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A bespoke analytical workflow for the confident identification of sulfopeptides and their discrimination from phosphopeptides

https://doi.org/10.1101/2023.07.15.549150

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Negative Ion Mass Spectra of [M-H]− Ions Derived From Caeridin and Dynastin Peptides. Internal Backbone Cleavages Directed Through Asp and Asn Residues

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Probability-based protein identification by searching sequence databases using mass spectrometry data

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The primary structure of human secretogranin I (chromogranin B): comparison with chromogranin A reveals homologous terminal domains and a large intervening variable region.

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Tyrosine O‐sulfation promotes proteolytic processing of progastrin.

inferredcites →https://doi.org/10.1002/jms.1599openalex-snapshot

Phosphopeptide fragmentation and analysis by mass spectrometry

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Collision‐induced fragmentations of the (M‐H)− parent anions of underivatized peptides: An aid to structure determination and some unusual negative ion cleavages

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Reactions of polypeptide ions with electrons in the gas phase

inferredcites →https://doi.org/10.1002/mas.21501openalex-snapshot

Negative ion cleavages of (M–H)− anions of peptides. Part 3. Post‐translational modifications

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WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT

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Modification‐specific proteomics: Strategies for characterization of post‐translational modifications using enrichment techniques

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A summary of the measured p K values of the ionizable groups in folded proteins

inferredcites →https://doi.org/10.1002/rcm.3254openalex-snapshot

Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques

inferredcites →https://doi.org/10.1002/rcm.4950openalex-snapshot

Analysis of sulfated peptides from the skin secretion of the Pachymedusa dacnicolor frog using IMAC ‐Ga enrichment and high‐resolution mass spectrometry

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Comparison of the positive and negative ion electrospray mass spectra of some small peptides containing pyroglutamate

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Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography

inferredcites →https://doi.org/10.1007/978-1-60327-834-8_4openalex-snapshot

Enrichment and Characterization of Phosphopeptides by Immobilized Metal Affinity Chromatography (IMAC) and Mass Spectrometry

inferredcites →https://doi.org/10.1007/s00726-006-0443-6openalex-snapshot

Focus on phosphohistidine

inferredcites →https://doi.org/10.1007/s13361-011-0248-zopenalex-snapshot

Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

inferredcites →https://doi.org/10.1007/s13361-013-0770-2openalex-snapshot

Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C -Terminal Residue

inferredcites →https://doi.org/10.1007/s13361-014-0910-3openalex-snapshot

Direct Identification of Tyrosine Sulfation by using Ultraviolet Photodissociation Mass Spectrometry

inferredcites →https://doi.org/10.1007/s13361-017-1794-9openalex-snapshot

Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides

inferredcites →https://doi.org/10.1007/s13361-017-1854-1openalex-snapshot

Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry

inferredcites →https://doi.org/10.1016/0014-5793(94)00907-4openalex-snapshot

Tyrosine‐rich acidic matrix protein (TRAMP) is a tyrosine‐sulphated and widely distributed protein of the extracellular matrix

inferredcites →https://doi.org/10.1016/0014-5793(95)00710-qopenalex-snapshot

Separation of phospho‐ and non‐phosphopeptides using reverse phase column chromatography

inferredcites →https://doi.org/10.1016/j.ab.2005.06.047openalex-snapshot

Ion-selective enrichment of tyrosine-sulfated peptides from complex protein digests

inferredcites →https://doi.org/10.1016/j.ab.2006.12.003openalex-snapshot

Stability of tyrosine sulfate in acidic solutions

inferredcites →https://doi.org/10.1016/j.aca.2021.338857openalex-snapshot

A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis

inferredcites →https://doi.org/10.1016/j.bbapap.2006.07.002openalex-snapshot

Protein sulfation analysis—A primer

inferredcites →https://doi.org/10.1016/j.cell.2006.09.026openalex-snapshot

Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks

inferredcites →https://doi.org/10.1016/j.ijms.2015.05.005openalex-snapshot

Formation of c- and z-ions due to preferential cleavage at the NC bond of Xxx-Asp/Asn residues in negative-ion CID of peptides

