Dataset Information

In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides

ABSTRACT: Cross-linking/mass spectrometry has undergone a maturation process akin to standard proteomics by adapting key methods such as false discovery rate control and quantification. A seldom-used search setting in proteomics is the consideration of multiple (lighter) alternative values for the monoisotopic precursor mass to compensate for possible misassignments of the monoisotopic peak. Here, we show that monoisotopic peak assignment is a major weakness of current data handling approaches in cross-linking. Cross-linked peptides often have high precursor masses, which reduces the presence of the monoisotopic peak in the isotope envelope. Paired with generally low peak intensity, this generates a challenge that may not be completely solvable by precursor mass assignment routines. We therefore took an alternative route by ‘in-search assignment of the monoisotopic peak’ in the cross-linking search tool Xi (Xi-MPA), which considers multiple precursor masses during database search. We compare and evaluate the performance of established preprocessing workflows that partly correct the monoisotopic peak and Xi-MPA on three publicly available datasets. Xi-MPA always delivered the highest number of identifications with ~2 to 4-fold increase of PSMs without compromising identification accuracy as determined by FDR estimation and comparison to crystallographic models.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Chaetomium Thermophilum (strain Dsm 1495 / Cbs 144.50 / Imi 039719)

SUBMITTER: Swantje Lenz

LAB HEAD: Juri Rappsilber

PROVIDER: PXD011121 | Pride | 2019-04-05

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	B160803_02_Lumos_LK_IN_190_PC_BS3_HCD_DT_1.raw	Raw
	B160803_03_Lumos_LK_IN_190_PC_BS3_EThcD_DT_1.raw	Raw
	B160803_04_Lumos_LK_IN_190_PC_BS3_ETciD_DT_1.raw	Raw
	B160803_05_Lumos_LK_IN_190_PC_BS3_CID_DT_1.raw	Raw
	B160803_07_Lumos_LK_IN_190_PC_BS3_HCD_DT_2.raw	Raw

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Publications

In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides.

Lenz Swantje S Giese Sven H SH Fischer Lutz L Rappsilber Juri J

Journal of proteome research 20181024 11

Cross-linking/mass spectrometry has undergone a maturation process akin to standard proteomics by adapting key methods such as false discovery rate control and quantification. A poorly evaluated search setting in proteomics is the consideration of multiple (lighter) alternative values for the monoisotopic precursor mass to compensate for possible misassignments of the monoisotopic peak. Here, we show that monoisotopic peak assignment is a major weakness of current data handling approaches in cro ...[more]

PMID: 30293428

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