XPRESS protocols

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XPRESS specifications

Information


Unique identifier OMICS_02488
Name XPRESS
Alternative name TPP distribution
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Ruedi Aebersold <>

Publication for XPRESS

XPRESS in pipelines

 (8)
2017
PMCID: 5620370
PMID: 28794267
DOI: 10.1091/mbc.E17-02-0093

[…] frame of 20 s following the fragmentation event. full-scan data were acquired in profile, and fragments were analyzed in centroid mode by xcalibur software. the lc unit was controlled by chromeleon xpress software., for data analysis, maxquant 1.5.3.30 (), perseus 1.5.4.1 (), and excel (microsoft office 2013) were used. the enzyme specificity was set to trypsin, and missed cleavages […]

2015
PMCID: 4518706
PMID: 26220445
DOI: 10.1186/s12864-015-1768-x

[…] [] at a confidence level of > 95 %. peptides were assembled to proteins using proteinprophet [] with a false discovery rate (fdr) < 1.0 %. for relative peptide and protein quantification xpress [] was used. mass tolerance for quantification was 0.02 da. xpress data was log2-transformed yielding fold change (fc)–values. for the ccrcc replicate analyses, protein abundance […]

2015
PMCID: 4632068
PMID: 26392412
DOI: 10.1534/g3.115.021444

[…] heavy lysine: 13c6-15n2 (mw = 8.01). after assessment of peptide and protein identifications by peptideprophet () and proteinprophet (), quantitative silac ratios for proteins were determined using xpress software (). precursor ion elution profiles of heavy vs. light peptides were determined with a mass tolerance of 0.05 (>5 sec) and the area under the curve was used to determine a silac […]

2015
PMCID: 4705380
PMID: 26582203
DOI: 10.1074/jbc.M115.691097

[…] 32.06 da; heavy formaldehyde, 36.08 da). x! tandem results were further validated by peptideprophet () at a confidence level of >95%. peak areas for relative quantitation were calculated by xpress (). semispecific peptides that are increased >8-fold in the klk2-treated samples were considered as klk2 cleavage products. the corresponding prime or non-prime sequences were determined […]

2013
PMCID: 3852494
PMID: 24119551
DOI: 10.1186/1755-8794-6-40

[…] profiling using the ion ampliseq cancer panel, ion torrent sequencing, and the ion variant caller (life technologies) was performed by ait biotech (singapore). libraries were barcoded using the ion xpress barcode kit and eight samples were sequencing together in a single ion torrent sequencing run using ion 318 chips (all life technologies). default ion variant caller settings were employed, […]


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XPRESS in publications

 (1279)
PMCID: 5953318
PMID: 29785135
DOI: 10.2147/TACG.S155955

[…] primer sequences and phosphorylate the amplicons at 50°c for 10 min, followed by 55°c for 10 min, then 60°c for 20 min. the amplicons were ligated to adapters with the diluted barcodes of the ion xpress™ barcode adapters kit (thermo fisher scientific) for 30 min at 22°c, then 72°c for 10 min. adaptor-ligated amplicon libraries were purified using agencourt ampure xp (cat no. a63881) reagents […]

PMCID: 5940699
PMID: 29739964
DOI: 10.1038/s41598-018-25071-x

[…] in the intermediate pvl group. this procedure captured 424 variants distributed in 279 genes (supplementary table )., barcoded-library dna samples from the 42 animals were prepared with an ion xpress plus fragment library kit and ion xpress barcode adaptors 1–96 kit according to the manufacture’s protocol for 200 base-read sequencing (life technologies/thermo fisher scientific). five […]

PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] were generated using the ion torrent pgm (thermo fisher scientific, san francisco, california, usa) next-generation sequencing (ngs) platform. the sequencing libraries were prepared using the ion xpress plus gdna fragment library preparation kit for 200 bp or 400 bp libraries. the library amplification and dna sequencing were conducted by either ion pgm template ot2 200 or 400 kits and ion […]

PMCID: 5920182
PMID: 29700161
DOI: 10.1128/genomeA.00348-18

[…] purification kit (promega). dna quality and concentration were determined by gel electrophoresis and spectrophotometry (nanodrop, thermo scientific). a dna library was prepared using the ion torrent xpress plus fragment library kit (400 bp), templated using the ion torrent ot2 400 template kit, and sequenced on the ion torrent pgm platform using the ion torrent pgm 400 sequencing kit (thermo […]

PMCID: 5919930
PMID: 29700339
DOI: 10.1038/s41598-018-24780-7

[…] scientific) as described by the manufacturer. dna from pd1 and pd5 and their associated lscc (lscc1 and lscc5) were sequenced as a pool. for each sample, 100-ng of dna was barcoded using the ion xpress barcode adapter kit and multiplexed for emulsion pcr. the resulting amplicons were sequenced using the ion sequencing kit v. 2.0 and an ion 316 chip (8 samples/chip) on an ion torrent personal […]


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XPRESS institution(s)
University of Connecticut Health Center, Farmington, CT, USA; Institute for Systems Biology, Seattle, WA, USA

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