PaesLeme - SRM Saliva

PaesLeme - SRM Saliva
Clustergrammer Heatmap
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MRM-C26-CT_2020-05-26_10-19-25.sky.zip2020-05-26 01:26:17217715461713
MRM-BaF-CT_2020-05-26_10-12-57.sky.zip2020-05-26 01:17:00217815662512
STORI_COHORT_2020-05-26_09-26-46.sky.zip2020-05-26 00:28:3173154154616102
Intra-day QC_2020-05-26_09-25-29.sky.zip2020-05-26 00:26:00731541546166
Inter-day QC_2020-05-26_09-23-53.sky.zip2020-05-26 00:24:21731541546165
Instrumental set-up QC_2020-05-26_09-21-49.sky.zip2020-05-26 00:22:31731541546165
ARMeD_NEDP1_2019-11-02_13-41-15.sky.zip2020-05-25 20:17:53751481622,58918
Batch1412_2020-05-12_15-21-49.sky.zip2020-05-19 20:17:272141254
Batch1553_2020-05-12_15-28-16.sky.zip2020-05-19 20:17:272141263
Batch1508_2020-05-12_15-31-44.sky.zip2020-05-19 20:17:272151639
Batch1015_2020-05-12_15-39-40.sky.zip2020-05-19 20:17:272151631
Batch1134_2020-05-12_15-41-42.sky.zip2020-05-19 20:17:272141235
Batch1139_2020-05-12_15-45-12.sky.zip2020-05-19 20:17:272141238
Batch1039_2020-05-12_15-46-04.sky.zip2020-05-19 20:17:272141265
Batch1039b_2020-05-12_15-47-09.sky.zip2020-05-19 20:17:272141211
Batch1135_2020-05-12_15-49-04.sky.zip2020-05-19 20:17:262141264
Batch1553rep_2020-05-12_15-50-08.sky.zip2020-05-19 20:17:262141213
Batch1059_2020-05-12_15-51-24.sky.zip2020-05-19 20:17:262041284
Batch 1143_2020-05-12_15-53-25.sky.zip2020-05-19 20:17:262141265
Precision_2020-05-18_19-01-24.sky.zip2020-05-19 20:17:262141219
PRM_60min_2020-05-12_18-57-21.sky.zip2020-05-19 20:16:45417201228
PRM_9min_2020-05-18_21-07-56.sky.zip2020-05-19 20:16:44299668
PRM_9min_2020-05-19_07-53-44.sky.zip2020-05-19 20:16:10299668
LINCS_P100_DIA_Plate29_annotated_minimized_2020-05-18_18-50-11.sky.zip2020-05-18 15:59:1690961921,02896
DIAassayLibrary_Gasac-Gill_Rev2_2020-05-15_18-31-25.sky.zip2020-05-15 19:31:421,6914,7464,87926,1230
DIAassayLibrary_Gasac-Gill_Rev1_2020-05-15_17-01-05.sky.zip2020-05-15 17:38:291,5075,0745,10425,3220
Inflammatory_peptides_2020-05-13_13-35-09.sky.zip2020-05-13 10:58:1317494921860
Manually_filtered_peptides_2020-05-13_08-27-56.sky.zip2020-05-13 05:51:586253,2053,20513,12660
Prefiltering_CSF_document_2020-05-12_09-28-28.sky.zip2020-05-12 07:21:051,2225,9545,95422,91166
ResponseCurve-EGFR-LTQLGTFEDHFLSLQR_2020-01-28_09-46-19.sky.zip2020-05-11 16:35:09112434
ResponseCurve-CCND1-AYPDANLLNDR_2020-01-28_09-46-04.sky.zip2020-05-11 16:35:09112644
ResponseCurve-FOLH1-TYSVSFDSLFSAVK_2020-01-28_09-46-45.sky.zip2020-05-11 16:35:09112638
ResponseCurve-MUC1-DISEMFLQIYK_2020-01-28_09-47-16.sky.zip2020-05-11 16:35:09112428
ResponseCurve-PSA-LSEPAETDAVK_2020-01-28_09-47-42.sky.zip2020-05-11 16:35:09112644
ResponseCurve-SPINK1-QTSILIQK_2020-01-28_09-48-12.sky.zip2020-05-11 16:35:09112632
ResponseCurve-MMP9-LGLGADVAQVTGALR_2020-01-28_09-47-01.sky.zip2020-05-11 16:35:09112643
ResponseCurve-NCOA2-LLQDSSSPVDLAK_2020-01-28_09-47-28.sky.zip2020-05-11 16:35:09112442
ResponseCurve-SPRC-LEAGDHPVELLAR_2020-01-28_09-48-25.sky.zip2020-05-11 16:35:09112442
ResponseCurve-TGFB1-GGEIEGFR_2020-01-28_09-48-56.sky.zip2020-05-11 16:35:09112436
ResponseCurve-VEGFA-FMDVYQR_2020-01-28_09-49-13.sky.zip2020-05-11 16:35:09112433
ResponseCurve-CAMKK2-SLSAPGNLLTK_2020-01-28_09-45-49.sky.zip2020-05-11 16:35:09112442
ResponseCurve-ERG_pan-VIVPADPTLWSTDHVR_2020-01-28_09-46-32.sky.zip2020-05-11 16:35:09112643
