MOESM2 of Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Additional file 2. Shared peptides between replicates and peptide amounts. (A) Peptide overlap between replicates. (B) Peptide amounts measured by BCA assay after tryptic digestion

MOESM4 of Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Additional file 4. Proteome overlaps and Pearson correlation coefficients between all DTR and FASP replicates. (A) Percent of shared proteins between all replicates. (B) Pearson correlation coefficients of LFQ intensities between all replicates

MOESM1 of Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Additional file 1. Shared proteins between the replicates and peptide numbers per protein. (A) Overlap between identified proteins. (B) Frequency of shared proteins between the replicates. (C) Average peptide numbers for each protocol and proteins depending on their appearance in multiple replicates

MOESM3 of Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Additional file 3. Distribution of LFQ intensities for the DTR and FASP protocols. Log2 transformed LFQ intensity distribution depicted for all replicates with DTR in black, FASP 10 k in dark grey and FASP 30 k in light grey

MOESM5 of Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Additional file 5. Distribution of LFQ intensities for the differently stained tissues processed with the DTR protocol. Distribution of log2 transformed LFQ intensities for all replicates stained with H&E (purple), hematoxylin (blue), hemalaun (pink) or unstained (white)

Additional file 2 Table S2. of ESOPEC: prospective randomized controlled multicenter phase III trial comparing perioperative chemotherapy (FLOT protocol) to neoadjuvant chemoradiation (CROSS protocol) in patients with adenocarcinoma of the esophagus (NCT02509286)

Visit schedule Arm B (CROSS). (DOCX 25 kb

Additional file 4: of Identification of a blood-borne miRNA signature of synovial sarcoma

Illustration of the miRNA-expression levels of the two active synovial sarcoma patients who received chemotherapy (Patient 2 and 3 of the screening cohort of active synovial sarcoma patients as depicted in Additional file 3 ) marked with a triangle, patients receiving anticoagulation (Patient 3 of the screening cohort of active synovial sarcoma patients and Patient 1 of the independent cohort of active synovial sarcoma patients as depicted in Additional file 3 ) marked in green and patients receiving radiotherapy/presenting localized disease (Patient 1 of the screening cohort of active synovial sarcoma patients as depicted in Additional file 3 ) marked in red. A, C, E, G, I, K and M include the screening cohort of active synovial sarcoma patients, B, D, F, H, J, L and N depict the independent cohort (IC) of synovial sarcoma patients. (JPEG 5044 kb

Additional file 1: of Identification of a blood-borne miRNA signature of synovial sarcoma

Demographic patient data and blood count of patients with active sarcoma and control groups. Demographic patient data (age, BMI) and blood count (hemoglobin level, platelet count and leukocyte count) of patients with active synovial sarcoma compared to healthy donors, patients with synovial sarcoma in remission and patients with active leiomyosarcoma, MPNST, Ewing sarcoma and liposarcoma. Data are presented as mean value ± standard error of mean (SEM). p- values were determined using a Student’s t-test for independent samples. Hb = Hemoglobin. BMI = Body Mass Index. (PPTX 68 kb

Additional file 2: of Identification of a blood-borne miRNA signature of synovial sarcoma

Demographic patient data and blood count of patients with active sarcoma (Individual Cohort (IC)) and control groups. Demographic patient data (age, BMI) and blood count (hemoglobin level, platelet count and leukocyte count) of patients with active synovial sarcoma (Individual Cohort (IC)) compared to healthy donors and patients with synovial sarcoma in remission. Data are presented as mean value ± standard error of mean (SEM). p- values were determined using a Student’s t-test for independent samples. Hb = Hemoglobin. BMI = Body Mass Index. IC = Independent Cohort. (PPTX 66 kb

Additional file 5: of Identification of a blood-borne miRNA signature of synovial sarcoma

Comparison of whole blood miRNA expression levels of patients with active synovial sarcoma and miRNA expression levels of corresponding synovial sarcoma tissue. MiRNA-expression of patients with synovial sarcoma expressing SS18-SSX2 are marked in purple. A. miR-99a-5p. B. miR-146b-5p. C. miR-148b-3p. D. miR-195-5p. E. miR-223-3p. F. miR-500b-3p. G. miR-505-3p. (JPEG 2837 kb