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Bioinformatics for Comparative Proteomics 1st Edition
Chuming Chen Digital Instant Download
Author(s): Chuming Chen, Hongzhan Huang, Cathy H. Wu (auth.), Cathy H.
Wu, Chuming Chen (eds.)
ISBN(s): 9781607619765, 1607619768
Edition: 1
File Details: PDF, 17.32 MB
Year: 2011
Language: english

Me t h o d s i n Mo l e c u l a r Bi o l o g y ™
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For other titles published in this series, go to
www.springer.com/series/7651

Bioinformatics for Comparative
Proteomics
Edited by
Cathy H.Wu
DepartmentofComputerandInformationSciences,
CenterforBioinformaticsandComputationalBiology,
UniversityofDelaware,Newark,DE,USA
Chuming Chen
DepartmentofComputerandInformationSciences,
CenterforBioinformaticsandComputationalBiology,
UniversityofDelaware,Newark,DE,USA

Editors
Cathy H. Wu, Ph.D.
Center for Bioinformatics
and Computational Biology
University of Delaware
15 Innovation Way, Suite 205
Newark, DE 19711
USA
wuc@dbi.udel.edu
Chuming Chen, Ph.D.
Center for Bioinformatics
and Computational Biology
University of Delaware
15 Innovation Way, Suite 205
Newark, DE 19711
USA
chenc@dbi.udel.edu
ISSN 1064-3745 e-ISSN 1940-6029
ISBN 978-1-60761-976-5 e-ISBN 978-1-60761-977-2
DOI 10.1007/978-1-60761-977-2
Springer New York Dordrecht Heidelberg London
© Springer Science+Business Media, LLC 2011
All rights reserved. This work may not be translated or copied in whole or in part without the written permission of
the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013,
USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of
information storage and retrieval, electronic adaptation, computer software, or by similar or
dissimilar methodology
now known or hereafter developed is forbidden.
The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified
as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.
While the advice and information in this book are believed to be true and accurate at the date of going to press,
neither
the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may
be made. The publisher makes no warranty, express or implied, with respect to the material contained herein.
Printed on acid-free paper
Humana Press is part of Springer Science+Business Media (www.springer.com)

v
Preface
With the rapid development of proteomic technologies in life sciences and in clinical appli-
cations, many bioinformatics methodologies, databases, and software tools have been
developed to support comparative proteomics study. This volume aims to highlight the
current status, challenges, open problems, and future trends in developing bioinformatics
tools and resources for comparative proteomics research and to serve as a definitive source
of reference providing both the breadth and depth needed on the subject of Bioinformatics
for Comparative Proteomics.
The volume is structured to introduce three major areas of research methods: (1)
basic bioinformatics frameworks related to comparative proteomics, (2) bioinformatics
databases and tools for proteomics data analysis, and (3) integrated bioinformatics systems
and approaches for studying comparative proteomics in the systems biology context.
Part I (Bioinformatics Framework for Comparative Proteomics) consists of seven
chapters:
Chapter 1 presents a comprehensive review (with categorization and description) of
major protein bioinformatics databases and resources that are relevant to comparative
proteomics research.
Chapter 2 provides a practical guide to the comparative proteomics community for
exploiting the knowledge captured from and the services provided in UniProt databases.
Chapter 3 introduces the InterPro protein classification system for automatic protein
annotation and reviews the signature methods used in the InterPro database.
Chapter 4 introduces the Reactome Knowledgebase that provides an integrated view
of the molecular details of human biological processes.
Chapter 5 introduces eFIP (extraction of Functional Impact of Phosphorylation), a
Web-based text mining system that can aid scientists in quickly finding abstracts from lit-
erature related to the phosphorylation (including site and kinase), interactions, and func-
tional aspects of a given protein.
Chapter 6 presents a tutorial for the Protein Ontology (PRO) Web resources to help
researchers in their proteomic studies by providing key information about protein diver-
sity in terms of evolutionary-related protein classes based on full-length sequence conser-
vation and the various protein forms that arise from a gene along with the specific functional
annotation.
Chapter 7 describes a method for the annotation of functional residues within experi-
mentally uncharacterized proteins using position-specific site annotation rules derived
from structural and experimental information.
Part II (Proteomic Bioinformatics) consists of ten chapters:
Chapter 8 describes how the detailed understanding of information value of mass
spectrometry-based proteomics data can be elucidated by performing simulations using
synthetic data.
Chapter 9 describes the concepts, prerequisites, and methods required to analyze a
shotgun proteomics data set using a tandem mass spectrometry search engine.

