Investigation of Effects of the Spectral Library on Analysis of diaPASEF Data

Wen, Chengwen; Gan, Guohong; Xu, Xiao; Lin, Guanzhong; Chen, Xi; Wu, Yaying; Xu, Zheni; Wang, Jinglin; Xie, Changchuan; Wang, Hongrui; Zhong, Chuan-Qi

doi:10.1021/acs.jproteome.1c00899

Cited by 12 publications

(13 citation statements)

References 38 publications

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“…When compared, 1182 proteins were identified in both approaches, 485 proteins (27%) were additionally identified when using the spectral library (Figure 4B). The increased protein identifications are in agreement with another comparison performed recently on diaPASEF data [37].…”

Section: Impact Of Using a Spectral Library On Protein Identificationsupporting

confidence: 91%

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

et al. 2023

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A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing fourdimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio, and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on tim-sTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer's disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.

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Section: Impact Of Using a Spectral Library On Protein Identificationsupporting

confidence: 91%

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

et al. 2023

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“…S3 , technical versus biological replicates). CVs at the neuropeptide level, as seen in our experiments, are typically higher than those observed in proteomics workflows ( 76 , 77 ), especially for low-abundant neuropeptides ( supplemental Fig. S3 ).…”

Section: Discussionmentioning

confidence: 42%

Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes

Cockx

Bael

Boelen

et al. 2023

Molecular & Cellular Proteomics

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“…A spectral library is usually important for DIA MS data analysis. Compared with library-free analysis strategy (directDIA), an appropriate spectral library can remarkably increase the quantified precursors and proteins from the same MS data [47,48]. In our work, we found that compared with directDIA, protein identification can indeed benefit from a project-specific spectral library, especially as the amount of starting material increases.…”

Section: Discussionmentioning

confidence: 86%

Ultrasensitive Proteomics Depicted an In-depth Landscape for Mouse Embryo

Gu¹,

Li²,

Zhu

et al. 2023

Preprint

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In recent years, single-cell or low-input multi-omics techniques have brought a revolution in the study of pre-implantation embryo development. However, single-cell or low-input proteome research in this field is relatively underdeveloped, due to the limited source of mammalian embryo samples, the objective reality of high abundance zona pellucida proteins, and the lack of hypersensitive proteome technology. Here, a comprehensive solution of ultrasensitive proteome technology was developed for single-cell or low-input mouse embryos. Both deep coverage route and high-throughput route could significantly reduce the starting material and enhance the proteomic depth without any customized instrument. Using the deep coverage route, an average of 2,665 or 4,585 protein groups can be identified from 1 or 20 mouse zygotes respectively. Using the high-throughput route, 300 single mouse zygotes can be analysis in 8 days with an average of 2,371 proteins identified. With its popularization, we believe researchers can choose deep coverage or high-throughput technology routes according to their own conditions.

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Investigation of Effects of the Spectral Library on Analysis of diaPASEF Data

Cited by 12 publications

References 38 publications

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes

Ultrasensitive Proteomics Depicted an In-depth Landscape for Mouse Embryo

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