XDIA: improving on the label-free data-independent analysis

Carvalho, Paulo C.; Han, Xuemei; Xu, Tao; Cociorva, Daniel; Carvalho, Maria da Glória da Costa; Barbosa, Valmir C.; Yates, John R.

doi:10.1093/bioinformatics/btq031

Cited by 88 publications

(66 citation statements)

References 5 publications

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“…Those methods operate via unbiased "data-independent acquisition" (DIA), in the cyclic recording, throughout the LC time range, of consecutive survey scans and fragment ion spectra for all the precursors contained in predetermined isolation windows. Various implementations of DIA methods have already been described using isolation windows of various widths, ranging from the complete m/z range to few Daltons (17)(18)(19)(20)(21)(22)(23)(24) (Table I). Using such scans, the link between the fragment ions and the precursors from which they originate is lost, complicating the analysis of the acquired data sets.…”

Section: Liquid Chromatography Coupled To Tandem Mass Spectrometry (Lmentioning

confidence: 99%

“…1B). Similar to other windowed DIA methods (20,23), consecutive swaths were acquired with some precursor isolation window overlap to ensure the transfer of the complete isotopic pattern of any given precursor ion in at least one isolation window and to thereby maintain optimal correlation between parent and fragment isotopes peaks at any LC time point (supplemental Fig. S1, a-f).…”

Section: Data-independent Data Acquisitionmentioning

confidence: 99%

See 1 more Smart Citation

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

Gillet

Navarro

Tate³

et al. 2012

Molecular & Cellular Proteomics

2,384

2,636

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Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-offlight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400 -1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics. Molecular & Cellular Proteomics 11: 10.1074/mcp.O111.016717, 1-17, 2012. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)1 is considered the method of choice for the identification and quantification of proteins and proteomes (1-4) and for the analysis of metabolites, lipids, glycans, and many other types of (bio)molecules. For proteomics, two main LC-MS/MS strategies have been used thus far. They have in common that the sample proteins are converted by proteolysis into peptides, which are then separated by (capillary) liquid chromatography. They differ in the mass spectrometric method used. The first and most widely used strategy is known as shotgun or discovery proteomics. For this method, the MS instrument is operated in data-dependent acquisition (DDA) mode, where fragment ion (MS2) spectra for selected precursor ions detectable in a survey (MS1) scan are generated (5). The resulting fragment ion spectra are then assigned to their corresponding peptide sequences by sequence data...

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Section: Liquid Chromatography Coupled To Tandem Mass Spectrometry (Lmentioning

confidence: 99%

Section: Data-independent Data Acquisitionmentioning

confidence: 99%

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

Gillet

Navarro

Tate³

et al. 2012

Molecular & Cellular Proteomics

2,384

2,636

View full text Add to dashboard Cite

show abstract

“…Thus, they are DIA. DIA, data-independent analysis/acquisition; SWATH, sequential window acquisition of all theoretical mass spectra MS1 and sequential MS2 windowed acquisitions [5]. At the time, windows of 20 m/z overlapping by 1 m/z.…”