vi Preface
Chapter 10 presents computational methods for quantification and comparison of
peptides by label-free LC–MS analysis, including data preprocessing, multivariate statisti-
cal methods, and detection of differential protein expression.
Chapter 11 proposes an alternative to MS/MS spectrum identification by combining
the uninterpreted MS/MS spectra from overlapping peptides and then determining the
consensus identifications for sets of aligned MS/MS spectra.
Chapter 12 describes the Trans-Proteomic Pipeline, a freely available open-source
software suite that provides uniform analysis of LC–MS/MS data from raw data to quanti-
fied sample proteins.
Chapter 13 provides an overview of a set of open-source software tools and steps
involved in ELISA microarray data analysis.
Chapter 14 presents the state of the art on the Proteomics Databases and Repositories.
Chapter 15 is a brief guide to preparing both large- and small-scale protein interaction
data for publication.
Chapter 16 demonstrates a new graphical user interface tool called PRIDE Converter,
which greatly simplifies the submission of MS data to PRIDE database for submitted pro-
teomics manuscripts.
Chapter 17 presents a method for describing a protein’s posttranslational modifications
by integrating the top–down and bottom–up MS data using the Protein Inference Engine.
Chapter 18 describes an integrated top–down and bottom–up approach facilitated by
concurrent liquid chromatography–mass spectrometry analysis and fraction collection for
comprehensive high-throughput intact protein profiling.
Part III (Comparative Proteomics in Systems Biology) consists of four chapters:
Chapter 19 gives an overview of the content and usage of the PhosphoPep database,
which supports systems biology signaling research by providing interactive interrogation
of MS-derived phosphorylation data from four different organisms.
Chapter 20 describes “omics” data integration to map a list of identified proteins to a
common representation of the protein and uses the related structural, functional, genetic,
and disease information for functional categorization and pathway mapping.
Chapter 21 describes a knowledge-based approach relying on existing metabolic path-
way information and a direct data-driven approach for a metabolic pathway-centric inte-
gration of proteomics and metabolomics data.
Chapter 22 provides a detailed description of a method used to study temporal changes
in the endoplasmic reticulum (ER) proteome of fibroblast cells exposed to ER stress agents
(tunicamycin and thapsigargin).
This volume targets the readers who wish to learn about state-of-the-art bioinformat-
ics databases and tools, novel computational methods and future trends in proteomics
data analysis, and comparative proteomics in systems biology. The audience may range
from graduate students embarking upon a research project, to practicing biologists work-
ing on proteomics and systems biology research, and to bioinformaticians developing
advanced databases, analysis tools, and integrative systems. With its interdisciplinary
nature, this volume is expected to find a broad audience in biotechnology and pharmaceu-
tical companies and in various academic departments in biological and medical sciences
(such as biochemistry, molecular biology, protein chemistry, and genomics) and compu-
tational sciences and engineering (such as bioinformatics and computational biology,
computer science, and biomedical engineering).

vii
Preface
We thank all the authors and coauthors who had contributed to this volume. We
thank our series editor, Dr. John M. Walker, for reviewing all the chapter manuscripts and
providing constructive comments. We also thank Dr. Winona C. Barker from Georgetown
University for reviewing the manuscripts. We thank Dr. Qinghua Wu for proof reading the
book draft. Finally, we would like to extend our thanks to David C. Casey and Anne
Meagher of Springer US, Jeya Ruby and Ravi Amina of SPi for their help in the compila-
tion of this book.
Newark, DE, USA Cathy H. Wu and Chuming Chen

ix
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
Part I: Bioinformatics Framework for Comparative Proteomics
1 Protein Bioinformatics Databases and Resources . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chuming Chen, Hongzhan Huang, and Cathy H. Wu
2 A Guide to UniProt for Protein Scientists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Claire O’Donovan and Rolf Apweiler
3 InterPro Protein Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Jennifer McDowall and Sarah Hunter
4 Reactome Knowledgebase of Human Biological
Pathways and Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Peter D’Eustachio
5 eFIP: A Tool for Mining Functional Impact
of Phosphorylation from Literature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Cecilia N. Arighi, Amy Y. Siu, Catalina O. Tudor,
Jules A. Nchoutmboube, Cathy H. Wu, and Vijay K. Shanker
6 A Tutorial on Protein Ontology Resources for Proteomic Studies . . . . . . . . . . . . 77
Cecilia N. Arighi
7 Structure-Guided Rule-Based Annotation of Protein
Functional Sites in UniProt Knowledgebase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Sona Vasudevan, C.R. Vinayaka, Darren A. Natale,
Hongzhan Huang, Robel Y. Kahsay, and Cathy H. Wu
Part II: Proteomic Bioinformatics
8 Modeling Mass Spectrometry-Based Protein Analysis . . . . . . . . . . . . . . . . . . . . . . 109
Jan Eriksson and David Fenyö
9 Protein Identification from Tandem Mass Spectra
by Database Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Nathan J. Edwards
10 LC-MS Data Analysis for Differential
Protein Expression Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Rency S. Varghese and Habtom W. Ressom
11 Protein Identification by Spectral Networks Analysis . . . . . . . . . . . . . . . . . . . . . . 151
Nuno Bandeira
12 Software Pipeline and Data Analysis for MS/MS Proteomics:
The Trans-Proteomic Pipeline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Andrew Keller and David Shteynberg