inferredcites →https://doi.org/10.1016/j.ijms.2019.116186openalex-snapshot

Characterization of collision-induced dissociation of deprotonated peptides of 4–16 amino acids using high-resolution mass spectrometry

inferredcites →https://doi.org/10.1016/j.jasms.2007.06.002openalex-snapshot

Sulfopeptide fragmentation in electron-capture and electron-transfer dissociation

inferredcites →https://doi.org/10.1016/j.jasms.2008.05.019openalex-snapshot

QCAL—a novel standard for assessing instrument conditions for proteome analysis

inferredcites →https://doi.org/10.1016/j.ygcen.2007.12.006openalex-snapshot

Early postnatal pulmonary failure and primary hypothyroidism in mice with combined TPST-1 and TPST-2 deficiency

inferredcites →https://doi.org/10.1016/s0006-3495(01)75850-xopenalex-snapshot

Tyrosine Sulfation Enhances but Is Not Required for PSGL-1 Rolling Adhesion on P-Selectin

inferredcites →https://doi.org/10.1016/s0021-9258(17)34149-2openalex-snapshot

Alternative splicing governs sulfation of tyrosine or oligosaccharide on peptidylglycine alpha-amidating monooxygenase.

inferredcites →https://doi.org/10.1016/s0021-9258(17)35234-1openalex-snapshot

Sulfation of Tyr1680 of human blood coagulation factor VIII is essential for the interaction of factor VIII with von Willebrand factor.

inferredcites →https://doi.org/10.1016/s0021-9258(17)43311-4openalex-snapshot

Synthetic tyrosine polymers as substrates and inhibitors of tyrosine-specific protein kinases.

inferredcites →https://doi.org/10.1016/s0021-9258(18)61471-1openalex-snapshot

Sulfation of a tyrosine residue in the plasmin-binding domain of alpha 2-antiplasmin.

inferredcites →https://doi.org/10.1016/s0021-9258(18)88991-8openalex-snapshot

Tyrosine sulfation of yolk proteins 1, 2, and 3 in Drosophila melanogaster.

inferredcites →https://doi.org/10.1016/s0021-9258(19)38920-3openalex-snapshot

Analysis of the substrate specificity of tyrosylprotein sulfotransferase using synthetic peptides.

inferredcites →https://doi.org/10.1016/s0092-8674(00)80577-2openalex-snapshot

Tyrosine Sulfation of the Amino Terminus of CCR5 Facilitates HIV-1 Entry

inferredcites →https://doi.org/10.1021/ac0400414openalex-snapshot

Protein Tyrosine-O-Sulfation Analysis by Exhaustive Product Ion Scanning with Minimum Collision Offset in a NanoESI Q-TOF Tandem Mass Spectrometer

inferredcites →https://doi.org/10.1021/ac061352copenalex-snapshot

Electron Capture Dissociation of Tyrosine O-Sulfated Peptides Complexed with Divalent Metal Cations

inferredcites →https://doi.org/10.1021/ac061457fopenalex-snapshot

Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors

inferredcites →https://doi.org/10.1021/ac203430uopenalex-snapshot

Analysis of the Acidic Proteome with Negative Electron-Transfer Dissociation Mass Spectrometry

inferredcites →https://doi.org/10.1021/ac301536ropenalex-snapshot

Characterization of O-Sulfopeptides by Negative Ion Mode Tandem Mass Spectrometry: Superior Performance of Negative Ion Electron Capture Dissociation

inferredcites →https://doi.org/10.1021/ac3025366openalex-snapshot

Toward Full Peptide Sequence Coverage by Dual Fragmentation Combining Electron-Transfer and Higher-Energy Collision Dissociation Tandem Mass Spectrometry

inferredcites →https://doi.org/10.1021/acs.analchem.0c01342openalex-snapshot

Development of a Sample-Preparation Workflow for Sulfopeptide Enrichment: From Target Analysis to Challenges in Shotgun Sulfoproteomics

inferredcites →https://doi.org/10.1021/acs.analchem.1c05621openalex-snapshot

The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry

inferredcites →https://doi.org/10.1021/acs.analchem.5b04123openalex-snapshot

Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

inferredcites →https://doi.org/10.1021/acs.jproteome.0c00508openalex-snapshot

Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment

inferredcites →https://doi.org/10.1021/acs.jproteome.7b00337openalex-snapshot

Evaluation of Parameters for Confident Phosphorylation Site Localization Using an Orbitrap Fusion Tribrid Mass Spectrometer

