GNPS - Glutamicibacter_arilaitensis_Penicillium_solitum_CoCulture
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF fleX
ORGANISM(S): Penicillium Solitum (ncbitaxon:60172) Glutamicibacter Arilaitensis (ncbitaxon:256701)
SUBMITTER: 
Laura M. Sanchez
PROVIDER: MSV000097837 | GNPS | Thu May 08 19:04:00 BST 2025
REPOSITORIES: GNPS
Similar Datasets
Project description:This dataset contains matrix assisted laser desorption/ionization imaging parallel reaction monitoring - parallel accumulation serial fragmentation (MALDI iprm-PASEF) data from a co-culture of G. arilaitensis(JB182) and P. solitum (#12). File descriptions are as follows:
MALDI-TIMS-MS1: 250321_JB182_Pen12.d
MALDI iprm-PASEF with precursor list 1: 250321_JB182_Pen12_Precursors1.d
MALDI iprm-PASEF with precursor list 2: 250321_JB182_Pen12_Precursors2.d
MALDI iprm-PASEF with precursor list 3: 250321_JB182_Pen12_Precursors3.d
imzML versions of each of the raw data files can be found with the corresponding file names in the Supplementary Files Folder.
2025-05-08 | MSV000097836 | MassIVE
Project description:This dataset contains matrix assisted laser desorption/ionization imaging parallel reaction monitoring - parallel accumulation serial fragmentation (MALDI iprm-PASEF) data from a co-culture of G. arilaitensis(JB182) and P. solitum (#12). File descriptions are as follows: MALDI-TIMS-MS1: 250321_JB182_Pen12.d; MALDI iprm-PASEF with precursor list 1- 250321_JB182_Pen12_Precursors1.d; MALDI iprm-PASEF with precursor list 2- 250321_JB182_Pen12_Precursors2.d; MALDI iprm-PASEF with precursor list 3- 250321_JB182_Pen12_Precursors3.d. imzML versions of each of the raw data files can be found with the corresponding file names in the Supplementary Files Folder.
2025-05-08 | MSV000097837 | MassIVE
Project description:Data independent acquisition methods have become increasingly popular in mass spectrometry (MS)-based proteomics because they enable parallel and continuous acquisition of fragment spectra. However, these advantages come with the challenge of correctly reconstructing the precursor-fragment relationship in these highly multiplexed spectra for reliable identification and quantification. Here we introduce a scan mode for the combination of trapped ion mobility spectrometry (TIMS) with parallel accumulation – serial fragmentation (PASEF) that naturally and continuously follows the ion cloud in ion mobility and peptide mass dimensions as opposed to the step functions we employed before. Termed synchro-PASEF, it increases fragment yield several fold at sub-second cycle times. The quadrupole selection window moves synchronously through the mass and ion mobility range, deconvoluting the DIA spectra and defining precursor-quadrupole relationships. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor – fragment relationship in ion mobility and mass dimensions. Importantly, the two parts of the fragment ion transitions in synchro-PASEF provide a further dimension of specificity via a lock and key mechanism. This is especially advantageous for quantification, where signals from interfering precursors in the dia selection window only affect the top or bottom part of the fragment ion, allowing them to be filtered out. In this paper, we establish the defining features of synchro-PASEF and explore its potential for proteomics analyses.
2023-03-10 | PXD037766 | Pride
Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
All Datasets are uploaded separateley. This file contains the dataset for mouse kidney MS1 data.
On the same slice a mouse liver was measured for a different experiment.
2024-11-11 | MSV000096373 | MassIVE
Project description:NIST1950 SRM samples analyzed on timsTOF Pro in Parallel-Accumulation Serial Fragmentation (PASEF) mode. Data provided by Bruker's team.
2019-10-01 | MSV000084402 | GNPS
Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
The datasets will be uploaded separately. This data set contains the PDX MS1 data. There are two tissues vissible on the.tif image. The relevant one is on the left side of the slide (away from the barcode).
2024-11-11 | MSV000096374 | MassIVE
Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
The datasets will be uploaded separately. This data set contains the Kidney MSMS data. There is an additional Liver tissue vissible on the .tif image. This was used for another experiment
2024-11-11 | MSV000096375 | MassIVE
Project description:RATIONALE
In spatial proteomics, matrix-assisted laser desorption/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS/MS imaging.
METHODS
An initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS/MS imaging. Finally, precursors are identified by peptide to spectrum matching.
RESULTS
This study presents the first multiplexed MALDI TIMS MS/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.
CONCLUSIONS
In the present study, we demonstrate the feasibility of TIMS-based MALDI MS/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.
The datasets will be uploaded separately. This data set contains the PDX MSMS data. There are two tissues vissible on the.tif image. The relevant one is on the left side of the slide (away from the barcode).
2024-11-11 | MSV000096376 | MassIVE
Project description:In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time-of-fight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive due to its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation – serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 800,000 fragmentation spectra in standard 120 min LC runs are easily achievable, which can be used for near exhaustive precursor selection in complex mixtures or re-sequencing weak precursors. MaxQuant identified more than 6,000 proteins in single run HeLa analyses without matching to a library, and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,000 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.
2018-11-06 | PXD010012 | Pride
Project description:Metaproteomics is gaining momentum in microbiome research due to the multi-dimensional information it provides. However, current approaches have reached their detection limits. We present a highly-sensitive metaproteomic workflow using the extra information captured by Parallel Accumulation-Serial Fragmentation (PASEF) technology. The comparison of different acquisition modes and data analysis software packages showed that DIA-PASEF and DIA-NN doubled protein identifications in the mouse gut microbiota and, importantly, also in the host proteome compared to DDA-PASEF. DIA-PASEF significantly improved peptide detection reproducibility and quantification accuracy, which resulted in more than twofold identified taxa, reaching depths comparable to metagenomic studies. Consequently, DIA-PASEF exhibited improved coverage of functional networks revealing 131 additional pathways compared to DDA-PASEF. We applied our optimized workflow to a pre-clinical mouse model of chronic pain, in which we deciphered novel host-microbiome interactions. In summary, we present here a metaproteomic approach that paves the way for increasing the functional characterization of microbiome ecosystems and is applicable to diverse fields of biological research.
2023-05-04 | PXD040947 | Pride