x Contents
13 Analysis of High-Throughput ELISA Microarray Data . . . . . . . . . . . . . . . . . . . . 191
Amanda M. White, Don S. Daly, and Richard C. Zangar
14 Proteomics Databases and Repositories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Lennart Martens
15 Preparing Molecular Interaction Data for Publication . . . . . . . . . . . . . . . . . . . . . 229
Sandra Orchard and Henning Hermjakob
16 Submitting Proteomics Data to PRIDE Using PRIDE Converter . . . . . . . . . . . . 237
Harald Barsnes, Juan Antonio Vizcaíno, Florian Reisinger,
Ingvar Eidhammer, and Lennart Martens
17 Automated Data Integration and Determination of
Posttranslational Modifications with the Protein Inference Engine . . . . . . . . . . . . 255
Stuart R. Jefferys and Morgan C. Giddings
18 An Integrated Top-Down and Bottom-Up Strategy
for Characterization of Protein Isoforms and Modifications . . . . . . . . . . . . . . . . . 293
Si Wu, Nikola Tolic¢, Zhixin Tian, Errol W. Robinson,
and Ljiljana Paša-Tolic¢
Part III: Comparative Proteomics in Systems Biology
19 Phosphoproteome Resource for Systems Biology Research . . . . . . . . . . . . . . . . . 307
Bernd Bodenmiller and Ruedi Aebersold
20 Protein-Centric Data Integration for Functional Analysis of
Comparative Proteomics Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Peter B. McGarvey, Jian Zhang, Darren A. Natale,
Cathy H. Wu, and Hongzhan Huang
21 Integration of Proteomic and Metabolomic Profiling
as well as Metabolic Modeling for the Functional
Analysis of Metabolic Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
Patrick May, Nils Christian, Oliver Ebenhöh,
Wolfram Weckwerth, and Dirk Walther
22 Time Series Proteome Profiling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
Catherine A. Formolo, Michelle Mintz, Asako Takanohashi,
Kristy J. Brown, Adeline Vanderver, Brian Halligan,
and Yetrib Hathout
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379

xi
Contributors
Ruedi Aebersold • Institute of Molecular Systems Biology, ETH Zurich, Zurich,
Switzerland
Rolf Apweiler • The European Bioinformatics Institute, Cambridge, UK
Cecilia N. Arighi • Department of Computer and Information Sciences, University
of Delaware, Newark, DE, USA
Nuno Bandeira • Center for Computational Mass Spectrometry, University of
California, San Diego, La Jolla, CA, USA
Harald Barsnes • Department of Informatics, University of Bergen, Bergen, Norway
Bernd Bodenmiller • Institute of Molecular Systems Biology, ETH Zurich, Zurich,
Switzerland
Kristy J. Brown • Center for Genetic Medicine Research, Children’s National
Medical Center, Washington, DC, USA
Chuming Chen • Department of Computer and Information Sciences, University of
Delaware, Newark, DE, USA
Nils Christian • Max-Planck-Institute for Molecular Plant Physiology,
Potsdam-Golm, Germany
Don S. Daly • Pacific Northwest National Laboratory, Richland, WA, USA
Peter D’Eustachio • Department of Biochemistry, New York University School of
Medicine, New York, NY, USA
Oliver Ebenhöh • Max-Planck-Institute for Molecular Plant Physiology,
Potsdam-Golm, Germany
Nathan J. Edwards • Department of Biochemistry and Molecular & Cellular Biology,
Georgetown University Medical Center, Washington, DC, USA
Ingvar Eidhammer • Department of Informatics, University of Bergen, Bergen, Norway
Jan Eriksson • Swedish University of Agricultural Sciences, Uppsala, Sweden
David Fenyö • The Rockefeller University, New York, NY, USA
Catherine A. Formolo • Center for Genetic Medicine Research, Children’s National
Morgan C. Giddings • Departments of Microbiology & Immunology and Biomedical
Engineering, The University of North Carolina at Chapel Hill, Chapel Hill,
NC, USA
Brian Halligan • Bioinformatics, Human and Molecular Genetics Center, Medical
College of Wisconsin, Milwaukee, WI, USA
Yetrib Hathout • Center for Genetic Medicine Research, Children’s National
Henning Hermjakob • EMBL Outstation, European Bioinformatics Institute (EBI),
Cambridge, UK
Hongzhan Huang • Department of Computer and Information Sciences, University
of Delaware, Newark, DE, USA

