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Structured Review

Matrix Science mascot v2.4
Mascot V2.4, supplied by Matrix Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/mascot+v2%2E4/mascot+software/pmc10089177__pnas__2213886120__sapp-215-16-18
Average 90 stars, based on 1 article reviews
mascot v2.4 - by Bioz Stars, 2026-10
90/100 stars

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Injection:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Generated:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Recombinant:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Cell Culture:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Synthesized:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Luciferase:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

RNA Library Preparation:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Isolation:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Multiplex Assay:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Software:


Article Title: Supporting Information for Lysosome-targeted multi-functional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant (8) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy
Article Snippet: MS2 spectra were acquired with the Orbitrap with a resolution of 30.000 and a max injection time of 86 ms. Acquired data were analyzed using IsobarQuant [ ] and Mascot V2.4 (Matrix Science) using a reverse in house generated FASTA database from Sf21 ( Spodoptera frugiperda ) including common contaminants.

Article Title: A protein corona modulates the function of mineralization-competent matrix vesicles
Article Snippet: The dynamic exclusion was set to 45 s. Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Homo sapiens database (UP000005640) including common contaminants.

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer
Article Snippet: Acquired data were analyzed using IsobarQuant and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, ) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGGSLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVPKHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSAQVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNAGGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDHDIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).

Article Title: Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer.
Article Snippet: Acquired data were analyzed using IsobarQuant85 and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Mus musculus database (UP000000589, downloaded in May 2016, 59.754 entries including common contaminants).

Article Title: MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress.
Article Snippet: Acquired data were analyzed using IsobarQuant (Franken et al, 2015) and Mascot V2.4 (Matrix Science) using a reverse UniProt FASTA Saccharomyces cerrevisiae database (UP000002311), including common contaminants and the following Rtn1-myc-3C-3xFLAG-tagged (bait) protein employed for the enrichment of subcellular membranes: sp|P1707_RE | P1707_RE MSASAQHSQAQQQQQQKSCNCDLLLWRNPVQTGKYFGG SLLALLILKKVNLITFFLKVAYTILFTTGSIEFVSKLFLGQGLITKYGPKECPNIAGFIKPHIDEALKQLPVFQAHIRKTVFAQVP KHTFKTAVALFLLHKFFSWFSIWTIVFVADIFTFTLPVIYHSYKHEIDATVAQGVEISKQKTQEFSQMACEKTKPYLDKVESKLGPISNLVKSKTAPVSSTAGPQTASTSKLAADVPLEPESKAYTSSA QVMPEVPQHEPSTTQEFNVDELSNELKKSTKNLQNELEKNNA GGGGGGEQKLISEEDLGSGLEVLFQGPGSGDYKDHDGDYKDH DIDYKDDDDK The following modifications were considered: Carbamidomethyl (C, fixed), TMT10plex (K, fixed), Acetyl (N-term, variable), Oxidation (M, variable) and TMT10plex (N-term, variable).



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