PXD029416

PXD029416 is an original dataset announced via ProteomeXchange.

Title	Formic acid and Acetic acid for peptide LC-MS
Description	Despite 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.
HostingRepository	jPOST
AnnounceDate	2022-12-10
AnnouncementXML	Submission_2022-12-15_14:38:17.813.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kosuke Ogata
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; alpha-amino acetylated residue; O4'-phospho-L-tyrosine; O-phospho-L-threonine; O-phospho-L-serine
Instrument	instrument; TripleTOF 5600; instrument

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-29 00:01:53	ID requested
⏵ 1	2022-12-15 14:38:18	announced

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]

submitter keyword: Reversed phase chromatography, ESI, peptide, phosphopeptide

Oleg Krokhin
lab head
Kosuke Ogata
contact affiliation	Kyoto university
dataset submitter

jPOST dataset URI

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