xii Contributors
Sarah Hunter • EMBL Outstation, European Bioinformatics Institute (EBI),
Cambridge, UK
Stuart R. Jefferys • Department of Bioinformatics & Computational Biology,
The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Robel Y. Kahsay • DuPont Central Research & Development,
Wilmington, DE, USA
Andrew Keller • Rosetta Biosoftware, Seattle, WA, USA
Lennart Martens • EMBL Outstation, European Bioinformatics Institute (EBI),
Cambridge, UK
Patrick May • Max-Planck-Institute for Molecular Plant Physiology, Potsdam-Golm,
Germany
Jennifer McDowall • EMBL Outstation, European Bioinformatics Institute (EBI),
Cambridge, UK
Peter B. McGarvey • Department of Biochemistry and Molecular & Cellular Biol-
ogy, Georgetown University Medical Center, Washington, DC, USA
Michelle Mintz • Center for Genetic Medicine Research, Children’s National Medi-
cal Center, Washington, DC, USA
Darren A. Natale • Department of Biochemistry and Molecular & Cellular Biology,
Jules A. Nchoutmboube • Department of Computer and Information Sciences,
University of Delaware, Newark, DE, USA
Claire O’Donovan • The European Bioinformatics Institute, Cambridge, UK
Sandra Orchard • EMBL Outstation, European Bioinformatics
Institute (EBI), Cambridge, UK
Ljiljana Paša-Tolic
¢ • Pacific Northwest National Laboratory, Richland, WA, USA
Florian Reisinger • EMBL Outstation, European Bioinformatics Institute (EBI),
Cambridge, UK
Habtom W. Ressom • Department of Oncology, Georgetown University Medical
Center, Washington, DC, USA
Errol W. Robinson • Pacific Northwest National Laboratory, Richland, WA, USA
Vijay K. Shanker • Department of Computer and Information Sciences, University of
Delaware, Newark, DE, USA
David Shteynberg • Institute for Systems Biology, Seattle, WA, USA
Amy Y. Siu • Department of Computer and Information Sciences, University of Dela-
ware, Newark, DE, USA
Asako Takanohashi • Center for Genetic Medicine Research, Children’s National
Zhixin Tian • Pacific Northwest National Laboratory, Richland, WA, USA
Nikola Tolic
¢ • Pacific Northwest National Laboratory, Richland, WA, USA
Catalina O. Tudor • Department of Computer and Information Sciences,
Adeline Vanderver • Center for Genetic Medicine Research, Children’s National
Rency S. Varghese • Department of Oncology, Georgetown University Medical
Center, Washington, DC, USA

xiii
Contributors
Sona Vasudevan • Department of Biochemistry and Molecular & Cellular Biology,
C.R. Vinayaka • Department of Biochemistry and Molecular & Cellular Biology,
Juan Antonio Vizcaíno • EMBL Outstation, European Bioinformatics Institute
(EBI), Cambridge, UK
Dirk Walther • Max-Planck-Institute for Molecular Plant Physiology, Potsdam-
Golm, Germany
Wolfram Weckwerth • Molecular Systems Biology, University of Vienna, Vienna,
Austria
Amanda M. White • Pacific Northwest National Laboratory, Richland, WA, USA
Cathy H. Wu • Department of Computer and Information Sciences,
Si Wu • Pacific Northwest National Laboratory, Richland, WA, USA
Richard C. Zangar • Pacific Northwest National Laboratory, Richland, WA, USA
Jian Zhang • Department of Biochemistry and Molecular & Cellular Biology,

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The Project Gutenberg eBook of Catty Atkins

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Title: Catty Atkins
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The Project Gutenberg eBook, Catty Atkins, by Clarence Budington
Kelland
Books by CLARENCE BUDINGTON KELLAND
CATTY ATKINS
THE HIDDEN SPRING
THE HIGHFLYERS
THE LITTLE MOMENT OF HAPPINESS
MARK TIDD
MARK TIDD IN BUSINESS
MARK TIDD’S CITADEL
MARK TIDD, EDITOR
MARK TIDD, MANUFACTURER
MARK TIDD IN THE BACKWOODS
THE SOURCE
SUDDEN JIM
THIRTY PIECES OF SILVER
HARPER & BROTHERS, NEW YORK

All of a sudden he jumped at Skoodles and quicker than a cat he hit him
twice, once on the nose and once on the stummick, and Skoodles sat down to
think it over

CATTY ATKINS
By
Clarence Budington Kelland
Author of “MARK TIDD”, “MARK TIDD, MANUFACTURER”
Illustrated
HARPER & BROTHERS PUBLISHERS
NEW YORK AND LONDON

Catty Atkins
Copyright 1919 by Harper & Brothers
Printed in the United States of America
Published, January, 1920

