ProSightPD Software

Name: ProSightPD Software
SKU: OPTON-30903

Complete characterization of intact proteoforms to unlock all the biological complexity present in your samples.

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Catalog Number	Description
OPTON-30903	Thermo Scientific ProSightPD software.
OPTON-30918	ProSightPD software.
OPTON-31090	ProSightPD 4.2 software
OPTON-31091	Upgrade ProSightPD 4.1 to ProSightPD 4.2
OPTON-31092	Upgrade ProSightPD before 4.1 to ProSightPD 4.2
OPTON-31093	Upgrade ProSightPD 4.2 from ProSightPC

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Catalog number OPTON-30903

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Description:

Thermo Scientific ProSightPD software.

Perform comprehensive analysis of top-down proteomics data with Thermo Scientific™ ProSightPD™ software. ProSightPD features robust proteomic search engines for proteoform characterization, including proteoforms with PTMs or truncations. ProSightPD software accommodates proteomic data generated by fragmentation techniques present in any Thermo Scientific mass spectrometer. ProSightPD software is the only proteomics software that allows the user to easily search MS/MS data against proteome databases containing the complete biological complexity found in UniProt.

Broad Functionality

A fast and flexible proteomics search engine for both targeted and high-throughput protein identification, designed specifically for top-down proteomics data.

Includes five different database search modes – Sequence Tag, Single Protein, and Gene Restricted search-for exceptional intact protein characterization.
Performs false discovery rate calculations at the protein, isoform, proteoform, and proteoform hit level.
Processes many different types of fragmentation data, including data generated using ETD, HCD, EThcD, UVPD, ECD, IRMPD, or CID.
Enables merging of graphical fragment maps, even those with different ion types.
Includes proprietary ProSight containing all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs).
Offers more robust precursor mass analysis, with FAIMS and PTR data now readily analyzable using ProSightPD software. Both high- and low-resolution data can be processed with the Xtract and ReSpect algorithms embedded in ProSightPD software, allowing analysis of masses from a wide range of masses (∼1 kDa to >150 kDa).
Imports XML and FASTA databases and shotgun annotates them with all possible modifications.
Allows users to experience unparalleled, versatile visualization for reviewing search results and customizing modifications to find better result fits.

Specifications

TypeSoftware

Software2

DescriptionThermo Scientific ProSightPD software.

For Use With (Equipment)Mass Spectrometers

Unit SizeEach

Frequently asked questions (FAQs)

What is E-Value referring to in ProSightPC/PD software?

The E-value is a Bonferroni corrected P Score. Bonferroni correction is a very conservative probability correction factor used to correct for multiple comparisons.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

What is the P-Score used in ProSightPC/PD software?

The P Score is a statistical model of MS/MS matching based on the Poisson Distribution. Learn more and view equations here.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

For a protein of interest, I see multiple proteoforms in my data. Why does ProSightPC/PD software only identify some of them?

Some modifications may not be included in the PTM annotation in the database and may need to be added manually. Additionally, it is common to find a few abundant proteoforms and several low abundance proteoforms. Low abundance proteoforms often do not yield sufficient fragment ion signal to make a confident PrSM. In this case, it may be beneficial to use additional scan averages when fragmenting weak or low abundant proteoforms to improve the fragment ion signal to noise ratio.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Why did I identify so few proteoforms overall while using ProSightPC/PD software?

There are several possible reasons for this. One common issue is the user defined database. Database selection/creation is a critical step in Top-Down data analysis. Foremost, the database must include the organisms in the sample or closely related ones. Equally important is the inclusion of PTMs in the database. A protein database made from a FASTA file will not include any PTMs and the result of a search will only return the unmodified protein. In order to screen for modified proteoforms, it is recommended that the database be constructed from Uniprot .xml or Uniprot .txt file files, or download from the database warehouse mentioned above (use complex for most comprehensive searches.)

Alternatively, users can reduce the confidence required to return a result. In the event that the MS2 data quality is poor it is likely that any PrSMs achieved are lower scoring and may be filtered out by default.
Lastly, ensure that all parameters in the ProSight software match the data collection parameters (e.g., activation method, resolving power, etc.)

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

How do I search my infusion data in ProSightPC Software?

Click the Add Experiment icon, or choose Tools > Experiment Adder to open the Experiment Adder dialog box

In the Fragmentation Methods area, select the fragmentation method.

In the Precursor Ion Data/Type box, select the precursor mass type, either Manual or Upload. If you select Manual in the Precursor Ion Data/Type list, select the mass type of the precursor ion in the Mass Type box (either Monoisotopic or Average) and enter the precursor mass. If you select Upload in the Precursor Ion Data/Type list, enter the path and name of the ASCII text file or files containing the precursor ion data in the Text File box, or click Browse to browse for them.

(Optional) Select a predefined search in the box near the bottom of the dialog box.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

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