inferredcites →https://doi.org/10.1021/bi800965mopenalex-snapshot

Sequential Tyrosine Sulfation of CXCR4 by Tyrosylprotein Sulfotransferases

inferredcites →https://doi.org/10.1021/la980894popenalex-snapshot

Phosphate Adsorption onto TiO 2 from Aqueous Solutions: An in Situ Internal Reflection Infrared Spectroscopic Study

inferredcites →https://doi.org/10.1021/pr200153kopenalex-snapshot

PeaksPTM: Mass Spectrometry-Based Identification of Peptides with Unspecified Modifications

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Stabilization of a tyrosine O‐sulfate residue by a cationic functional group: formation of a conjugate acid–base pair

inferredcites →https://doi.org/10.1038/204931a0openalex-snapshot

The antral Hormone Gastrin: Structure of Gastrin

inferredcites →https://doi.org/10.1038/nbt.2377openalex-snapshot

A cross-platform toolkit for mass spectrometry and proteomics

inferredcites →https://doi.org/10.1038/ncb0502-e127openalex-snapshot

The origins of protein phosphorylation

inferredcites →https://doi.org/10.1038/nmeth1056openalex-snapshot

Determination of the sites of tyrosine O-sulfation in peptides and proteins

inferredcites →https://doi.org/10.1038/nprot.2006.185openalex-snapshot

Highly selective enrichment of phosphorylated peptides using titanium dioxide

inferredcites →https://doi.org/10.1038/nprot.2008.211openalex-snapshot

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

inferredcites →https://doi.org/10.1038/s41598-021-81986-yopenalex-snapshot

Proteome-wide profiling and mapping of post translational modifications in human hearts

inferredcites →https://doi.org/10.1042/bcj20180265openalex-snapshot

New tools for carbohydrate sulfation analysis: heparan sulfate 2- O -sulfotransferase (HS2ST) is a target for small-molecule protein kinase inhibitors

inferredcites →https://doi.org/10.1042/bcj20180266openalex-snapshot

New tools for evaluating protein tyrosine sulfation: tyrosylprotein sulfotransferases (TPSTs) are novel targets for RAF protein kinase inhibitors

inferredcites →https://doi.org/10.1042/bcj20200309openalex-snapshot

Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics

inferredcites →https://doi.org/10.1042/bcj20200952openalex-snapshot

Mobility shift-based electrophoresis coupled with fluorescent detection enables real-time enzyme analysis of carbohydrate sulfatase activity

inferredcites →https://doi.org/10.1042/bcj20220089openalex-snapshot

Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance

inferredcites →https://doi.org/10.1042/bcj20220102openalex-snapshot

Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway

inferredcites →https://doi.org/10.1053/j.gastro.2021.12.260openalex-snapshot

Inhibition of p53 Sulfoconjugation Prevents Oxidative Hepatotoxicity and Acute Liver Failure

inferredcites →https://doi.org/10.1073/pnas.82.18.6143openalex-snapshot

(Glu62, Ala30, Tyr8)n serves as high-affinity substrate for tyrosylprotein sulfotransferase: a Golgi enzyme.

inferredcites →https://doi.org/10.1073/pnas.97.11.5762openalex-snapshot

Specific interaction of CCR5 amino-terminal domain peptides containing sulfotyrosines with HIV-1 envelope glycoprotein gp120

inferredcites →https://doi.org/10.1074/jbc.m306061200openalex-snapshot

Sulfation of Tyrosine 174 in the Human C3a Receptor Is Essential for Binding of C3a Anaphylatoxin

inferredcites →https://doi.org/10.1074/jbc.m308689200openalex-snapshot

Identification of Tyrosine Sulfation in Extracellular Leucine-rich Repeat Proteins Using Mass Spectrometry

inferredcites →https://doi.org/10.1074/jbc.m808179200openalex-snapshot

Structure of the Tyrosine-sulfated C5a Receptor N Terminus in Complex with Chemotaxis Inhibitory Protein of Staphylococcus aureus

