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ProteomicsComparison of LFQ and IPTL for protein identification and relative quantification
Mass spectrometry-based quantitative proteome profiling is most commonly performed by label-free quantification (LFQ), stable isotopic labeling with amino acids in cell culture (SILAC), and reporter-ion based isobaric labeling methods (TMT and iTRAQ). Isobaric peptide termini labeling (IPTL) was des...
ORGANISM(S): Homo sapiens (Human) 
2022-02-17 | PXD026942 | Pride
Tmt Silac Lfq Quantitative proteomics Iptl 
ProteomicsLarge scale intact glycopeptide identification by Mascot database search
We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) pr...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-07-02 | MSV000082567 | MassIVE
ProteomicsProteogenomics analysis unveils a novel TFG-RET gene fusion and druggable targets in papillary thyroid carcinomas
Papillary thyroid cancer (PTC) is the most common type of endocrine malignancy. From a set of PTC patients whose tumor did not harbour any BRAF or RAS mutations, a 35 years old male patient’s normal, primary tumor and lymph node (LN) metastatic tissues were subjected to genomics and proteomics analy...
ORGANISM(S): Homo sapiens (Human) 
2020-04-02 | PXD016828 | Pride
Ptc/ ret/ huwe1/ usp7/ usp9x / precision medicine/ tfg-ret 
ProteomicsLC-MS peptide mapping of monoclonal antibodies using the mirror proteases trypsin and Tryp-N
Accurate characterization of the amino acid sequence and post-translational modifications (PTMs) of monoclonal antibodies (mAbs) is essential for evaluating product quality. Peptide mapping through bottom-up LC/MS analysis is a key methodology for this purpose. While trypsin is commonly the first ch...
ORGANISM(S): Homo Sapiens (human) 
2026-04-15 | PXD072803 | JPOST Repository
ProteomicsHalf decimal place rule
Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the first digit after the decimal point to the full molecular mass and results in a re...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080727 | MassIVE
ProteomicsA regulatory network comprising let-7 miRNA and SMUG1 is associated with good prognosis in breast cancer survival
Cytosine deamination to uracil in DNA leads to mutations if the DNA lesion is not corrected. Base excision repair (BER) initiated by single-strand selective uracil-DNA glycosylase 1 (SMUG1) primarily recognizes uracil and oxidized pyrimidines, and processes them to restore the correct bases. SMUG1 s...
ORGANISM(S): Homo sapiens (Human) 
2023-03-09 | PXD025929 | Pride
Smug1 Breast cancer Dna repair Rna and ribonucleoprotein biogenesis Hsa-let-7b-5p Modified bases 
ProteomicsAbsolute quantitation of proteins by two-point quantitation using dimethylated proteotypic peptides
Absolute targeted proteomics typically employs known amounts of synthetic stable isotopically labeled peptides which are mixed with the analyte and analysed by LC-MS. In order to obtain accurate data, we evaluated the use of two different stable isotopes of the same peptide as spike-in for absolute ...
ORGANISM(S): Homo sapiens (Human) 
2018-11-27 | PXD007894 | Pride
Absolute quantitation Dimethylation  mass spectrometry Parallel reaction monitoring Targeted proteomics 
ProteomicsQuantitative phosphoproteome analysis of cisplatin-induced apoptosis in Jurkat T cells
Reversible protein phosphorylation is one of the most important posttranslational modifications (PTMs) due to its vital role in cellular functions and signaling pathways. Protein phosphorylation is also known to be involved in the regulation of apoptosis. Previously, we have performed a SILAC-based ...
ORGANISM(S): Homo sapiens (Human) 
2017-05-11 | PXD004415 | Pride
: apoptosis Mass spectrometry Phosphorylation Cisplatin Phosphoproteomics 
ProteomicspTyr-CoIP HP/AGS - Quantitative analysis of H. pylori induced phosphotyrosine signaling upon infection.
Quantitative analysis of H. pylori induced phosphotyrosine signaling upon infection.
ORGANISM(S): Homo sapiens (Human) 
2014-07-09 | PXD000722 | Pride
Human Helicobacter Ptyr 
ProteomicsLarge scale intact glycopeptide identification by Mascot database search
We present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) pr...
ORGANISM(S): Homo sapiens (Human) 
2018-02-08 | PXD005931 | Pride
Mascot Glycoproteomics Higher-energy collisional induced dissociation (hcd) Prostate cancer Serum 
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