CHAPTER I
I put a bottle on a box against the side of the barn and aimed as
careful as all-git-out. My idea was to bust it right at the neck. Well, I
jerked on the trigger and the gun went off and I looked at the
bottle. It was still there, neck and all.
After the aim I took it didn’t seem possible, so I walked up close to
find out if maybe I hadn’t slammed a hole right through it that
couldn’t be seen—but there wasn’t any hole. I knew right off there
must be something wrong with that gun. It was the very first time
I’d ever shot it, and if a gun don’t shoot straight the first time, when
it’s spang-whang new, what kind of shooting will it do when it gets
to be old and worn? I was dog-gone disappointed.
Dad gave me that rifle for my birthday and I’d come hustling out
right after breakfast to give it a try—and it wasn’t any good! I put in
another cartridge and got some closer to the bottle and tried again.
The bottle never wiggled. I came some closer and shot again, and
then I came still closer and shot again. Six times I shot before I hit
the danged thing and then I was so close I could have knocked it
over with the rifle-barrel.
“Pretty middlin’ shootin’,” says somebody behind me, and I turned
around quick. There was a kid I’d never seen. He was kind of small,
with bare feet and clothes that looked as if he’d found them in an
ash-barrel and then slept in them. His hair was kind of bristly, and
he didn’t have on any hat. He wasn’t smiling or making fun of me as
far as I could see, for his face was as sober as a houseful of
deacons. It was a kind of a thin face with a sharp chin and a straight
nose and funny crinkles around the eyes. But the eyes were gray
and kind of sparkly. I looked at him a minute, wondering who he
was, before I said anything. Then I says:

“Calc’late this gun ain’t much good.”
“Is it a reg’lar gun,” says he, “or jest a kind of a cap pistol?”
That made me mad, so I says, sarcastic: “Naw, this ain’t a gun. This
is a pan of mush and milk.”
“Maybe,” says he, kind of slow and solemn, like he was thinking it
over mighty careful—“maybe you could hit things better with it if it
was mush and milk. It would spatter more.”
“Say,” says I, “who are you, anyhow?”
“I wa’n’t brung up to give anythin’ away free,” says he, “but I’ll trade
you—my name for yourn.”
“It’s a trade,” says I. “Mine’s Moore. Mostly the kids call me Wee-
wee.”
“Mine’s Atkins,” says he, “and folks call me Catty because I can climb
like one.”
“One what?” says I.
“Mud turtle,” says he; “that’s plain. C-a-t-t-y—mud turtle. Spells it
every time where I come from.”
“Where’d you come from?”
“Different places.”
“Goin’ to live here?”
“Maybe.”
“Don’t you know?”
“Hain’t thought about it much.”
“If you’re not goin’ to live here, what made you come here?”
“A body’s got to go some place,” says he, very solemn. “Dad and me
wasn’t p’tic’lar. We didn’t start out to come here, we just got here,
and here we be!”
“What’s your Dad do?”

“Dad don’t do much. He calc’lates to be shiftless.”
“Don’t he work?”
“I’ve seen him,” says Catty, “but it hain’t usual.”
“Are you rich?”
“Well—we got our health and these here clothes is mine, free and
clear. No mortgages on ’em nor nothin’. Dad’s clothes is his’n, too,
but they hain’t so gaudy as mine.”
“Kind of tramps?” says I, getting interested.
“Not tramps—j’st shiftless. Didn’t I tell you?”
“Where you sleepin’?”
“If you ain’t careful,” he says, as solemn as an owl, “you’ll ketch
yourself askin’ a question. We been livin’,” says he, “in a little house
down by the bayou.”
“That tumble-down shanty not far from the waterworks?”
“That’s the one.”
“There isn’t any furniture in it,” says I. “Movin’ about like Dad and
me, furniture would be a nuisance.”
“There’s no glass in the windows.”
“We’re partial to fresh air.”
“Huh!” says I. “You’re dog-gone easy suited. If your Dad doesn’t
work, how do you get to eat?”
“Well, there’s times when we have more mealtimes than we do
meals, but Dad he gits an odd job, and I git an odd job and mostly
we do pretty well, thank you kindly.” Just then Dad came out
through the back gate, and right here I want to say something about
my Dad. I heard a couple of women say one day that they guessed
he was a little crazy, but I want to let you know that he ain’t crazy a
bit, and I can lick any feller that says he is. Dad ain’t old, either. He
ain’t forty yet. Only thing I got to complain about is the way he

