Journal: Cell Reports

Article Title: Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry

doi: 10.1016/j.celrep.2019.06.046

Figure Lengend Snippet:

Article Snippet: Trans-Proteomic Pipeline (TPP) 4.6.0 , ( ) , https://sourceforge.net/projects/sashimi/files/.

Techniques: Plasmid Preparation, Recombinant, Data-independent acquisition, Mass Spectrometry, Microarray, Sequencing, Software, Hydrophilic Interaction Liquid Chromatography

Journal: Molecular Endocrinology

Article Title: Minireview: Progress and Challenges in Proteomics Data Management, Sharing, and Integration

doi: 10.1210/me.2012-1180

Figure Lengend Snippet: Proteomics elucidates function and mechanism in molecular endocrinology. The schematic shows events on which proteomics reports in general functional models of G protein-coupled receptor and NR signaling. The binding of a variety of peptide ligands to G protein-coupled receptors (GPCR) induces recruitment of intracellular interacting partner proteins, touching off a variety of kinase cascades with functional endpoints in the cytoplasm (phosphorylated target protein) and nucleus. Nuclear targets of kinase cascades include transcription factors (TF), NR, and coregulators (CoR), which collectively modulate target gene expression and de novo protein synthesis. NR ligands bind directly to NR (the classic genomic model), inducing the recruitment of coregulators and modulating expression of target genes. Certain NR ligands have also been reported to elicit rapid cellular effects via cross talk with cellular kinase cascades (the nongenomic model). Phosphorylation events upon which phosphoproteomics reports are indicated.

Article Snippet: Name Description URL (Ref.) Central Proteomics Facilities Pipeline (CPFP) Suite for labeled or label-free quantitation in core proteomics facilities http://cpfp.sourceforge.net ( 124 ) LabKey Server Suite to identify and quantify proteins using its Computational Proteomics System (CPAS) and integrating with a variety of search engines and TPP components http://labkey.com ( 125 ) MaxQuant Suite for high-resolution labeled or label-free MS data with Andromeda search engine and a Viewer for visualization http://maxquant.org ( 68 ) Open Comprehensive Analysis Pipeline (OCAP) Suite for iTRAQ quantitative MS data analysis incorporating a variety of search engines and visualization components http://code.google.com/p/ocap ( 126 ) PhoMSVal Suite for MS/MS phosphopeptide data http://csbi.itdk.helsinki.fi/phomsval ( 127 ) The OpenMS Proteomic Pipeline (TOPP) Suite for creating custom analytic pipelines of HPLC/MS data http://open-ms.sourcefourge.net/topp/ ( 128 ) TPP (Trans-Proteomic Pipeline) Suite for validation, quantitation, and visualization of MS and MS/MS data, incorporating a variety of search engines http://sourceforge.net/projects/sashimi ( 129 ) with a guided tour ( 130 ) Open in a separate window Selected MS data analysis pipeline suites.

Techniques: Functional Assay, Binding Assay, Targeted Gene Expression, Expressing, Phospho-proteomics

Journal: Molecular Endocrinology

Article Title: Minireview: Progress and Challenges in Proteomics Data Management, Sharing, and Integration

doi: 10.1210/me.2012-1180

Figure Lengend Snippet: Selected MS data analysis pipeline suites

Article Snippet: Name Description URL (Ref.) Central Proteomics Facilities Pipeline (CPFP) Suite for labeled or label-free quantitation in core proteomics facilities http://cpfp.sourceforge.net ( 124 ) LabKey Server Suite to identify and quantify proteins using its Computational Proteomics System (CPAS) and integrating with a variety of search engines and TPP components http://labkey.com ( 125 ) MaxQuant Suite for high-resolution labeled or label-free MS data with Andromeda search engine and a Viewer for visualization http://maxquant.org ( 68 ) Open Comprehensive Analysis Pipeline (OCAP) Suite for iTRAQ quantitative MS data analysis incorporating a variety of search engines and visualization components http://code.google.com/p/ocap ( 126 ) PhoMSVal Suite for MS/MS phosphopeptide data http://csbi.itdk.helsinki.fi/phomsval ( 127 ) The OpenMS Proteomic Pipeline (TOPP) Suite for creating custom analytic pipelines of HPLC/MS data http://open-ms.sourcefourge.net/topp/ ( 128 ) TPP (Trans-Proteomic Pipeline) Suite for validation, quantitation, and visualization of MS and MS/MS data, incorporating a variety of search engines http://sourceforge.net/projects/sashimi ( 129 ) with a guided tour ( 130 ) Open in a separate window Selected MS data analysis pipeline suites.

Techniques: Labeling, Quantitation Assay, Multiplex sample analysis, Phospho-proteomics, Biomarker Discovery

Journal: World Journal of Gastroenterology

Article Title: Recent advances in mass spectrometry-based proteomics of gastric cancer

doi: 10.3748/wjg.v22.i37.8283

Figure Lengend Snippet: Summary of recent proteomic analyses of gastric cancer

Article Snippet: GC tissue , Global proteome , LTQ Orbitrap XL , Label-free, Bioworks Browser (v3.3.1), Trans-Proteomic Pipeline (v4.0) , Shen et al[ ], 2015 .

Techniques: Membrane, Multiplex sample analysis, Peptide Mass Fingerprinting, Targeted Proteomics, Glycoproteomics, Labeling

Journal: Analytical and bioanalytical chemistry

Article Title: Employing proteomics to understand the effects of nutritional intervention in cancer treatment

doi: 10.1007/s00216-018-1219-z

Figure Lengend Snippet: Examples of proteomic studies in nutritional intervention in cancer

Article Snippet: Dayon et al. , A scalable automated proteomic pipeline (ASAP 2 ), a sample preparation procedure that automates the depletion and general shotgun proteomics workflow for biomarker discovery , Serum , • Untargeted LC-MS/MS , [ 128 ].

