MassIVE MSV000094407

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TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics

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Description

E. coli proteins (300 ng) extracted from the sample were analyzed using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) coupled with an Ultimate 3000 (Thermo Fisher Scientific) reversed-phase liquid chromatography (RPLC) separation system with a C2 column (60 cm length, CoAnn Inc.). In the RPLC system, phase A was water with 0.1% formic acid (FA), and phase B was 60% acetonitrile (ACN) and 15% isopropanol (IPA) with 0.1% FA. A 98-min gradient of mobile phase B (0-5 min 5%, 5-7 min for 5% to 35%, 7-10 min for 35% to 50%, 10-97 min for 50% to 80%, 97-98 min from 80% to 99%) was applied with a flow rate of 400 nL/min. E. coli proteins were analyzed using both DDA and DIA modes. In each mode, six runs were performed separately, with each targeting a specific m/z range within the MS1 scan: 720-800, 800-880, 880-960, 960-1040, 1040-1120, and 1120-1200 m/z. MS1 spectra were collected with a resolution of 240,000 (at 200 m/z), 4 microscans, an automatic gain control (AGC) target value of 1x106, and a maximum injection time of 200 ms. MS/MS spectra were obtained with a scan range of 400-2000 m/z, a resolution of 60,000 (at 200 m/z), 1 microscan, an AGC target value of 1x106, and a maximum injection time of 500 ms. Fragmentation was performed using higher-energy collisional dissociation (HCD) with 30% NCE. In the DDA runs, the top six precursor ions from each MS1 scan were isolated with a 3 m/z window for MS/MS analysis. The dynamic exclusion was set to 60 seconds. In the DIA runs, a 4 m/z isolation window was used, resulting in a total of 20 MS/MS spectra for each cycle. Three technical replicates were obtained for each experiment. [doi:10.25345/C5TB0Z615] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: data independent acquisition ; top down proteomics ; TDP ; DIA ; TopPIC ; TopFD ; TopDIA

Contact

Principal Investigators:
(in alphabetical order) 		Xiaowen Liu, Tulane University School of Medicine, United States
Submitting User: ARBasharat
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.