PaesLeme - SRM Saliva

PaesLeme - SRM Saliva
Clustergrammer Heatmap
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Streptavidin Peptides_2020-09-30_15-13-28.sky.zip2020-10-27 13:35:32148240
BSA-QC_68fmol_Sep2020_Impact-II_2020-10-03_14-17-45.sky.zip2020-10-03 14:18:51131402166
Stergachis-SupplementaryData_2_b.sky2020-09-30 16:33:31101241248761
Stergachis-SupplementaryData_2_a.sky2020-09-30 16:32:35101151158461
Genome-scale metabolic rewiring to improve titers, rates and yields of the non-native non-ribosomal peptide product indigoidine at scale_2020-02-17_12-40-25.sky.zip2020-09-18 14:56:4716414118645
iPSC_Markers-LINCS-v4-2020august12_2020-08-14_19-21-16.sky.zip2020-09-15 09:50:341866,5536,03437,4446
Tier3_2020-09-10_18-48-08.sky.zip2020-09-13 11:03:112339869
200720_0845_2020-09-10_18-55-02.sky.zip2020-09-13 11:02:072351545
200721_1119_2020-09-10_18-56-20.sky.zip2020-09-13 11:02:072351545
200722_1408_2020-09-10_18-57-32.sky.zip2020-09-13 11:02:072351537
200723_1126_2020-09-10_18-58-38.sky.zip2020-09-13 11:02:072351544
200724_1047_2020-09-10_18-59-46.sky.zip2020-09-13 11:02:072351541
200727_1254r_2020-09-10_19-00-53.sky.zip2020-09-13 11:02:072351544
200728_0950r_2020-09-10_19-09-04.sky.zip2020-09-13 11:02:072351545
200729_1036_2020-09-10_19-17-39.sky.zip2020-09-13 11:02:072351546
200804_0953_2020-09-10_19-18-30.sky.zip2020-09-13 11:02:062351546
200805_1136_2020-09-10_19-19-12.sky.zip2020-09-13 11:02:062351546
200806_1428_2020-09-10_19-20-01.sky.zip2020-09-13 11:02:062351535
200820_1557_2020-09-10_19-21-02.sky.zip2020-09-13 11:02:062351548
200821_1134_2020-09-10_19-21-42.sky.zip2020-09-13 11:02:062351539
200821_1358_2020-09-10_19-22-30.sky.zip2020-09-13 11:02:062351536
PRM_9min_2020-09-11_15-50-27.sky.zip2020-09-13 11:01:28299668
PRM_60min_2020-09-11_15-51-41.sky.zip2020-09-13 11:01:28417201228
OSCA_TiO2enrich_12_OrderedBySample_Panorama_2020-08-08_17-37-31.sky.zip2020-09-10 07:07:581021219127
BSA-QC_68fmol_Aug2020_Impact-II_2020-09-02_08-08-32.sky.zip2020-09-02 08:10:11131402165
LMR0015_Oreni-Kidney_minPanorama_2020-08-28_19-19-59.sky.zip2020-08-31 23:56:542,1209,2269,22652,36112
microglia_grouped_2020-07-07_10-11-36.sky.zip2020-08-30 20:23:302,91827,68533,602100,80615
BP_MyoMuscle_241017_2020-06-01_21-42-31.sky.zip2020-08-17 15:30:326011011016
Determine_linkage_BP_2020-06-01_23-44-28.sky.zip2020-08-17 15:30:3220663
BP_CA_Nglycanlibrary_final_2020-06-03_01-02-34.sky.zip2020-08-17 15:30:3240898924
BP_GlycoT_Quantcheck_addstruc_2020-06-03_01-13-03.sky.zip2020-08-17 15:30:3240979712
E4HN 69 Wk F_M_120k.sky.zip2020-08-11 12:22:4620283984
E4HN 69 Wk F_M_240k_for Cit+9.sky.zip2020-08-11 12:22:39106684
Pilot Experiment APOE3 3 Mice (21 DBS_3Plasma_2Brain).sky.zip2020-08-11 12:22:3620273829
Pilot Experiment APOE3 3 Mice (21 DBS_3Plasma_2Brain)_240k.sky.zip2020-08-11 12:22:33106625
Pilot Kinetics Experiment CVN Mice 120k.sky.zip2020-08-11 12:22:322018248
5572_Plate1LC2_07232020.sky.zip2020-08-11 12:19:3890505099
5572_Plate2LC1_07222020.sky.zip2020-08-11 12:19:2310122123113
5572_Plate2LC2_07232020.sky.zip2020-08-11 12:18:4990505099
5572_Plate3LC1_07282020.sky.zip2020-08-11 12:18:3210122123113
5572_Plate3LC2_07282020.sky.zip2020-08-11 12:17:5590505099
5572_Plate4LC1_07302020.sky.zip2020-08-11 12:17:3510122123113
5572_Plate4LC2_07312020.sky.zip2020-08-11 12:17:0090505099
5572_Plate1LC1_07222020.sky.zip2020-08-11 12:16:4510122123113
vanGelder_Kinase_phosphorylation_2020-07-30_16-35-41.sky.zip2020-08-06 12:03:144510502
Common_Wheat_2020-07-30_13-16-10.sky.zip2020-08-03 08:35:4013224418648
