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ProteomicsHeLa benchmark datasets DirectMS1 MSGF+
This technical dataset contains LC-MS runs of HeLa protein digest analyzed with a common shotgun proteomics pipeline based on MSGF+ and Percolator and DirectMS1 pipeline.
ORGANISM(S): Homo sapiens (Human) 
2023-09-25 | PXD045495 | Pride
Hela Proteomics Technical Directms1 
UnknownPrevention of platelet aggregation and arterial thrombosis using a modified Shenzhu Guanxin Formula.
Not available
S-EPMC7586491 | biostudies-literature
ProteomicsProteomic profiling in fibrolamellar carcinoma patient tumor tissue
Fibrolamellar carcinoma (FLC) is a rare, early-onset liver cancer. The five-year survival rate is low, and there is a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore,...
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD051527 | Pride
Primary Cancer Flc Non-malignant Human Liver Fibrolamellar carcinoma Frozen tissue Metastatic 
ProteomicsErythrocyte Proteome & Terminome
Proteins and protein N termini were isolated and enriched from human erythrocytes following the TAILS procedure with heavy dimethyl labeling of free N-termini (Kleifeld et al. Nat Biothech 2010). Following LC-MS/MS analysis on a Thermo Orbitrap XL spectra were matched using Mascot, X!Tandem and MSGF...
ORGANISM(S): Homo sapiens (Human) 
2014-02-24 | PXD000434 | Pride
Human Red blood cell Acetylation N termini Terminus Rbc Erythrocyte 
UnknownAccurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy.
Not available
S-EPMC7217331 | biostudies-literature
ProteomicsOuter membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440
Lignin modifications and the exoproteome of three aromatic catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MSGF+ and abundances inferred using PNNL's DMS an...
ORGANISM(S): Pseudomonas Putida Kt2440 (ncbitaxon:160488) Amycolatopsis Sp. Atcc 39116 (ncbitaxon:385957) Rhodococcus Jostii Rha1 (ncbitaxon:101510) 
2019-11-01 | MSV000084524 | MassIVE
UnknownA peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities.
Not available
S-EPMC4117239 | biostudies-literature
ProteomicsProteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic (NOD) mouse
Using plasma samples collected from pre-diabetic non-obese diabetic (NOD) mice (an experimental model of T1D) we performed parallel analysis of whole plasma samples and plasma-derived extracellular vesicle (EV) fractions using mass spectrometry (MS). Whole plasma samples were depleted of abundant pr...
ORGANISM(S): Mus musculus (Mouse) 
2022-10-20 | PXD033867 | Pride
Biomarkers  extracellular vesicles  exosomes  mass spectrometry  mouse  non-obese diabetic (nod) mouse  plasma  type 1 diabetes 
UnknownData from proteome analysis of Lasiodiplodia theobromae (Botryosphaeriaceae).
Not available
S-EPMC5447515 | biostudies-literature
ProteomicsA systematic evaluation of semispecific peptide search parameter enables identification of previously undescribed N-terminal peptides and conserved proteolytic processing in cancer cell lines
Background: Liquid chromatography- tandem mass spectrometry (LC-MS/MS) has become the most commonly used technique in explorative proteomic research. A variety of open-source tools for peptide-spectrum matching have become available. Most analyses of explorative MS data are performed using conventio...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2021-03-11 | MSV000087034 | MassIVE
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