inferredcites →https://doi.org/10.1074/jbc.r300008200openalex-snapshot

The Biology and Enzymology of Protein Tyrosine O-Sulfation

inferredcites →https://doi.org/10.1074/mcp.m115.049726openalex-snapshot

The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD)

inferredcites →https://doi.org/10.1074/mcp.m500135-mcp200openalex-snapshot

Phosphorylation Analysis by Mass Spectrometry

inferredcites →https://doi.org/10.1074/mcp.m600314-mcp200openalex-snapshot

Using Phage Display to Select Antibodies Recognizing Post-translational Modifications Independently of Sequence Context

inferredcites →https://doi.org/10.1074/mcp.t500007-mcp200openalex-snapshot

Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns

inferredcites →https://doi.org/10.1074/mcp.tir117.000516openalex-snapshot

Stable Isotope Dynamic Labeling of Secretomes (SIDLS) Identifies Authentic Secretory Proteins Released by Cancer and Stromal Cells

inferredcites →https://doi.org/10.1084/jem.193.9.1059openalex-snapshot

Sulfated Tyrosines Contribute to the Formation of the C5a Docking Site of the Human C5a Anaphylatoxin Receptor

inferredcites →https://doi.org/10.1093/emboj/21.4.504openalex-snapshot

Tyrosine sulfation is required for agonist recognition by glycoprotein hormone receptors

inferredcites →https://doi.org/10.1093/nar/gkab1062openalex-snapshot

HMDB 5.0: the Human Metabolome Database for 2022

inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot

UniProt: the Universal Protein knowledgebase

inferredcites →https://doi.org/10.1126/science.1075762openalex-snapshot

The Protein Kinase Complement of the Human Genome

inferredcites →https://doi.org/10.1126/scisignal.aax2713openalex-snapshot

Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity

inferredcites →https://doi.org/10.1126/scisignal.abf6685openalex-snapshot

Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α

inferredcites →https://doi.org/10.1182/blood.v76.5.946.946openalex-snapshot

Sulfation of tyrosine residues in coagulation factor V

inferredcites →https://doi.org/10.1371/journal.pgen.1005885openalex-snapshot

Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization

inferredcites →https://doi.org/10.1371/journal.pone.0057804openalex-snapshot

Hydrogen Bond Strengths in Phosphorylated and Sulfated Amino Acid Residues

inferredcites →https://doi.org/10.15252/embj.2018100847openalex-snapshot

Strong anion exchange‐mediated phosphoproteomics reveals extensive human non‐canonical phosphorylation

inferredcites →https://doi.org/10.2144/000112201openalex-snapshot

Analysis of Posttranslational Modifications of Proteins by Tandem Mass Spectrometry

inferredcites →https://doi.org/10.2174/138920309789630598openalex-snapshot

Focus on Phosphoarginine and Phospholysine

inferredcites →https://doi.org/10.3892/ijmm.2017.3036openalex-snapshot

The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review)

inferredcites →https://doi.org/10.4049/jimmunol.165.9.5295openalex-snapshot

Monocyte Chemotactic Protein-1 Receptor CCR2B Is a Glycoprotein That Has Tyrosine Sulfation in a Conserved Extracellular N-Terminal Region

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1039/d3cc02909copenalex-snapshot

Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond

inferred← citeshttps://doi.org/10.7554/elife.92536openalex-snapshot

Redox regulation and dynamic control of brain-selective kinases BRSK1/2 in the AMPK family through cysteine-based mechanisms

inferred← citeshttps://doi.org/10.7554/elife.92536.1openalex-snapshot

Redox Regulation of Brain Selective Kinases BRSK1/2: Implications for Dynamic Control of the Eukaryotic AMPK family through Cys-based mechanisms

inferred← citeshttps://doi.org/10.7554/elife.92536.2openalex-snapshot

Redox Regulation of Brain Selective Kinases BRSK1/2: Implications for Dynamic Control of the Eukaryotic AMPK family through Cys-based mechanisms

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Redox Regulation of Brain Selective Kinases BRSK1/2: Implications for Dynamic Control of the Eukaryotic AMPK family through Cys-based mechanisms

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