Section: Abstract: Data-dependent Analysis / Data-independent Analysismentioning

confidence: 99%

DIA is not a new mass spectrometry acquisition method

2017

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Contrary to what is being said by several colleagues (and even advertised), data-independent analysis/acquisition (DIA) is not a new mass spectrometry acquisition method. Here we draw a timeline of events showing that DIA has been around since the early 2000s. Keywords: Data-dependent analysis / Data-independent analysisIt is commonly heard in conference talks or read in a few papers [1] that data-independent analysis/acquisition (DIA) is a new way of analyzing proteomes in a shotgun fashion. That is not quite accurate. Back in 2004, Venable et al. proposed a modified method for MS/MS "based on the sequential isolation and fragmentation of precursor windows (of 10 m/z)", which was referred as "not data dependent" [2]. About a year later, Silva et al., while looking for a precise relative quantification method, proposed the quantitation of peptides based on MS acquisition without any previous isolation [3]. Here, they proposed to alternate the collision energy in low and high energy during MS acquisition. These data are then collected in two channels: one containing the signals of intact peptides and the other the chimeric fragmented peptides [4]. This is the so called MS E method.Both methods, described more than 10 years ago, are not dependent on MS data for fragmentation. Thus, they are DIA. DIA, data-independent analysis/acquisition; SWATH, sequential window acquisition of all theoretical mass spectra MS1 and sequential MS2 windowed acquisitions [5]. At the time, windows of 20 m/z overlapping by 1 m/z. More recently, the concept of SWATH (sequential window acquisition of all theoretical mass spectra) reverberated the use of DIA [6]. Gillet et al., while describing SWATH, actually cited Venable's paper from 2004, supporting the idea that DIA was already something existent. Not only that, but a simple PubMed search can show hundreds of papers using MS E in the past decade, in all kinds of different questions. The main differences in these methods rely on the data processing (spectral library vs. deconvolution) and the use or not of a selection window in the quadrupole. It is true though that SWATH has awaken DIA as a possibility for any mass spectrometer, in times where DDA started reaching its limits in proteomics, which is the focus on the identification of high-abundant proteins in a limited dynamic range. Another contributing factor was the significant developments around MS-based targeted proteomics using SRM and, more recently, PRM [7]. Empathy for DIA became stronger, and new developments on algorithms to deal with DIA data such as and Skyline DIA is now evolving even more. A few months ago, a new strategy proposed multiplexing narrowband and wideband DIA acquisitions in a single analytical workflow [12]. One could risk saying that this is a combination of SWATH and MS E . This multimode acquisition (MMA) strategy would avoid DIA drawbacks on sensitivity and chimeric C

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“…Alternatively, spectra deconvolution approaches have been applied to separate co-eluting peptides transmitted through the same mass-isolation window followed by using MS/MS database searching programs for peptide and protein identification. To date, tandem spectra have been deconvoluted by the following procedures: a) matching precursors detected with similar elution time that fall within the mass-isolation window of MS/MS spectra generated -thereby reassigning mass-isolation windows with vast numbers of possible precursor m/z values with accurate mass values; [18] b) eliminating fragment-ions in MS/MS spectra that do not have similar chromatographic behavior (e.g., lift-off, touchdown, or maximum elution time); [19] c) matching fragment-ions with similar elution profiles to precursors with similar elution time that fall within the same isolation window; [20][21] d) a two-stage identification procedure where (b) and (c) are applied and the search results from both rounds of identification are combined. [22] In this study, we assessed sequential windowed precursor acquisition with three isolation window sizes and various precursor ranges in trypsin digests from E. coli on a Sciex 5600+ QTOF to provide an optimized prototype DIA method for maximizing sensitivity in single injection LC-DIA studies.…”

Section: Introductionmentioning

confidence: 99%

Systematic evaluation of data‐independent acquisition for sensitive and reproducible proteomics‐a prototype design for a single injection assay

Heaven¹,

Funk²,

Cobbs³

et al. 2016

J. Mass Spectrom.

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Data-independent acquisition (DIA) based proteomics has become increasingly complicated in recent years due to the vast number of workflows described, coupled with a lack of studies indicating a rational framework for selecting effective settings to use. To address this issue and provide a resource for the proteomics community, we compared twelve DIA methods that assay tryptic peptides using various mass-isolation windows. Our findings indicate the most sensitive single injection LC-DIA method uses 6 m/z isolation windows to analyze the densely populated tryptic peptide range from 450-730 m/z, which allowed quantification of 4,465 E. coli peptides. In contrast, using the sequential windowed acquisition of all theoretical fragment-ions (SWATH) approach with 26 m/z isolation windows across the entire 400-1200 m/z range, allowed quantification of only 3,309 peptides. This reduced sensitivity with 26 m/z windows is caused by an increase in co-eluting compounds with similar precursor values detected in the same tandem MS spectra, which lowers the signal-to-noise of peptide fragment-ion chromatograms and reduces the amount of low abundance peptides that can be quantified from 410-920 m/z. Above 920 m/z, more peptides were quantified with 26 m/z windows due to substantial peptide 13 C isotope distributions that parse peptide ions into separate isolation windows. Since reproducible quantification has been a long-standing aim of quantitative proteomics, and is a so-called trait of DIA, we sought to determine whether precursor-level chromatograms used in some methods rather than their fragment-level counterparts have similar precision. Our data show extracted fragmention chromatograms are the reason DIA provides superior reproducibility.

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XDIA: improving on the label-free data-independent analysis

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 88 publications

References 5 publications

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

DIA is not a new mass spectrometry acquisition method

Systematic evaluation of data‐independent acquisition for sensitive and reproducible proteomics‐a prototype design for a single injection assay

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