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PXD029416

PXD029416 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleFormic acid and Acetic acid for peptide LC-MS
DescriptionDespite the general acceptance of formic acid as the additive of choice for peptide reversed-phase LC-MS/MS applications, some still argue that the selection of acetic acid represents a better option. To settle this debate, we investigated both the difference in MS sensitivity and chromatographic behaviour of peptides between these two systems. This interlaboratory study was performed using different MS setups and C18 separation media employing both 0.1% formic and 0.5% acetic acid as ion pairing modifier. Relative to formic acid, we find an overall ~2.2-2.5x increase in MS signal and slight decrease in RP LC retention (-0.7% acetonitrile on average) for acetic acid conditions. While these two features have opposing effects on peptide detectability, we find that acetic acid produces up to 60% higher peptide ID output depending on the type of sample. The drop in RPLC retention increases with peptide net charge at acidic pH. MS signal is dependent on the difference between charge of the precursor ion and charge of peptide in solution, favoring species with low pI. Lower peptide retention under acetic acid conditions demonstrates its higher hydrophilicity and as expected, leads to composition and sequence-dependent character of the observed retention shift. A custom version of SSRCalc retention prediction model has been developed to accommodate these charges, with formic and acetic acid models showing identical results independent of the origin of data collection.
HostingRepositoryjPOST
AnnounceDate2022-12-10
AnnouncementXMLSubmission_2022-12-15_14:38:17.813.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKosuke Ogata
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListS-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; alpha-amino acetylated residue; O4'-phospho-L-tyrosine; O-phospho-L-threonine; O-phospho-L-serine
Instrumentinstrument; TripleTOF 5600; instrument
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-10-29 00:01:53ID requested
12022-12-15 14:38:18announced
Publication List
Battellino T, Ogata K, Spicer V, Ishihama Y, Krokhin O, Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid. J Proteome Res, 22(1):272-278(2023) [pubmed]
Keyword List
submitter keyword: Reversed phase chromatography, ESI, peptide, phosphopeptide
Contact List
Oleg Krokhin
lab head
Kosuke Ogata
contact affiliationKyoto university
dataset submitter
Full Dataset Link List
jPOST dataset URI
Dataset FTP location
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