cusses over my grammar. He always talks as correct as Mother does,
only more so, and he’s got manners. Not the kind of manners folks
put on at a party or in church, but the kind you have always and use
always and that look to people as if you didn’t really try to have ’em,
but as if they came natural.
The reason those women said he was kind of crazy is because he
don’t act just like everybody else in town. He’s polite even to the
man that comes to get our garbage, and he treats boys as if they
were just as old as he is, and don’t call them “My boy” and “Bub”
and such like names. And he fusses around with me just like he was
a kid. Why, he can do more things than any kid I ever saw!
“How’s the gun?” says he.
“Somethin’ seems to be wrong with it,” I says. “It don’t hit things.”
“Let me see,” he says, and just then a big rat went running along
the alley. Well, sir, quick as a wink Dad snapped the gun to his
shoulder, and off it went, and the rat went end over end. I ran over
and picked it up by the tail. It was shot right plumb through the
head.
“Huh!” says I.
“Maybe,” says Dad, “something was wrong with the way you aimed
it.”
“Maybe,” says I.
Dad looked over at Catty and smiled. “Good morning,” says he.
“Good morning,” says Catty.
“Don’t believe I know you,” says Dad.
“He’s Catty Atkins,” says I. “He and his Dad just came to town.
They’re shiftless.” Dad looked quick at Catty to see if I’d said
something that hurt his feelings, but Catty only nodded that I was
right.
“Do you find it hard work, being shiftless?” says Dad.

“We make out to enjoy it,” says Catty. “It must be pleasant,” says
Dad. “I’ve often wished I was fixed so I could be shiftless. But when
you’ve a family—”
Catty nodded. “There’s just Dad and me. He didn’t used to be
shiftless till Ma died, so he says.”
“Are you going to make a profession of it,” Dad says, “or do you plan
to do something else when you grow up?”
“Hain’t thought about it,” says Catty. “It must be fine,” says Dad, “to
start off in the morning and not know where you are going, and not
to care, and not to feel that you’ve ever got to come back. It must
be splendid to go fishing when you want to, or to lie on your back in
the sun when you want to, and to know that there’s no reason why
you shouldn’t. Somehow it seems to me that if I could be shiftless
I’d rather work at it in the country, in the woods or mountains, than
around towns.” He nodded his head and so did Catty. “I’d rather be
shiftless like a squirrel than like an alley cat,” Dad says.
“The bear’s the feller,” says Catty. “He pokes around and does what
he wants to all summer when it’s fine, and then he goes to sleep
warm and comfortable all winter, with no bother about grub or fuel.
I wisht I was a bear.”
“Do you like corners?” says Dad, and I didn’t know what he meant,
but Catty did.
“Dad and me talk a lot about corners,” says he. “Seems like corners
is the most int’restin’ things in the world. Country roads is full of
’em. Heaps of times Dad and me will set down when we’re comin’ to
a corner and argue about it for half an hour—about what we’ll see
when we come to turn it. It’s a funny thing, but there’s a different
thing around every corner you turn. No two of ’em’s alike.”
“And brooks,” said Dad, “especially mountain brooks.”
“They’re jest like stories,” says Catty. “Like them intrestin’ stories
that you can’t git to sleep till you finish. I’d rather foller down a
brook than anything.”

“Shoot?” says Dad.
“Never shot a gun.”
“Try it.”
Catty aimed at my bottle and missed it as far as I did. He sort of
wrinkled his nose and says something to himself and waggled his
head. You could see he didn’t like missing. When I got to know him
better I found out that he was always like that. He didn’t like not
being able to do things, and if he found out he couldn’t do
something, he wouldn’t rest till he could do it. He went over and
snooped around the ground till he had picked up six cartridges that
had been shot, and sat them in a row on top of the fence. Then he
walked off a ways and took a piece of rubber band out of his pocket.
There was a leather pocket on it.
“What’s that?” says I.
“A beanie,” says he.
I’d never seen one. In our part of the country we used a sling-shot
made of two rubber bands and a crotch.
Catty fingered in his pocket and piffled out a round pebble and fixed
it in the leather. Then he drew back the rubber over the first finger
of his left hand and shot quick. The pebble knocked off the first
cartridge. And then, almost quicker than I can say it, he shot five
more times, and every pebble knocked off a cartridge. I never saw
such shooting.
“There!” says he.
“Fine shooting,” says Dad, and Dad’s eyes were shining like they
always do when he’s pleased. “I’m glad I saw that.”
Then Dad put in about half an hour showing Catty and me how to
shoot a gun, and we got so we could do a little better.
“The only way to get to be a marksman,” he says, “is to stick to it
and shoot and shoot. Isn’t that so, Catty?”
“Yes,” says Catty.

