least two multiplets per protein and a unique peptide per protein. A protein was identified as a single protein species in neighbouring OFFGEL-fractions, whereas, a protein was identified as a separate protein species or isoform in several non side-by-side OFFGEL-fractions. In total 3222 protein species were detected in all 24 fractions of the first OFFGEL-analysis (645 unique protein species). However, because many of the proteins have been found in several fractions, this number was reduced to 131. In the second technical replicate, 3734 protein species were detected in total in all 24 fractions of the OFFGEL-analysis (734 unique protein species). Likewise proteins appearing in several fractions were removed, with 146 proteins left over. Eight-two proteins were identical in both technical replicates. In the first analysis of the not-fractionated samples, from in total 291 detected protein species, 62 unique proteins were identified. The second analysis of the non-fractionated samples could not be included in the evaluation, because that generated by the LC-MS/MS spectra did not permit reliable statements. A repeat of the experiment could not be performed due to insufficient sample amount. Forty-two of the identified proteins were found in all analyses (fractionated and non-fractionated). The identified proteins were classified as differentially expressed with a regulation value of 1.5 \(\geq\) 1 \(\geq\) 0.66, with at least two quadruplets per protein and a unique peptide per protein (CV \(\leq\) 30%). The analysis for nCRT I and nCRT II was carried out separately because of the different chemotherapy regimens added to radiation therapy. Thus, in the data set of nCRT I, 201 proteins (non-redundant) were identified in 2 \(\times\) 24 OFFGEL fractions and in the non-fractionated sample and the corresponding protein IDs are allocated from the IPI database; of these, 140 proteins could meet the described regulation value. Out of these 140 differentially regulated proteins, 79 proteins are downregulated in the proteome of poor/moderate responses of nCRT I and 61 proteins were upregulated. In the data set of nCRT II, and 201 proteins (non-redundant) were identified in 2 \(\times\) 24 OFFGEL fractions and in the non-fractionated sample, and the corresponding protein IDs are allocated from the IPI database. Of these, 114 proteins met the described regulation values. Out of these 114 differentially regulated proteins, 91 proteins are downregulated in the proteome of poor/moderate responses of nCRT I and 23 proteins were upregulated. Fourteen of these proteins showed a synchronous regulation after nCRT I and 2: A high expression of FLNB Isoform 1 of Filamin-B, Transketolase, PKM2 Isoform M2 of Pyruvate kinase isozymes M1/M2 and SERPINB1 Leukocyte elastase inhibitor and a low expression of IGHG2, Putative uncharacterized protein DKFZp686C15213 was particularly predictive for nCRT without any preference to the added chemotherapy throughout the applied RCT regiments. Thirty-five proteins were completely reciprocally regulated in response to nCRT I _vs._ nCRT II. Transgelin, LOC440786 Ig kappa chain V-II region TEW and kappa light chain variable region (Fragment) were highly expressed in good responders to nCRT II and expressed at very low levels in good responders to nCRT I. But heterogeneous nuclear ribonucleoprotein F, Adenine phosphoribosyltransferase (APRT) or Tubulin \(\alpha\)-1C chain (TUBA1C) were highly expressed in response to nCRT I and expressed at very low levels in response to nCRT II. Eighty-nine proteins were regulated either in response to nCRT I or II.