Software:SuperHirn

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h3. Parameters: h3. Parameters:
-{| class="wikitable"+'''Other Compatible MS File Formats:'''
 + 
 +{| class="wikitable" style="text-align:center;" border="2" cellpadding="2"
|- |-
-! Parameter name+! Parameter name !! Description !! Suggested Value !! Comment
-! Description +
-! Suggested Value+
-! Comment+
|- |-
-! GENERAL:+| GENERAL:
|- |-
- +| MS1 retention time tolerance || RT tolerance between MS1 features used for the alignment (min) || 1.0 || -
-!MS1 retention time tolerance +
-! RT tolerance between MS1 features used for the alignment (min) +
-!1.0 +
-!-+
|- |-
 +|MS1 m/z tolerance|| Mass tolerance between MS1 features used for the alignment (ppm) || 10 || -
 +
|} |}
 +
| h6.General:||| | h6.General:|||
-|MS1 retention time tolerance| RT tolerance between MS1 features used for the alignment (min)| 1.0 |- 
|MS1 m/z tolerance| Mass tolerance between MS1 features used for the alignment (ppm)| 10|- |MS1 m/z tolerance| Mass tolerance between MS1 features used for the alignment (ppm)| 10|-
|MS2 PPM m/z tolerance| Mass tolerance for annotation of MS1 features with MS/MS identifications (ppm)| 20|- |MS2 PPM m/z tolerance| Mass tolerance for annotation of MS1 features with MS/MS identifications (ppm)| 20|-

Revision as of 09:58, 30 January 2009

Contents

Description

SuperHirn is a novel tool to quantitatively analyze multi dimensional LC-MS data in a label-free approach and was developed by the group of Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology (ETHZ, Switzerland). The software is programmed in C++ and is compatible with Unix platforms (tested on Linux and OSX). LC-MS data are preprocessed by a MS1 feature extraction routine and the different LC-MS runs are then combined by a multi dimensional LC-MS alignment into a general repository called MasterMap. SuperHirn then offers several modules for post data analysis of the MasterMap:

  • LC-MS similarity analysis: Binary similarity analysis of LC-MS runs (intensity reproducibility, feature overlap)
  • Feature intensity normalization: global MS1 feature intensity normalization across LC-MS runs
  • Unsupervised feature profiling: Kmeans cluster analysis of MS1 features
  • Targeted peptide/protein profiling: Correlate peptide/protein profile vs. a given target profile
  • MS1 feature annotation: Annotation of MS1 features in the MasterMap (inclusion list etc.)

Avaliablity

The source code of SuperHirn can now be downloaded from the download page: go to download page

Supporting material to this software:

  • For questions, suggestions and general comments visit the Google Groups "SuperHirn" .
  • To access the benchmark Latin Square profiling data from the SuperHirn technical manuscript (Mueller et al.), follow this link.
  • For more details about SuperHirn, please read the corresponding publication (Mueller et al.) or download the SuperHirn User Manual.
  • For an example data set of SuperHirn, please download from this link: Example Test Set.
  • For additional readings for experimental wetlab procedures in combination with SuperHirn data processing: Experimental Tips.

Reference

Software Article:

  • Mueller, LN, Rinner, O, Schmidt, A, Letarte, S, Bodenmiller, B, Brusniak, MY, Vitek, O, Aebersold, R and Muller, M, SuperHirn - a novel tool for high resolution LC-MS based peptide/protein profiling, Proteomics, accepted for publication (2007) go to article





Applications of SuperHirn:

  • Mueller, LN and Rinner, O, Hubálek, M, Müller, M, Gstaiger, M and Aebersold, R, An integrated mass spectrometric and computational framework for the comprehensive analysis of protein interaction networks, Nature Biotechnology 25, 345 - 352 (2007) go to article
  • Bodenmiller, B, Mueller, LN, Mueller, M, Domon, B and Aebersold, R, Reproducible Isolation of Distinct, Overlapping Segments of the Phospho-Proteome. Nature Methods - 4, 231 - 237 (2007) go to article
  • Rinner, O, Seebacher, J, Walzthoeni, T, Mueller, LN, Beck, M, Schmidt, A, Mueller, M, Aebersold, R, Identification of cross-linked peptides from large sequence databases. Nature Methods - 5, 315 - 323 (2008) go to article
  • Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B., An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. MCP, 2008 Nov;7(11):2138-5 go to article
  • Schiess R, Mueller LN, Mueller M, Wollscheid, B, Aebersold R, Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. MCP, 2008 Nov;7(11):2138-5 go to article
  • Mueller LN, Brusniak M, Mani DR, Aebersold R, An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 2008 Jan;7(1):51-61 go to article
  • Urwyler S, Nyfeler Y, Ragaz C, Lee H, Mueller LN, Aebersold R, Hilbi H, Proteome analysis of Legionella vacuoles purified by magnetic immuno-separation reveals secretory and endosomal GTPases. Traffic 2008 Oct 29, AOP, go to article
  • Letarte S, Brusniak M, Campbell D, Eddes J, Kemp C, Lau H, Mueller LN, Schmidt A, Shannon P, Kelly-Spratt, Vitek O, Zhang H, Aebersold R, Watts J, Differential Plasma Glycoproteome of p19ARF Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clinical Proteomics, Volume 4, Numbers 3-4 / December, 2008, go to article

