Dataset Information

Confident identification of citrullination and carbamylation assisted by peptide retention time prediction

ABSTRACT: We used 2D-LC-MS/MS methods to examine the impact of the biologically important PTM citrullination and its analogue carbamylation on peptide retention. Three first-dimension separation systems were evaluated: high-pH, HILIC and SCX, with the instrument interface separation happening at low-pH RP for all three. As we have well developed models for all of these separation systems, our goal was to enhance peptide assignment using retention prediction. We induced the PTMs citrullination and carbamylation on a mixture of integrins using PAD2 and urea respectively. As deamidation often confounds the assignment of citrullination we also examined its retention properties. Identified peptides were organized into pairwise modified and unmodified counterparts to assign shifts in both separation dimensions. Under both HILIC and SCX separations peptide retention times were significantly shifted by both PTMs, with SCX exhibiting shift magnitudes greater than the prediction error of our current computational model. Conversely deamidation's retention impact across all separation models was small. These findings gave us the capacity to assign the target PTMs without needing to identify their unmodified counterparts. We applied this approach to an un-depleted sample of human synovial fluid from an RA patient, identifying 14 citrullinated peptides which were supported by prior RA literature.

INSTRUMENT(S): TripleTOF 5600, Q Exactive HF

ORGANISM(S): Bos Taurus (ncbitaxon:9913) Sus Scrofa (ncbitaxon:9823) Gallus Gallus (ncbitaxon:9031) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Oleg Krokhin

PROVIDER: MSV000086214 | MassIVE |

REPOSITORIES: MassIVE

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Publications

Compendium of Chromatographic Behavior of Post-translationally and Chemically Modified Peptides in Bottom-Up Proteomic Experiments.

Neale Quinn Q Prefontaine Alexandre A Battellino Taylor T Mizero Benilde B Yeung Darien D Spicer Victor V Budisa Nediljko N Perreault Helene H Zahedi Rene P RP Krokhin Oleg V OV

Analytical chemistry 20230922 39

We have systematically evaluated the chromatographic behavior of post-translationally/chemically modified peptides using data spanning over 70 of the most relevant modifications. These retention properties were measured for standard bottom-up proteomic settings (fully porous C18 separation media, 0.1% formic acid as ion-pairing modifier) using collections of modified/nonmodified peptide pairs. These pairs were generated by spontaneous degradation, chemical or enzymatic treatment, analysis of syn ...[more]

PMID: 37739932

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