Then Dad went away after telling Catty to come around often. “Tell
your father I’ll drop in to see him—and talk about roads and brooks
and the pleasures of shiftlessness,” he said, as he went through the
gate.
I heard somebody whistle, and knew it was either Banty Gage or
Skoodles Gordon. I whistled back.
“Here come the fellers,” says I. “Now we kin have a reg’lar shootin’-
match.”
“Guess I’ll be moggin’ along,” says Catty.
“Why?”
“Oh, I dunno. Just guess I’ll be goin’.”
“I wisht you’d show those kids how you can shoot that beanie.”
“I ain’t much for kids. Don’t have much to do with ’em.”
“Why not? You stopped and talked with me.”
“I was sort of int’rested in the way you was missin’ that bottle. Glad
I stopped, too. I got to see your Dad. He’s mighty near as good a
Dad as mine.”
“Aw, rats!” says I. “Banty and Skoodles is heaps of fun.”
“I don’t git along with kids,” he says, stubborn. “Got so’s I never
have anythin’ to do with ’em. Mostly I never have anythin’ to do with
anybody but Dad.”
“Why?”
“We jest don’t git along. It’s on account of our bein’ shiftless. I’ve
had to lick a sight of kids on account of callin’ me or Dad names.
And then their Mas see ’em playin’ with me and makes ’em stop—
and I have to lick ’em on that account.”
“Why don’t their Mas want them to play with you?”
“’Cause we’re shiftless.”
“My mother wouldn’t care.”

“Bet she would.”
“Anyhow, Dad wouldn’t. You seen him. He told you to come around,
didn’t he?”
“I hain’t never seen anybody jest like your Dad before,” says Catty.
“Mostly I get told to clear out.”
“Aw, shucks!” says I.
“Good-by,” says he. “Hope you git to shoot that gun like a
champeen. Maybe I’ll see you ag’in some day.”
“Come around any time,” says I; “and, if you hain’t got any
objection, I’ll drop around your place.”
“Come ahead,” says he. “Maybe we’ll still be there, and I guess I kin
stand it if you kin.” He started off, but he stopped and says: “Your
Dad—die’s all right. I like your Dad.”

CHAPTER II
It was a day or two afterward that I run across Catty Atkins poking
along the road on the edge of town, all alone. I hollered to him and
he stopped.
“How’s things?” says I.
“Sich as there is, they’re perty fair,” says he. “Hain’t moved on yet?”
He sort of grinned. “Oh yes. We left for Philadelphy two days ago.
Arrived there about ten this mornin’.”
“Huh!” says I. “Come on back to my house and let’s shoot with my
rifle.”
“Don’t guess I better,” he said, kind of hesitating, but I could see he
wanted to come.
“Come on,” says I. “Dad was askin’ after you this mornin’.”
“Was he?” says Catty, and his eyes got bright as anything. “Was he
really?... I’ll come.”
When we got there Banty Gage, who lives next door, and Skoodles
Gordon were sitting on top of the shed, waiting for me to turn up. I
had told them about Catty Atkins, and they were interested to see
him and to watch him shoot with that beanie of his. When Catty saw
them he came close to turning around and going off, but I hung
onto him, and Skoodles and Banty came down off of the shed.
“This is Catty Atkins that I told you about,” says I, and then I told
him what their names were. He didn’t say much and acted sort of
offish and quiet, but that didn’t last. In a while we were shooting

away and having a bully time. Dad came out on the porch a minute
and asked how we were getting along, and spoke special to Catty,
and then sat down to read his paper.
About ten minutes after that Banty Gage’s mother came out and
stood looking at us. Then she called to Banty and he went over to
the fence. We could hear what she said.
“Who is that boy?” she asked, sort of cold and severe.
“Catty Atkins,” says Banty.
“Who is he? Where did you get acquainted with him?”
“Wee-wee brought him home with him.”
“Is he that boy you were talking about the other evening? The one
whose father is a tramp and who is hanging around that old shanty
down by the waterworks?”
“Yes, ’m.”
“Then you come right straight home. If Mrs. Moore wants her boy to
play with that sort of people, all right, but my boy can’t. No telling
what he’ll lead you into.” She stopped and looked hard at Catty, who
was standing very still, with his lips set and his eyes kind of like they
was made out of pieces of polished steel. “He’s a tramp, and there’s
no telling what else. Such people aren’t fit to be let at large. I don’t
see what the town is thinking of not to shut them up or make them
go away. You come right home, and never let me see you with that
boy again. Now march.”
Catty looked at Mrs. Gage and looked at me and looked at Dad, and
then he says to himself, “I sort of knew folks thought that about us,
but I didn’t ever hear one of ’em say it before.” And he turned
around and started for the back gate.
“Where you goin’?” says I, and I was good and mad.
He didn’t answer, but kept right on. Then Dad spoke from the porch.
“Catty,” says he, and his voice had something in it that sounded
good.