Techniques: Sample Prep, Biomarker Discovery, Marker, Targeted Proteomics, Cell Culture, Inhibition

Journal: bioRxiv

Article Title: Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex

doi: 10.1101/2025.10.20.683548

Figure Lengend Snippet: a , Structures of parent and alkynylated tryptoline acrylamide stereoprobes used previously . b, Heatmap showing DFT calculations for elaborated tryptoline acrylamide stereoprobes compared to unelaborated counterparts (* parent stereoprobes, ** other analogs included for analysis), suggesting minimal impact of C6-and C7-substitution on tryptoline acrylamide core geometry. c, Workflow for cysteine-directed ABPP experiments where stereoprobe reactivity with cysteines is determined by blockade of iodoacetamide-desthiobiotin (IA-DTB) labeling, streptavidin enrichment, and identification and quantification by multiplexed (tandem mass tagging, TMT 10p lex ) MS-based proteomics, as described previously . d, Bar graph showing the number of experiments in which stereoprobe-liganded cysteines were quantified (shown for all cysteines liganded by elaborated, parent, and/or alkyne stereoprobes). e, Bar graphs showing representative liganding profiles for cysteines preferentially engaged by elaborated (left) or parent stereoprobes (right) or showing no preference (middle). Data represent average values ± SD of four independent experiments. f, Pie chart showing number of cysteines preferentially engaged (> 1.5-fold) by elaborated stereoprobes or alkyne stereoprobes. Cysteines not quantified in either elaborated or alkyne stereoprobe datasets were excluded from the analysis (12 total cysteines). g, Bar graph comparing the number of liganded cysteines for each elaborated tryptoline acrylamide stereoprobe where blue and grey designate cysteines that were engaged solely by the indicated stereoprobe vs multiple stereoprobes, respectively.

Article Snippet: Raw files were uploaded to the Integrated Proteomics Pipeline (IP2, version 6.0.2) available at http://ip2.scripps.edu/ ip2/mainMenu.html, and MS2 and MS3 files were extracted from the raw files using RAW Converter (version 1.1.0.22, available at http://fields.scripps.edu/rawconv/ ) and searched using the ProLuCID algorithm using a reverse concatenated, non-redundant variant of the Human UniProt database (release 2016-07).

Techniques: Labeling

Journal: bioRxiv

Article Title: Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex

doi: 10.1101/2025.10.20.683548

Figure Lengend Snippet: a , Colocalization of MTS-EGFP and Mitotracker Deep Red FM for 10 images from a single independent experiment performed in MTS-EGFP-inducible parental HCT-116 cells treated with doxycycline (0.5 µg/mL) and DMSO or WX-71b or WX-71d (20 µM, 8 h) as described in . Data represent average values ± SD of ten technical replicates. b, Generation of sgGRPEL1 cells. HCT-116 cells stably expressed Flag epitope-tagged WT or C124A-GRPEL1 were subject to CRISPR/Cas9 disruption of endogenous GRPEL1 and analyzed at the population level. c, Workflow for pulsed-SILAC labeling with tandem-mass tag (TMT 16p lex )-based multiplexing. sgGRPEL1 HCT-116 cells expressing Flag-epitope tagged WT-or C124A-GRPEL1 were pretreated in light media with DMSO or WX-71b or WX-71d (20 µM, 4 h) followed by shifting the cells to heavy amino acid media in the continued presence of stereoprobes (5 µM, 8 h). Mitochondria were biochemically enriched and analyzed by quantitative proteomics. d, Violin plot showing heavy-labeled protein abundance for the indicated treatment groups in pulse-SILAC experiments. Protein signals were corrected to light-labeled protein signals and normalized to heavy-labeled DMSO-treated WT-GRPEL1 or C124A-GRPEL1 signals. Statistical significance evaluated with parametric, two-tailed, paired t-test. e, Violin plot showing relative heavy-labeled protein abundance for WT-GRPEL1 cells across the indicated submitochondrial localizations as annotated from MitoCarta3.0 in combination with information retrieved from Uniprot and Human Protein Atlas. OMM, outer mitochondrial membrane; IMS, mitochondrial intermembrane space; IMM, inner mitochondrial membrane. f, Histograms (cell count (y axis)) versus mt-mKeima excitation (x axis)) showing mitophagy induction in (left) parental HCT-116 cells or sgGRPEL1 cells expressing WT-GRPEL1 (middle) or C124A-GRPEL1 (right) and also expressing mt-mKeima and Parkin treated with DMSO or WX-71b or WX-71d (20 µM, 8 h). Data show a single experiment representative of three independent experiments ( , present quantification).

Article Snippet: Raw files were uploaded to the Integrated Proteomics Pipeline (IP2, version 6.0.2) available at http://ip2.scripps.edu/ ip2/mainMenu.html, and MS2 and MS3 files were extracted from the raw files using RAW Converter (version 1.1.0.22, available at http://fields.scripps.edu/rawconv/ ) and searched using the ProLuCID algorithm using a reverse concatenated, non-redundant variant of the Human UniProt database (release 2016-07).

Techniques: Stable Transfection, FLAG-tag, CRISPR, Disruption, Multiplex sample analysis, Labeling, Multiplexing, Expressing, Quantitative Proteomics, Two Tailed Test, Membrane, Cell Counting