Developers

Other Stuff

Das SuperHirn:: http://www.youtube.com/watch?v=LPj6cfX_U9o


About SuperHirn Parameters

h5. Description about the most important SuperHirn parameters:

The following table describes the most important SuperHirn processing parameters. These are stored in the Root-Parameter file and mostly optimized for FT profile data. To modify a parameter, do as following:

1.) copy the parameter in this format to your param.def file:

MS1 retention time tolerance=1.0

2.) adjust the parameters as you wish:

MS1 retention time tolerance=2.0

3.) run SuperHirn 4.) if you do not need the parameter anymore, just delete it or comment it out by //MS1 retention time tolerance ...


h3. Parameters:

Other Compatible MS File Formats:

Parameter name Description Suggested Value Comment
GENERAL:
MS1 retention time tolerance RT tolerance between MS1 features used for the alignment (min) 1.0 -
MS1 m/z tolerance Mass tolerance between MS1 features used for the alignment (ppm) 10 -


| h6.General:||| |MS1 m/z tolerance| Mass tolerance between MS1 features used for the alignment (ppm)| 10|- |MS2 PPM m/z tolerance| Mass tolerance for annotation of MS1 features with MS/MS identifications (ppm)| 20|- |MS2 mass matching modus| if theoretical peptide mass (1) or precursor mass (0) used to mapp MS/MS ids to MS1 features| 0|- |Peptide Prophet Threshold| Peptide Prophet Threshold, see peptide prophet paper | 0.9|- |MS2 SCAN tolerance| Scan tolerance for annotation of MS1 features with MS/MS identifications (# scans)| 100|- |MS2 retention time tolerance| RT tolerance for annotation of MS1 features with MS/MS identifications (min), if set to -1.0, then value from MS1 retention time tolerance parameter used | -1.0|- |INCLUSIONS LIST MS2 SCAN tolerance| Scan tolerance for annotation of MS1 features with inclusion list MS/MS identifications (# scans)| 100000|- | h6.LC-MS Alignment:||| |retention time window| RT window to search for common MS1 feature across LC-MS runs before the alignment, i.e. maximal RT shift possible (min)| 5.0 |- |mass / charge window| Mass window to search for common MS1 feature across LC-MS runs before the alignment, i.e. maximal mass shift possible (ppm)| 20 |- | h6.Peak Detection:||| |MS1 external isotopic distribution file|Path to XML file containing external Isotopic Peptide Distributions, use only if abnormal peptide distributions expected| "" |- |MS1 data centroid data| If MS1 data is in centroid (1) or raw (0) format| 0 |- |Save MS/MS sequenced MS1 monoisotopic peaks| Option to keep detected Monoisotopic peaks which have been selected for MS/MS but do NOT fullfill the LC elution peak criteria (i.e. times detected, ∆RT between the detected peaks): on(1) or off(0)| 1 |- |Precursor detection scan levels| MS scan from which level should be submitted for peak extraction, example for scan level 1 and 2: 1,2| 1 |- |FT peak detect MS1 m/z tolerance| Mass tolerance to cluster detected monoisotopic peaks into RT elution clusters, i.e. MS1 featuers (ppm)| 10 |- |MS1-to-MS2 precursor tolerance| Mass tolerance to associate MS/MS precursors to extracted mono isotopic peaks (ppm)| 15 |- |FT peak detect MS1 min nb peak members| Minimal number of detected mono isotopic peaks for a MS1 featuer| 4 |- |MS1 max inter scan distance| Maximal allowed RT distance between detected mono isotopic peak (min)| 0.2 |- |FT peak detect MS1 intensity min threshold| Minimal intensity of a detected mono isotopic peak (counts)| 1000 |- |Absolute isotope mass precision| Mass precision used in the detection of isotopic distributions (Da)| 0.01 |- |Relative isotope mass precision| Mass precision used in the detection of isotopic distributions (ppm)| 10 |- |IntensityCV| Coefficient of variance used to correlate a theoretical isotopic distributions to the observed one, i.e. the closer to one the better these two distributions need to coorelate | 0.9 |- |Detectable isotope factor| At which % of the highest Isotope other isotopes to not need to be detected anymore | 0.1 |- |Min. RAW MS Signal Intensity| Minimal intensity of a raw signal (before centroiding) | 10 |- |Minimal peak height| Minimal intensity of a peak signal (after centroiding) | 0 |- | h6.MS1 Feature Merging:||| |Activation of MS1 feature merging post processing| Turn peak merging on(1) or off(0) | 1 |- |PPM value for the m/z clustering of merging candidates| Mass tolerance to merge MS1 features (ppm) | 10 |- |Initial Apex Tr tolerance| RT window to search for MS1 feature candidates which should be merged (min) | 5.0 |- |MS1 feature Tr merging tolerance| Final RT tolerance for MS1 feature to be merged (min), measured from their start/end elution points | 1.0 |- |Percentage of intensity variation between LC border peaks| Maximal log10 Intensity variation between start/end elution points of 2 features which should be merged | 50.0 |- | h6.KMeans Profile Clustering Parameters :||| |number of clusters| Number of initial start clusters, really depends on how many number of profile trends (or biological groups) you expect from your data | |- |min. nb. of profile data points| How many profile points a MS1 features needs (same as how many times aligned) to be integrated into the clustering analysis | |- |min. nb. of cluster members| How many members a build cluster needs minimally to survive the next clustering iteration | |-

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