Catty stopped and looked at him, very sober, with his lips shut tight.
“Wait just a moment, Catty,” says Dad, and then he turned to Mrs.
Gage.
“Mrs. Gage,” says Dad, “Catty is my guest, and as my guest he is
entitled to the courtesy of those who are my friends and neighbors. I
know Catty, and I am very glad to have him come to my home and
play with my son. I am going to give myself the pleasure of calling
on Catty’s father. I am sure you spoke hastily and had no wish to
hurt this boy as you have hurt him.”
“Mr. Moore,” said Mrs. Gage, as sharp as a needle, “you can have
any tramp or criminal or anybody you want to play with your family,
but you can’t force them on mine.... You heard me tell you to come
home, Thomas.” Banty’s right name was Thomas.
“I know, Mrs. Gage,” said father, in a gentle sort of way he has, “that
you will be sorry you have hurt this boy. If you knew him, when you
know him, I am sure you will want to apologize.”
“Know him!... Apologize to a young tramp!...” Mrs. Gage turned and
went into the house, slamming the screen after her, and Banty
followed. Then she gave Banty what for, and didn’t take a bit of
trouble to lower her voice. “You heard what I said,” she says. “You
keep away from that ragamuffin.”
“But Mr. Moore says—”
“I don’t care what Mr. Moore says. I sha’n’t put up with his crazy
ideas. The idea! Mr. Moore ought to know better, but he doesn’t
seem to. After this you keep away from the Moores.”
Dad looked down at me and smiled sort of humorous and at the
same time sort of sad, and then he came down off the porch and
walked right up to Catty.
“I can’t tell you how sorry I am that this thing happened,” he said,
and looked straight into Catty’s eyes. “I know Mrs. Gage didn’t
intend to be cruel. She doesn’t understand, that’s all. You mustn’t be
hard on the rest of us because some people don’t understand things.

You won’t, will you?... And remember that you are always welcome
here and that I am glad to have Wee-wee play with you. We’re going
to have dinner in a few minutes and I shall be very glad indeed if
you will stay and eat with us.”
“Eat with you!” says Catty, and looked down at his clothes.
“Of course.”
“I hain’t never been invited to dinner no-wheres. I wouldn’t know
how to act.”
“Catty, there’s folks in this world who always know how to act. The
finest manners I ever saw were shown by a French lumberjack who
couldn’t write his name. Being a gentleman doesn’t consist in
knowing which fork to use first, Catty. Those things are just
trimmings, but a gentleman is a gentleman because he’s got
something inside—something that I know you’ve got. Do you know
what a gentleman is, Catty, and what it is that makes any man good
enough to dine with any other man, or to do anything else in the
world with any other man?”
“No, sir,” says Catty.
“It’s a feeling inside him that he wants to act toward everybody just
as he wants everybody to act toward him.”
“I thought,” said Catty, “that a gentleman was somebody with a
white shirt who thought most folks was beneath him.”
Dad laughed. “Come on in and wash for dinner—and meet Wee-
wee’s mother.”
“Will she—will she want me, sir?”
Dad laughed again, and I laughed this time, because that was really
funny. If Dad was to bring home a hippopotamus to dinner Mother
would be glad of it—just because Dad brought him. I’ve took notice
that Mother always thought that whatever Dad did was just right,
and, now that I come to think it over, she thought so because
everything that Dad did was just right.

Mother shook hands with Catty just as if nothing out of the ordinary
run was happening at all, and acted just as she would act if Catty
had been the Presbyterian minister or president of the bank, or
anybody else. Then Catty and me washed up and came down to
dinner, and Dad talked a lot until pretty soon he got Catty to talking
some, and what he said was mighty interesting to me—all about
walking around the country, and what they saw, and how they lived.
I kept my eye on him jest to find out what kind of table manners he
had, but I couldn’t find out, because he kept his eyes on my mother
all the time, and never did a thing until he saw her do it first, and
then did it just like she did. I saw Dad grin to himself a couple of
times.
“Mr. Moore,” said Catty, serious as all-git-out, “I wonder kin I ask you
a piece of advice?”
“Fire ahead, Catty.”
“Well, I’m wonderin’ if I ought to lick that kid before Dad and me
goes away.”
“What kid?”
“Banty Gage.”
Dad kept his face very straight, but I knew by the looks of him that
he wanted to laugh. “What has Banty done to you?”
“He didn’t do anythin’—but his Ma did. I can’t lick his Ma, because
fellers don’t pick fights with wimmin, but it seems as if I ought to lick
somebody, and, her bein’ his Ma, he comes closest to bein’ the right
person.”
“You feel like fighting, eh? Well, I don’t blame you.... You said before
you and your father went away. Are you going away?”
“When I git home I’m goin’ to tell Dad it’s time to move on.”
“And he’ll go?”
“’Course. Dad’s always willin’ to go.”
“And you’re going because of what Mrs. Gage said?”

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