ResponseCurve-SMAD4-YCQYAFDLK_2020-01-28_09-47-57.sky.zip2020-05-11 16:35:09112444
ResponseCurve-TFF3-VDCGYPHVTPK_2020-01-28_09-48-41.sky.zip2020-05-11 16:35:09112444
ResponseCurve-ANXA2-GLGTDEDSLIEIICSR_2020-01-28_09-49-31.sky.zip2020-05-11 16:35:09112441
CPDR-FFPE-ID-1193_2020-01-29_12-44-32.sky.zip2020-05-11 16:23:121616328224
CPDR-FFPE-ID-859_2020-01-29_12-41-32.sky.zip2020-05-11 16:23:121616328423
CPDR-FFPE-ID-1250_2020-01-29_12-41-18.sky.zip2020-05-11 16:23:121616328229
CPDR-FFPE-ID-1376_2020-01-29_14-56-40.sky.zip2020-05-11 16:23:121616328027
CPDR-FFPE-ID-1689_2020-01-29_12-40-48.sky.zip2020-05-11 16:23:121616328425
CPDR-FFPE-ID-636_2020-01-28_13-43-56.sky.zip2020-05-11 16:23:121616328632
CPDR-FFPE-ID-779_2020-01-28_13-41-34.sky.zip2020-05-11 16:23:121616328225
CPDR-FFPE-ID-850_2020-01-29_12-24-07.sky.zip2020-05-11 16:23:121616328223
CPDR-FFPE-ID-613_2020-01-28_13-47-05.sky.zip2020-05-11 16:23:121616328218
CPDR-FFPE-ID-623_2020-01-28_13-43-21.sky.zip2020-05-11 16:23:121616328244
CPDR-FFPE-ID-607_2020-01-28_13-42-17.sky.zip2020-05-11 16:23:121616328230
CPDR-FFPE-ID-573_2020-01-28_13-40-55.sky.zip2020-05-11 16:23:121616328415
CPDR-FFPE-ID-440_2020-01-28_13-27-00.sky.zip2020-05-11 16:23:121616328021
CPDR-FFPE-ID-497_2020-01-28_11-16-43.sky.zip2020-05-11 16:23:121616328430
CPDR-FFPE-ID-428_2020-01-28_11-16-26.sky.zip2020-05-11 16:23:121616328424
CPDR-FFPE-ID-1380_2020-01-29_14-57-50.sky.zip2020-05-11 16:23:121616328227
CPDR-FFPE-ID-1030_2020-01-29_14-49-38.sky.zip2020-05-11 16:23:121616328028
CPDR-FFPE-ID-726_2020-01-29_14-42-29.sky.zip2020-05-11 16:23:121616328229
CPDR-FFPE-ID-1217_2020-01-29_14-53-36.sky.zip2020-05-11 16:23:121616328224
CPDR-FFPE-ID-1059_2020-01-29_14-51-26.sky.zip2020-05-11 16:23:121616328425
CPDR-FFPE-ID-837_2020-01-29_14-45-59.sky.zip2020-05-11 16:23:121616328422
CPDR-FFPE-ID-835_2020-01-29_14-45-16.sky.zip2020-05-11 16:23:111616328428
CPDR-FFPE-ID-675_2020-01-29_14-30-10.sky.zip2020-05-11 16:23:111616328428
CPDR-FFPE-ID-659_2020-01-29_13-41-39.sky.zip2020-05-11 16:23:111616328224
CPDR-FFPE-ID-808_2020-01-29_12-41-02.sky.zip2020-05-11 16:23:111616328235
CPDR-FFPE-ID-1442_2020-01-29_12-40-36.sky.zip2020-05-11 16:23:111616328422
CPDR-FFPE-ID-928_2020-01-29_12-40-07.sky.zip2020-05-11 16:23:111616328225
CPDR-FFPE-ID-939_2020-01-29_12-39-50.sky.zip2020-05-11 16:23:111616328437
CPDR-FFPE-ID-1530_2020-01-29_12-38-39.sky.zip2020-05-11 16:23:111616328226
CPDR-FFPE-ID-796_2020-01-29_12-35-45.sky.zip2020-05-11 16:23:111616328429
CPDR-FFPE-ID-1090_2020-01-29_12-35-31.sky.zip2020-05-11 16:23:111616328427
CPDR-FFPE-ID-816_2020-01-29_12-35-04.sky.zip2020-05-11 16:23:111616328228
CPDR-FFPE-ID-831_2020-01-29_12-33-40.sky.zip2020-05-11 16:23:111616328239
CPDR-FFPE-ID-846_2020-01-29_12-34-49.sky.zip2020-05-11 16:23:111616328426
CPDR-FFPE-ID-1177_2020-01-29_12-34-34.sky.zip2020-05-11 16:23:111616328233
CPDR-FFPE-ID-958_2020-01-29_12-34-21.sky.zip2020-05-11 16:23:111616328228
CPDR-FFPE-ID-1502_2020-01-29_12-33-53.sky.zip2020-05-11 16:23:111616327831
CPDR-FFPE-ID-224_2020-01-29_12-33-29.sky.zip2020-05-11 16:23:111616328225
CPDR-FFPE-ID-912_2020-01-29_12-31-33.sky.zip2020-05-11 16:23:111616328231
CPDR-FFPE-ID-698_2020-01-29_12-26-45.sky.zip2020-05-11 16:23:111616328228
CPDR-FFPE-ID-769_2020-01-29_12-23-21.sky.zip2020-05-11 16:23:111616327823
CPDR-FFPE-ID-776_2020-01-29_12-44-15.sky.zip2020-05-11 16:23:111616328024
CPDR-FFPE-ID-1350_2020-01-29_12-40-21.sky.zip2020-05-11 16:23:101616328225
