PaesLeme - SRM Saliva

PaesLeme - SRM Saliva
Clustergrammer Heatmap
Flag FileDownloadCreatedProteinsPeptidesPrecursorsTransitionsReplicates (121 MB)2019-06-1390961922,76496 (12 MB)2019-06-10818116283018 (5 MB)2019-06-1081811628548 (81 MB)2019-06-1090961922,76266 (140 MB)2019-06-0890961922,76496 (110 MB)2019-06-0890961922,76491 (100 MB)2019-06-0790961922,75866 (7 MB)2019-06-04882417496 (8 MB)2019-06-04882418396 (7 MB)2019-06-03882316196 (140 MB)2019-06-0390961922,76496 (7 MB)2019-06-03882416596
all (46 MB)2019-05-31133575268,5337
20180518 multiplex quantification - APOA4 only (265 MB)2019-05-311364864
20180518 multiplex quantification only (380 MB)2019-05-3128357050268 (120 MB)2019-05-311613628684820
500 µE (PG-500uE_2ul_2019-05-16_15-23-09) (7 MB)2019-05-292710510555811 (3 MB)2019-05-2920611225758 (13 MB)2019-05-2931681366528
200µE (R5-8_V2_2019-05-16_15-31-29) (8 MB)2019-05-2928979751616 (1 GB)2019-05-283,22827,28927,28985,17542 (1 GB)2019-05-243,73136,39336,39395,63942 (162 MB)2019-05-2220989862412 (531 MB)2019-05-224,00716,22916,22947,85630 (1 GB)2019-05-223,48230,60230,60290,48842
Janschitz et al_PRM_results_Panorama (611 MB)2019-05-094475833712 (16 MB)2019-04-29818116287833 (43 MB)2019-04-26909619292496 (128 MB)2019-04-2690961921,00296 (52 MB)2019-04-18909619278892 (6 MB)2019-04-18882413292 (19 MB)2019-04-17818116291233 (26 MB)2019-04-16818116291233 (24 MB)2019-04-16808016080533 (24 MB)2019-04-16818116289433 (4 MB)2019-04-08882415666 (72 MB)2019-04-0890961922,76466 (5 MB)2019-04-08882415066
Dee Dee Luu et. al_The immunogenic microbial peptide RaxX represents an unclassified group of sulfated ribosomally synthesized and post-translationally modified (1 MB)2019-04-062221318 (75 MB)2019-04-0290961922,76466 (2 MB)2019-04-01882417436 (39 MB)2019-04-0190961922,76236 (5 MB)2019-03-28882416266 (6 MB)2019-03-27882417182 (98 MB)2019-03-2790961922,76284 (7 MB)2019-03-13882416596
HLF with (176 KB)2019-03-086045451
U87MG with (429 KB)2019-03-08901181181
IgA with (358 KB)2019-03-08801251251
HNE with (174 KB)2019-03-086038381
PGM OG with (370 KB)2019-03-08201061061
IgG with (228 KB)2019-03-087061611
Fet NG with (229 KB)2019-03-087063631
CBHI OG with (93 KB)2019-03-082020201
CBHI NG with (109 KB)2019-03-083028281
BLF with (302 KB)2019-03-088085851 (429 KB)2019-03-08901191191 (40 KB)2019-03-08103181 (797 KB)2019-03-0810151510 (63 MB)2019-03-088011634212 (6 MB)2019-03-0820183216
PRM-Identifying the N-terminal amino acid for a TAG start (3 MB)2019-03-05266583
PRM-Identifying the N-terminal amino acid for an ATG start (1 MB)2019-03-05266563 (5 MB)2019-03-01551332582,2633 (5 MB)2019-03-01631342602,0613 (51 MB)2019-02-2674730,02544,411576,8660 (17 MB)2019-02-261729,62414,598189,6470 (27 MB)2019-02-2637615,60123,172301,0320 (17 MB)2019-02-261729,62414,598189,6470 (23 MB)2019-02-0419192414469 (23 MB)2019-02-0319192414469 (1 GB)2019-01-309,04732,31233,292348,20120 (118 MB)2019-01-301851511728 (244 MB)2019-01-3017474713795 (2 MB)2019-01-2215107062 (2 MB)2019-01-2215107058 (2 MB)2019-01-1815107058 (2 MB)2019-01-1815107062 (815 KB)2019-01-1897971949311 (815 KB)2019-01-1897971949311 (758 KB)2019-01-162121422021
20160309_MouseV2B12M6& (15 MB)2019-01-16465110239039 (13 MB)2019-01-16535410851045 (294 KB)2019-01-161717341661 (334 KB)2019-01-1649501004831 (32 MB)2019-01-16979719496345 (62 MB)2019-01-161661703401,69045 (17 MB)2019-01-16676713462845 (1 MB)2019-01-161661703401,6501 (19 MB)2019-01-16717114269845 (929 KB)2019-01-161631603201,5481 (305 KB)2019-01-163946924561 (31 MB)2019-01-161311332661,26045 (34 MB)2019-01-161591603201,58445 (71 MB)2019-01-161131142281,06239
20190110 - Ajinomoto (23 MB)2019-01-1163434161238 (451 KB)2019-01-10819381369
20180406_180307CN1_Heavy& (2 MB)2019-01-108214214427
20180401_180307CN1_Heavy& (1 MB)2019-01-108214215027
20180329_180307CN1_Heavy& (558 KB)2019-01-10821421569
Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer

  • Organism: Homo sapiens
  • Instrument: Waters Xevo TQ-XS
  • SpikeIn: Yes
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