Representative_Response_2020-07-30_13-25-50.sky.zip2020-08-03 08:35:401322432137
Durum_Wheat_2020-07-30_13-31-28.sky.zip2020-08-03 08:35:4013224419648
Einkorn_2020-07-30_13-53-08.sky.zip2020-08-03 08:35:4013224419054
Emmer_2020-07-30_13-58-02.sky.zip2020-08-03 08:35:4013224418851
Spelt_2020-07-30_14-09-32.sky.zip2020-08-03 08:35:4013224418248
Identification_Peptides_2020-07-21_14-05-35.sky.zip2020-08-03 08:32:1713486483916
Identification_Peptides_Selection_2020-07-30_14-12-39.sky.zip2020-08-03 08:32:171234351754
BSA-QC_68fmol_Jul2020_Impact-II_minPanorama_2020-07-30_12-55-38.sky.zip2020-07-30 12:57:29131402167
NIST PTM.sky.zip2020-07-29 09:37:022501374113
200626_PRM_Validation_Samples_FilteredAssays_2020-07-13_11-22-54.sky.zip2020-07-22 15:25:2568683769417
Twiss_PRM_unmod_24.sky.zip2020-07-20 05:19:40841841841,71333
LINCS_P100_DIA_Plate97_annotated_minimized_2020-06-29_18-13-03.sky.zip2020-06-29 15:20:4490961922,76490
BSA-QC_68fmol_Jun2020_Impact-II_minPanorama_2020-06-28_22-05-23.sky.zip2020-06-28 22:10:23131402165
19_8_27_LARP1_Kinase_Reaction_2020-06-18_10-51-35.sky.zip2020-06-24 21:25:59264762373
Phospho_CDK2_Silencing_Experiment_Human_2020-06-23_16-21-00.sky.zip2020-06-24 21:25:5911921636
20_6_Phospho_SAMe_Combined.sky.zip2020-06-24 21:25:582,77924,31330,00390,00933
Sky0 ACE2 TMPRSS2 cell lines_2020-06-18_16-55-27.sky.zip2020-06-18 13:38:456252919732
LINCS_P100_DIA_Plate96_annotated_minimized_2020-06-11_19-02-30.sky.zip2020-06-11 16:24:3290961922,76493
AMBPb_2020-06-01_14-39-27.sky.zip2020-06-11 15:34:1311261
AMBP_2020-06-01_17-29-42.sky.zip2020-06-11 15:34:13112668
AMBPc_2020-06-02_12-38-26.sky.zip2020-06-11 15:34:1311262
B2Mb_2020-06-02_15-19-17.sky.zip2020-06-11 15:34:1311268
B2M_2020-06-02_17-56-29.sky.zip2020-06-11 15:34:13112663
HBB_2020-06-03_11-25-07.sky.zip2020-06-11 15:34:13112672
IGHA1_2020-06-03_14-07-57.sky.zip2020-06-11 15:34:131121069
IGHA1b_2020-06-03_16-47-13.sky.zip2020-06-11 15:34:13112101
IGHA1c_2020-06-04_12-45-14.sky.zip2020-06-11 15:34:13112102
LYZ_2020-06-04_15-26-23.sky.zip2020-06-11 15:34:13112460
LYZb_2020-06-04_18-12-30.sky.zip2020-06-11 15:34:13112412
SERPINF1_2020-06-05_12-55-50.sky.zip2020-06-11 15:34:13112669
SERPINF1b_2020-06-05_16-03-56.sky.zip2020-06-11 15:34:1311262
Sky1 Synthetic SARS-CoV2 proteome library_2020-05-30_00-33-22.sky.zip2020-06-09 13:21:56121431351,2121
Sky3 52 patients nano PRM-MS2 raw_2020-05-30_00-38-21.sky.zip2020-06-09 13:20:236345734055
Sky4 5 positive patients nano PRM-MS2 refined_2020-05-30_00-52-02.sky.zip2020-06-09 13:20:22634492945
Sky6 11 positive patients micro PRM-MS2 refined_2020-05-30_00-19-04.sky.zip2020-06-09 13:11:206345527311
Sky5 91 patients micro PRM-MS2 raw_2020-05-30_00-57-41.sky.zip2020-06-09 13:11:206345527391
Sky2 Dilution series SARS Cov2 nano and microflow_2020-05-30_00-30-29.sky.zip2020-06-09 13:04:536345737118
20191031_Cdc55AID_PRM_l1_manual3_2020-05-02_10-59-22.sky.zip2020-06-02 20:16:492828562164
20191031_Cdc55AID_PRM_l2_manual3_2020-05-13_10-32-35.sky.zip2020-06-02 20:16:492627542064
20191031_Cdc55AID_PRM_l3_manual3_2020-05-13_11-25-38.sky.zip2020-06-02 20:16:492424481824
STORI_COHORT_2020-06-02_14-14-43.sky.zip2020-06-02 05:40:5673154154616102
Intra-day QC_2020-06-02_14-13-40.sky.zip2020-06-02 05:39:45731541546166
Inter-day QC_2020-06-02_14-12-41.sky.zip2020-06-02 05:39:34731541546165
Instrumental set-up QC_2020-06-02_14-10-53.sky.zip2020-06-02 05:39:23731541546165
ARMeD_NEDP1_2019-11-02_13-41-15.sky.zip2020-05-25 20:17:53751481622,58918
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
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