CPDR-FFPE-ID-1660_2020-01-29_12-39-36.sky.zip2020-05-11 16:23:101616328436
CPDR-FFPE-ID-804_2020-01-29_12-39-10.sky.zip2020-05-11 16:23:101616328223
CPDR-FFPE-ID-995_2020-01-29_12-38-23.sky.zip2020-05-11 16:23:101616328422
CPDR-FFPE-ID-1423_2020-01-29_12-38-07.sky.zip2020-05-11 16:23:101616328024
CPDR-FFPE-ID-1552_2020-01-29_12-36-56.sky.zip2020-05-11 16:23:101616328224
CPDR-FFPE-ID-1137_2020-01-29_12-36-39.sky.zip2020-05-11 16:23:101616328026
CPDR-FFPE-ID-1147_2020-01-29_12-35-59.sky.zip2020-05-11 16:23:101616328462
CPDR-FFPE-ID-1103_2020-01-29_12-32-17.sky.zip2020-05-11 16:23:101616328235
CPDR-FFPE-ID-656_2020-01-29_12-30-34.sky.zip2020-05-11 16:23:101616328227
CPDR-FFPE-ID-651_2020-01-29_12-22-55.sky.zip2020-05-11 16:23:101616328421
CPDR-FFPE-ID-1145_2020-01-29_12-22-42.sky.zip2020-05-11 16:23:101616328421
CPDR-FFPE-ID-736_2020-01-29_12-22-25.sky.zip2020-05-11 16:23:101616328230
Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer

  • Organism: Homo sapiens
  • Instrument: Waters Xevo TQ-XS
  • SpikeIn: Yes
Abstract
Different regions of oral squamous cell carcinoma (OSCC) have particular histopathological and molecular characteristics limiting the standard tumor-node-metastasis prognosis classification. Therefore, the identification of biological signatures that assists in the prognostic outcomes for OSCC patients would be of great clinical significance. Here we show by histopathology-guided discovery proteomics differentially expressed proteins between invasive tumor front (ITF) and inner tumor in neoplastic islands and tumor stroma. Immunohistochemistry analysis indicates low expression level of cystatin-B in the ITF of neoplastic islands as an independent marker for local recurrence. Selected reaction monitoring mass spectrometry of saliva proteins combined with machine learning methods demonstrate the most relevant prognostic signature to distinguish patients with and without lymph node metastasis. Our results identify a robust prognostic signature, which may enhance prognostic decisions in OSCC and better guide appropriate treatment and reduction of tumor recurrence or lymph node metastasis.
Experiment Description
Saliva samples from 40 OSCC patients (Supplementary Table 23-25) were selected to monitor peptides derived from CSTB, NDRG1, LTA4H, PGK1, COL6A1, ITGAV and MB based on DDA analysis. The samples were divided into two groups: those without lymph node metastasis (N0) and those with lymph node metastasis (N+).
Sample Description
The saliva samples were centrifuged at 1,500 g for 5 min at 4°C to pellet the debris. The resulting supernatant was collected and quantified by the Bradford assay (Bio-Rad, Hercules, CA, USA). A volume corresponding to 10 µg of total protein was used for sample preparation, and the sample volumes were adjusted. Ten micrograms of total protein were denatured in urea buffer (at a final concentration of 100 mM Tris-HCl pH 7.5, 8 M urea, 2 M thiourea, 5 mM EDTA, 1 mM PMSF, 1 mM DTT) containing Protease Inhibitor Cocktail Complete Mini Tablets (Roche, Auckland New Zealand). The samples were sonicated for 10 min and then centrifuged at 10,000 g for 5 min. The supernatant was collected, and the proteins were reduced with DDT and alkylated with iodoacetamide. Proteins were digested overnight at 37°C using 1.8 µg of trypsin.
Created on 3/27/18, 11:45 AM